From tbooth at ceh.ac.uk  Mon Mar  2 05:21:46 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 2 Mar 2015 10:21:46 +0000
Subject: [Bio-Linux] shared folders disappeared after update
In-Reply-To: <CAHhAhShu-FSy8A3Tj6i7WhoQkRnWkZPyBWkkW8KQ43FK_i9oQg@mail.gmail.com>
References: <CAHhAhShu-FSy8A3Tj6i7WhoQkRnWkZPyBWkkW8KQ43FK_i9oQg@mail.gmail.com>
Message-ID: <1425291706.29012.142.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Parham,

Sorry to hear about this.  Let's check things through one step at a
time, though I'm sure you've done most of this already:

1) In the VM, check that all updates applied successfully.  You can do
this in the terminal like so:

sudo apt-get update
sudo apt-get dist-upgrade

You should see 0 to install and 0 errors.

2) Type 'groups' and see if the list includes the word 'vboxsf'.  If
not, run:

sudo usermod -aG vboxsf $USER

3) Shut down the VM

4) In the shared folder settings in the VM, remove the shared folder
definition and recreate it from scratch with the options 'auto-mount'
and 'make permanent' selected.

5) Boot up the VM

6) In the VM, open up a terminal and give the command:

sudo VBoxControl --nologo sharedfolder list

What do you see?

7) Also, give the command:

ls -l /media

Again, what do you see?

Cheers,

TIM

On Fri, 2015-02-27 at 22:00 +0000, Parham Pourbozorgi wrote:
> Hello all,
> I have been using biolinux 8 on VMware player 7.1.0 build-2496824.
> Yesterday after a biolinux (or may be Ubuntu) update the shared
> folders between VMware and my host (Windows 8.1) disappeared and no
> matter how many of the online tips I tried and how many times I
> re-installed the biolinux I couldn't figure out a solution. I was
> wondering if you know the cause and you can give any advise.
> 
> 
> I must add that biolinux is a fantastic job and I really appreciate
> the effort, thanks!
> 
> 
> 
> Cheers,
> Parham

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From papo0009 at gapps.umu.se  Mon Mar  2 09:43:45 2015
From: papo0009 at gapps.umu.se (Parham Pourbozorgi)
Date: Mon, 2 Mar 2015 15:43:45 +0100
Subject: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 1
In-Reply-To: <mailman.1.1425297601.18546.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1425297601.18546.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <CAHhAhSjuPFw54R8YMY+jVCZim7aVkFXL41-mj1fjEoUDq+PUsg@mail.gmail.com>

Hi,
Thanks for looking into it. I tried the steps, it seems there is no vboxsf
available. This is the output:
sudo usermod -aG vboxsf $USER
usermod: group 'vboxsf' does not exist

I must add that I installed VMware's tools with default values, in case
they had to be changed.

Cheers,
Parham

Kind regards,
Parham Pourbozorogi

PhD student,
Dept. of medical biochemistry and biophysics,
Ume? Unviersity,
Ume? - Sweden

On Mon, Mar 2, 2015 at 1:00 PM, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:

> Send Bio-Linux mailing list submissions to
>         bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
>         bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
>         bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
>    1. Re: shared folders disappeared after update (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 2 Mar 2015 10:21:46 +0000
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
> Subject: Re: [Bio-Linux] shared folders disappeared after update
> Message-ID:
>         <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Parham,
>
> Sorry to hear about this.  Let's check things through one step at a
> time, though I'm sure you've done most of this already:
>
> 1) In the VM, check that all updates applied successfully.  You can do
> this in the terminal like so:
>
> sudo apt-get update
> sudo apt-get dist-upgrade
>
> You should see 0 to install and 0 errors.
>
> 2) Type 'groups' and see if the list includes the word 'vboxsf'.  If
> not, run:
>
> sudo usermod -aG vboxsf $USER
>
> 3) Shut down the VM
>
> 4) In the shared folder settings in the VM, remove the shared folder
> definition and recreate it from scratch with the options 'auto-mount'
> and 'make permanent' selected.
>
> 5) Boot up the VM
>
> 6) In the VM, open up a terminal and give the command:
>
> sudo VBoxControl --nologo sharedfolder list
>
> What do you see?
>
> 7) Also, give the command:
>
> ls -l /media
>
> Again, what do you see?
>
> Cheers,
>
> TIM
>
> On Fri, 2015-02-27 at 22:00 +0000, Parham Pourbozorgi wrote:
> > Hello all,
> > I have been using biolinux 8 on VMware player 7.1.0 build-2496824.
> > Yesterday after a biolinux (or may be Ubuntu) update the shared
> > folders between VMware and my host (Windows 8.1) disappeared and no
> > matter how many of the online tips I tried and how many times I
> > re-installed the biolinux I couldn't figure out a solution. I was
> > wondering if you know the cause and you can give any advise.
> >
> >
> > I must add that biolinux is a fantastic job and I really appreciate
> > the effort, thanks!
> >
> >
> >
> > Cheers,
> > Parham
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 1
> ****************************************
>
-------------- next part --------------
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From tbooth at ceh.ac.uk  Mon Mar  2 11:46:53 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 2 Mar 2015 16:46:53 +0000
Subject: [Bio-Linux] VMWare player shared folders
In-Reply-To: <CAHhAhSjuPFw54R8YMY+jVCZim7aVkFXL41-mj1fjEoUDq+PUsg@mail.gmail.com>
References: <mailman.1.1425297601.18546.bio-linux@nebclists.nerc.ac.uk>
 <CAHhAhSjuPFw54R8YMY+jVCZim7aVkFXL41-mj1fjEoUDq+PUsg@mail.gmail.com>
Message-ID: <1425314813.29012.158.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Parham,

I do apologise - I didn't read your e-mail properly and sent
instructions for VirtualBox rather than VMWare.  You can ignore the
vboxsf stuff.

Given you already installed the VMWare drivers, please try this:

sudo apt-get install linux-headers-generic

sudo vmware-config-tools.pl

sudo mkdir -p /mnt/shared

sudo mount -t vmhgfs .host:/ /mnt/shared

ls /mnt/*

Any joy?  Or else what exact error messages do you get?

Cheers,

TIM

On Mon, 2015-03-02 at 14:43 +0000, Parham Pourbozorgi wrote:
> Hi, 
> Thanks for looking into it. I tried the steps, it seems there is no
> vboxsf available. This is the output:
> sudo usermod -aG vboxsf $USER                     
> usermod: group 'vboxsf' does not exist
> 
> 
> I must add that I installed VMware's tools with default values, in
> case they had to be changed. 
> 
> 
> Cheers,
> Parham
> 
> Kind regards,
> Parham Pourbozorogi
> 
> 
> PhD student,
> Dept. of medical biochemistry and biophysics,
> Ume? Unviersity,
> Ume? - Sweden
> 
> On Mon, Mar 2, 2015 at 1:00 PM,
> <bio-linux-request at nebclists.nerc.ac.uk> wrote:
>         Send Bio-Linux mailing list submissions to
>                 bio-linux at nebclists.nerc.ac.uk
>         
>         To subscribe or unsubscribe via the World Wide Web, visit
>                 http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         or, via email, send a message with subject or body 'help' to
>                 bio-linux-request at nebclists.nerc.ac.uk
>         
>         You can reach the person managing the list at
>                 bio-linux-owner at nebclists.nerc.ac.uk
>         
>         When replying, please edit your Subject line so it is more
>         specific
>         than "Re: Contents of Bio-Linux digest..."
>         
>         
>         Today's Topics:
>         
>            1. Re: shared folders disappeared after update (Tim Booth)
>         
>         
>         ----------------------------------------------------------------------
>         
>         Message: 1
>         Date: Mon, 2 Mar 2015 10:21:46 +0000
>         From: Tim Booth <tbooth at ceh.ac.uk>
>         To: Bio-Linux help and discussion
>         <bio-linux at nebclists.nerc.ac.uk>
>         Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
>         Subject: Re: [Bio-Linux] shared folders disappeared after
>         update
>         Message-ID:
>         
>         <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
>         Content-Type: text/plain; charset="UTF-8"
>         
>         Hi Parham,
>         
>         Sorry to hear about this.  Let's check things through one step
>         at a
>         time, though I'm sure you've done most of this already:
>         
>         1) In the VM, check that all updates applied successfully.
>         You can do
>         this in the terminal like so:
>         
>         sudo apt-get update
>         sudo apt-get dist-upgrade
>         
>         You should see 0 to install and 0 errors.
>         
>         2) Type 'groups' and see if the list includes the word
>         'vboxsf'.  If
>         not, run:
>         
>         sudo usermod -aG vboxsf $USER
>         
>         3) Shut down the VM
>         
>         4) In the shared folder settings in the VM, remove the shared
>         folder
>         definition and recreate it from scratch with the options
>         'auto-mount'
>         and 'make permanent' selected.
>         
>         5) Boot up the VM
>         
>         6) In the VM, open up a terminal and give the command:
>         
>         sudo VBoxControl --nologo sharedfolder list
>         
>         What do you see?
>         
>         7) Also, give the command:
>         
>         ls -l /media
>         
>         Again, what do you see?
>         
>         Cheers,
>         
>         TIM
>         
>         On Fri, 2015-02-27 at 22:00 +0000, Parham Pourbozorgi wrote:
>         > Hello all,
>         > I have been using biolinux 8 on VMware player 7.1.0
>         build-2496824.
>         > Yesterday after a biolinux (or may be Ubuntu) update the
>         shared
>         > folders between VMware and my host (Windows 8.1) disappeared
>         and no
>         > matter how many of the online tips I tried and how many
>         times I
>         > re-installed the biolinux I couldn't figure out a solution.
>         I was
>         > wondering if you know the cause and you can give any advise.
>         >
>         >
>         > I must add that biolinux is a fantastic job and I really
>         appreciate
>         > the effort, thanks!
>         >
>         >
>         >
>         > Cheers,
>         > Parham
>         
>         --
>         Tim Booth <tbooth at ceh.ac.uk>
>         NERC Environmental Bioinformatics Centre
>         
>         Centre for Ecology and Hydrology
>         Maclean Bldg, Benson Lane
>         Crowmarsh Gifford
>         Wallingford, England
>         OX10 8BB
>         
>         http://environmentalomics.org/bio-linux
>         +44 1491 69 2297
>         
>         
>         
>         ------------------------------
>         
>         Subject: Digest Footer
>         
>         _______________________________________________
>         Bio-Linux mailing list
>         Bio-Linux at nebclists.nerc.ac.uk
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         
>         
>         ------------------------------
>         
>         End of Bio-Linux Digest, Vol 78, Issue 1
>         ****************************************
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From papo0009 at gapps.umu.se  Tue Mar  3 07:41:09 2015
From: papo0009 at gapps.umu.se (Parham Pourbozorgi)
Date: Tue, 3 Mar 2015 13:41:09 +0100
Subject: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 2
In-Reply-To: <mailman.1.1425384002.25214.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1425384002.25214.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <CAHhAhSh9a8-aYpRw4pY2K+-XurRLyGY4PuLRszXPGo7LLFCFFQ@mail.gmail.com>

Hi Tim,
No worries thanks any way.
I tried the commands and here is the output again:

sudo mount -t vmhgfs .host:/ /mnt/shared
Error: cannot mount filesystem: No such device

I assumed vmware-config-tools.pl should be ran with default values. It
seems it's not working with VMware. I don't have any problem with
VirtualBox. I just prefer VM because it runs biolinux faster than
VirtualBox. At least a year ago that was my experience so then I switched
to VM. I must add that several places I read that VM has removed this
shared folder option from newer version. Could that be the reason?


Cheers,
Parham


Kind regards,
Parham Pourbozorogi

PhD student,
Dept. of medical biochemistry and biophysics,
Ume? Unviersity,
Ume? - Sweden

On Tue, Mar 3, 2015 at 1:00 PM, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:

> Send Bio-Linux mailing list submissions to
>         bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
>         bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
>         bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
>    1. Re: Bio-Linux Digest, Vol 78, Issue 1 (Parham Pourbozorgi)
>    2. VMWare player shared folders (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 2 Mar 2015 15:43:45 +0100
> From: Parham Pourbozorgi <papo0009 at gapps.umu.se>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 1
> Message-ID:
>         <
> CAHhAhSjuPFw54R8YMY+jVCZim7aVkFXL41-mj1fjEoUDq+PUsg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> Thanks for looking into it. I tried the steps, it seems there is no vboxsf
> available. This is the output:
> sudo usermod -aG vboxsf $USER
> usermod: group 'vboxsf' does not exist
>
> I must add that I installed VMware's tools with default values, in case
> they had to be changed.
>
> Cheers,
> Parham
>
> Kind regards,
> Parham Pourbozorogi
>
> PhD student,
> Dept. of medical biochemistry and biophysics,
> Ume? Unviersity,
> Ume? - Sweden
>
> On Mon, Mar 2, 2015 at 1:00 PM, <bio-linux-request at nebclists.nerc.ac.uk>
> wrote:
>
> > Send Bio-Linux mailing list submissions to
> >         bio-linux at nebclists.nerc.ac.uk
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > or, via email, send a message with subject or body 'help' to
> >         bio-linux-request at nebclists.nerc.ac.uk
> >
> > You can reach the person managing the list at
> >         bio-linux-owner at nebclists.nerc.ac.uk
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bio-Linux digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: shared folders disappeared after update (Tim Booth)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 2 Mar 2015 10:21:46 +0000
> > From: Tim Booth <tbooth at ceh.ac.uk>
> > To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> > Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
> > Subject: Re: [Bio-Linux] shared folders disappeared after update
> > Message-ID:
> >         <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Parham,
> >
> > Sorry to hear about this.  Let's check things through one step at a
> > time, though I'm sure you've done most of this already:
> >
> > 1) In the VM, check that all updates applied successfully.  You can do
> > this in the terminal like so:
> >
> > sudo apt-get update
> > sudo apt-get dist-upgrade
> >
> > You should see 0 to install and 0 errors.
> >
> > 2) Type 'groups' and see if the list includes the word 'vboxsf'.  If
> > not, run:
> >
> > sudo usermod -aG vboxsf $USER
> >
> > 3) Shut down the VM
> >
> > 4) In the shared folder settings in the VM, remove the shared folder
> > definition and recreate it from scratch with the options 'auto-mount'
> > and 'make permanent' selected.
> >
> > 5) Boot up the VM
> >
> > 6) In the VM, open up a terminal and give the command:
> >
> > sudo VBoxControl --nologo sharedfolder list
> >
> > What do you see?
> >
> > 7) Also, give the command:
> >
> > ls -l /media
> >
> > Again, what do you see?
> >
> > Cheers,
> >
> > TIM
> >
> > On Fri, 2015-02-27 at 22:00 +0000, Parham Pourbozorgi wrote:
> > > Hello all,
> > > I have been using biolinux 8 on VMware player 7.1.0 build-2496824.
> > > Yesterday after a biolinux (or may be Ubuntu) update the shared
> > > folders between VMware and my host (Windows 8.1) disappeared and no
> > > matter how many of the online tips I tried and how many times I
> > > re-installed the biolinux I couldn't figure out a solution. I was
> > > wondering if you know the cause and you can give any advise.
> > >
> > >
> > > I must add that biolinux is a fantastic job and I really appreciate
> > > the effort, thanks!
> > >
> > >
> > >
> > > Cheers,
> > > Parham
> >
> > --
> > Tim Booth <tbooth at ceh.ac.uk>
> > NERC Environmental Bioinformatics Centre
> >
> > Centre for Ecology and Hydrology
> > Maclean Bldg, Benson Lane
> > Crowmarsh Gifford
> > Wallingford, England
> > OX10 8BB
> >
> > http://environmentalomics.org/bio-linux
> > +44 1491 69 2297
> >
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> > ------------------------------
> >
> > End of Bio-Linux Digest, Vol 78, Issue 1
> > ****************************************
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150302/bfbf99a3/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Mon, 2 Mar 2015 16:46:53 +0000
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Subject: [Bio-Linux] VMWare player shared folders
> Message-ID:
>         <1425314813.29012.158.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Parham,
>
> I do apologise - I didn't read your e-mail properly and sent
> instructions for VirtualBox rather than VMWare.  You can ignore the
> vboxsf stuff.
>
> Given you already installed the VMWare drivers, please try this:
>
> sudo apt-get install linux-headers-generic
>
> sudo vmware-config-tools.pl
>
> sudo mkdir -p /mnt/shared
>
> sudo mount -t vmhgfs .host:/ /mnt/shared
>
> ls /mnt/*
>
> Any joy?  Or else what exact error messages do you get?
>
> Cheers,
>
> TIM
>
> On Mon, 2015-03-02 at 14:43 +0000, Parham Pourbozorgi wrote:
> > Hi,
> > Thanks for looking into it. I tried the steps, it seems there is no
> > vboxsf available. This is the output:
> > sudo usermod -aG vboxsf $USER
> > usermod: group 'vboxsf' does not exist
> >
> >
> > I must add that I installed VMware's tools with default values, in
> > case they had to be changed.
> >
> >
> > Cheers,
> > Parham
> >
> > Kind regards,
> > Parham Pourbozorogi
> >
> >
> > PhD student,
> > Dept. of medical biochemistry and biophysics,
> > Ume? Unviersity,
> > Ume? - Sweden
> >
> > On Mon, Mar 2, 2015 at 1:00 PM,
> > <bio-linux-request at nebclists.nerc.ac.uk> wrote:
> >         Send Bio-Linux mailing list submissions to
> >                 bio-linux at nebclists.nerc.ac.uk
> >
> >         To subscribe or unsubscribe via the World Wide Web, visit
> >                 http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >         or, via email, send a message with subject or body 'help' to
> >                 bio-linux-request at nebclists.nerc.ac.uk
> >
> >         You can reach the person managing the list at
> >                 bio-linux-owner at nebclists.nerc.ac.uk
> >
> >         When replying, please edit your Subject line so it is more
> >         specific
> >         than "Re: Contents of Bio-Linux digest..."
> >
> >
> >         Today's Topics:
> >
> >            1. Re: shared folders disappeared after update (Tim Booth)
> >
> >
> >
>  ----------------------------------------------------------------------
> >
> >         Message: 1
> >         Date: Mon, 2 Mar 2015 10:21:46 +0000
> >         From: Tim Booth <tbooth at ceh.ac.uk>
> >         To: Bio-Linux help and discussion
> >         <bio-linux at nebclists.nerc.ac.uk>
> >         Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
> >         Subject: Re: [Bio-Linux] shared folders disappeared after
> >         update
> >         Message-ID:
> >
> >         <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
> >         Content-Type: text/plain; charset="UTF-8"
> >
> >         Hi Parham,
> >
> >         Sorry to hear about this.  Let's check things through one step
> >         at a
> >         time, though I'm sure you've done most of this already:
> >
> >         1) In the VM, check that all updates applied successfully.
> >         You can do
> >         this in the terminal like so:
> >
> >         sudo apt-get update
> >         sudo apt-get dist-upgrade
> >
> >         You should see 0 to install and 0 errors.
> >
> >         2) Type 'groups' and see if the list includes the word
> >         'vboxsf'.  If
> >         not, run:
> >
> >         sudo usermod -aG vboxsf $USER
> >
> >         3) Shut down the VM
> >
> >         4) In the shared folder settings in the VM, remove the shared
> >         folder
> >         definition and recreate it from scratch with the options
> >         'auto-mount'
> >         and 'make permanent' selected.
> >
> >         5) Boot up the VM
> >
> >         6) In the VM, open up a terminal and give the command:
> >
> >         sudo VBoxControl --nologo sharedfolder list
> >
> >         What do you see?
> >
> >         7) Also, give the command:
> >
> >         ls -l /media
> >
> >         Again, what do you see?
> >
> >         Cheers,
> >
> >         TIM
> >
> >         On Fri, 2015-02-27 at 22:00 +0000, Parham Pourbozorgi wrote:
> >         > Hello all,
> >         > I have been using biolinux 8 on VMware player 7.1.0
> >         build-2496824.
> >         > Yesterday after a biolinux (or may be Ubuntu) update the
> >         shared
> >         > folders between VMware and my host (Windows 8.1) disappeared
> >         and no
> >         > matter how many of the online tips I tried and how many
> >         times I
> >         > re-installed the biolinux I couldn't figure out a solution.
> >         I was
> >         > wondering if you know the cause and you can give any advise.
> >         >
> >         >
> >         > I must add that biolinux is a fantastic job and I really
> >         appreciate
> >         > the effort, thanks!
> >         >
> >         >
> >         >
> >         > Cheers,
> >         > Parham
> >
> >         --
> >         Tim Booth <tbooth at ceh.ac.uk>
> >         NERC Environmental Bioinformatics Centre
> >
> >         Centre for Ecology and Hydrology
> >         Maclean Bldg, Benson Lane
> >         Crowmarsh Gifford
> >         Wallingford, England
> >         OX10 8BB
> >
> >         http://environmentalomics.org/bio-linux
> >         +44 1491 69 2297
> >
> >
> >
> >         ------------------------------
> >
> >         Subject: Digest Footer
> >
> >         _______________________________________________
> >         Bio-Linux mailing list
> >         Bio-Linux at nebclists.nerc.ac.uk
> >         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> >         ------------------------------
> >
> >         End of Bio-Linux Digest, Vol 78, Issue 1
> >         ****************************************
> >
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 2
> ****************************************
>
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From tbooth at ceh.ac.uk  Tue Mar  3 13:51:25 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 3 Mar 2015 18:51:25 +0000
Subject: [Bio-Linux] VMWare shared folders
In-Reply-To: <CAHhAhSh9a8-aYpRw4pY2K+-XurRLyGY4PuLRszXPGo7LLFCFFQ@mail.gmail.com>
References: <mailman.1.1425384002.25214.bio-linux@nebclists.nerc.ac.uk>
 <CAHhAhSh9a8-aYpRw4pY2K+-XurRLyGY4PuLRszXPGo7LLFCFFQ@mail.gmail.com>
Message-ID: <1425408685.9751.22.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Parham,

In the last day I've gone through and retried the setup on a fresh test
installation using VMWare Desktop (which I think uses exactly the same
drivers as the player) and indeed I was unable to get it working.

So I'm sorry my original answers were totally useless and I think you
are right that support has been discontinued.  I came to this page:

https://github.com/rasa/vmware-tools-patches

Which suggested that by installing the 3.16.x kernel package
"linux-image-virtual-lts-utopic" and applying the patches from that page
I should be able to get the necessary kernel module compiled, but I've
had no luck.

Did the articles you read suggest an alternative?  I'd imagine that
sharing the folders in Windows then connecting to them using either
gvfs-mount or mount.cifs would work, but as all the traffic will need to
go through the networking layer it won't be as fast as using shared
folders.

Cheers,

TIM

On Tue, 2015-03-03 at 12:41 +0000, Parham Pourbozorgi wrote:
> Hi Tim,
> No worries thanks any way. 
> I tried the commands and here is the output again:
> 
> 
> sudo mount -t vmhgfs .host:/ /mnt/shared         
> Error: cannot mount filesystem: No such device
> 
> 
> I assumed vmware-config-tools.pl should be ran with default values. It
> seems it's not working with VMware. I don't have any problem with
> VirtualBox. I just prefer VM because it runs biolinux faster than
> VirtualBox. At least a year ago that was my experience so then I
> switched to VM. I must add that several places I read that VM has
> removed this shared folder option from newer version. Could that be
> the reason? 
> 
> 
> 
> 
> Cheers,
> Parham
> 
> 
> 
> Kind regards,
> Parham Pourbozorogi
> 
> 
> PhD student,
> Dept. of medical biochemistry and biophysics,
> Ume? Unviersity,
> Ume? - Sweden
> 
> On Tue, Mar 3, 2015 at 1:00 PM,
> <bio-linux-request at nebclists.nerc.ac.uk> wrote:
>         Send Bio-Linux mailing list submissions to
>                 bio-linux at nebclists.nerc.ac.uk
>         
>         To subscribe or unsubscribe via the World Wide Web, visit
>                 http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         or, via email, send a message with subject or body 'help' to
>                 bio-linux-request at nebclists.nerc.ac.uk
>         
>         You can reach the person managing the list at
>                 bio-linux-owner at nebclists.nerc.ac.uk
>         
>         When replying, please edit your Subject line so it is more
>         specific
>         than "Re: Contents of Bio-Linux digest..."
>         
>         
>         Today's Topics:
>         
>            1. Re: Bio-Linux Digest, Vol 78, Issue 1 (Parham
>         Pourbozorgi)
>            2. VMWare player shared folders (Tim Booth)
>         
>         
>         ----------------------------------------------------------------------
>         
>         Message: 1
>         Date: Mon, 2 Mar 2015 15:43:45 +0100
>         From: Parham Pourbozorgi <papo0009 at gapps.umu.se>
>         To: bio-linux at nebclists.nerc.ac.uk
>         Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 1
>         Message-ID:
>                 <CAHhAhSjuPFw54R8YMY+jVCZim7aVkFXL41-mj1fjEoUDq
>         +PUsg at mail.gmail.com>
>         Content-Type: text/plain; charset="utf-8"
>         
>         Hi,
>         Thanks for looking into it. I tried the steps, it seems there
>         is no vboxsf
>         available. This is the output:
>         sudo usermod -aG vboxsf $USER
>         usermod: group 'vboxsf' does not exist
>         
>         I must add that I installed VMware's tools with default
>         values, in case
>         they had to be changed.
>         
>         Cheers,
>         Parham
>         
>         Kind regards,
>         Parham Pourbozorogi
>         
>         PhD student,
>         Dept. of medical biochemistry and biophysics,
>         Ume? Unviersity,
>         Ume? - Sweden
>         
>         On Mon, Mar 2, 2015 at 1:00 PM,
>         <bio-linux-request at nebclists.nerc.ac.uk>
>         wrote:
>         
>         > Send Bio-Linux mailing list submissions to
>         >         bio-linux at nebclists.nerc.ac.uk
>         >
>         > To subscribe or unsubscribe via the World Wide Web, visit
>         >
>          http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         > or, via email, send a message with subject or body 'help' to
>         >         bio-linux-request at nebclists.nerc.ac.uk
>         >
>         > You can reach the person managing the list at
>         >         bio-linux-owner at nebclists.nerc.ac.uk
>         >
>         > When replying, please edit your Subject line so it is more
>         specific
>         > than "Re: Contents of Bio-Linux digest..."
>         >
>         >
>         > Today's Topics:
>         >
>         >    1. Re: shared folders disappeared after update (Tim
>         Booth)
>         >
>         >
>         >
>         ----------------------------------------------------------------------
>         >
>         > Message: 1
>         > Date: Mon, 2 Mar 2015 10:21:46 +0000
>         > From: Tim Booth <tbooth at ceh.ac.uk>
>         > To: Bio-Linux help and discussion
>         <bio-linux at nebclists.nerc.ac.uk>
>         > Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
>         > Subject: Re: [Bio-Linux] shared folders disappeared after
>         update
>         > Message-ID:
>         >
>          <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
>         > Content-Type: text/plain; charset="UTF-8"
>         >
>         > Hi Parham,
>         >
>         > Sorry to hear about this.  Let's check things through one
>         step at a
>         > time, though I'm sure you've done most of this already:
>         >
>         > 1) In the VM, check that all updates applied successfully.
>         You can do
>         > this in the terminal like so:
>         >
>         > sudo apt-get update
>         > sudo apt-get dist-upgrade
>         >
>         > You should see 0 to install and 0 errors.
>         >
>         > 2) Type 'groups' and see if the list includes the word
>         'vboxsf'.  If
>         > not, run:
>         >
>         > sudo usermod -aG vboxsf $USER
>         >
>         > 3) Shut down the VM
>         >
>         > 4) In the shared folder settings in the VM, remove the
>         shared folder
>         > definition and recreate it from scratch with the options
>         'auto-mount'
>         > and 'make permanent' selected.
>         >
>         > 5) Boot up the VM
>         >
>         > 6) In the VM, open up a terminal and give the command:
>         >
>         > sudo VBoxControl --nologo sharedfolder list
>         >
>         > What do you see?
>         >
>         > 7) Also, give the command:
>         >
>         > ls -l /media
>         >
>         > Again, what do you see?
>         >
>         > Cheers,
>         >
>         > TIM
>         >
>         > On Fri, 2015-02-27 at 22:00 +0000, Parham Pourbozorgi wrote:
>         > > Hello all,
>         > > I have been using biolinux 8 on VMware player 7.1.0
>         build-2496824.
>         > > Yesterday after a biolinux (or may be Ubuntu) update the
>         shared
>         > > folders between VMware and my host (Windows 8.1)
>         disappeared and no
>         > > matter how many of the online tips I tried and how many
>         times I
>         > > re-installed the biolinux I couldn't figure out a
>         solution. I was
>         > > wondering if you know the cause and you can give any
>         advise.
>         > >
>         > >
>         > > I must add that biolinux is a fantastic job and I really
>         appreciate
>         > > the effort, thanks!
>         > >
>         > >
>         > >
>         > > Cheers,
>         > > Parham
>         >
>         > --
>         > Tim Booth <tbooth at ceh.ac.uk>
>         > NERC Environmental Bioinformatics Centre
>         >
>         > Centre for Ecology and Hydrology
>         > Maclean Bldg, Benson Lane
>         > Crowmarsh Gifford
>         > Wallingford, England
>         > OX10 8BB
>         >
>         > http://environmentalomics.org/bio-linux
>         > +44 1491 69 2297
>         >
>         >
>         >
>         > ------------------------------
>         >
>         > Subject: Digest Footer
>         >
>         > _______________________________________________
>         > Bio-Linux mailing list
>         > Bio-Linux at nebclists.nerc.ac.uk
>         > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         >
>         >
>         > ------------------------------
>         >
>         > End of Bio-Linux Digest, Vol 78, Issue 1
>         > ****************************************
>         >
>         -------------- next part --------------
>         An HTML attachment was scrubbed...
>         URL:
>         <http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150302/bfbf99a3/attachment-0001.html>
>         
>         ------------------------------
>         
>         Message: 2
>         Date: Mon, 2 Mar 2015 16:46:53 +0000
>         From: Tim Booth <tbooth at ceh.ac.uk>
>         To: Bio-Linux help and discussion
>         <bio-linux at nebclists.nerc.ac.uk>
>         Subject: [Bio-Linux] VMWare player shared folders
>         Message-ID:
>         
>         <1425314813.29012.158.camel at wllt1771.nerc-wallingford.ac.uk>
>         Content-Type: text/plain; charset="UTF-8"
>         
>         Hi Parham,
>         
>         I do apologise - I didn't read your e-mail properly and sent
>         instructions for VirtualBox rather than VMWare.  You can
>         ignore the
>         vboxsf stuff.
>         
>         Given you already installed the VMWare drivers, please try
>         this:
>         
>         sudo apt-get install linux-headers-generic
>         
>         sudo vmware-config-tools.pl
>         
>         sudo mkdir -p /mnt/shared
>         
>         sudo mount -t vmhgfs .host:/ /mnt/shared
>         
>         ls /mnt/*
>         
>         Any joy?  Or else what exact error messages do you get?
>         
>         Cheers,
>         
>         TIM
>         
>         On Mon, 2015-03-02 at 14:43 +0000, Parham Pourbozorgi wrote:
>         > Hi,
>         > Thanks for looking into it. I tried the steps, it seems
>         there is no
>         > vboxsf available. This is the output:
>         > sudo usermod -aG vboxsf $USER
>         > usermod: group 'vboxsf' does not exist
>         >
>         >
>         > I must add that I installed VMware's tools with default
>         values, in
>         > case they had to be changed.
>         >
>         >
>         > Cheers,
>         > Parham
>         >
>         > Kind regards,
>         > Parham Pourbozorogi
>         >
>         >
>         > PhD student,
>         > Dept. of medical biochemistry and biophysics,
>         > Ume? Unviersity,
>         > Ume? - Sweden
>         >
>         > On Mon, Mar 2, 2015 at 1:00 PM,
>         > <bio-linux-request at nebclists.nerc.ac.uk> wrote:
>         >         Send Bio-Linux mailing list submissions to
>         >                 bio-linux at nebclists.nerc.ac.uk
>         >
>         >         To subscribe or unsubscribe via the World Wide Web,
>         visit
>         >
>          http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         >         or, via email, send a message with subject or body
>         'help' to
>         >                 bio-linux-request at nebclists.nerc.ac.uk
>         >
>         >         You can reach the person managing the list at
>         >                 bio-linux-owner at nebclists.nerc.ac.uk
>         >
>         >         When replying, please edit your Subject line so it
>         is more
>         >         specific
>         >         than "Re: Contents of Bio-Linux digest..."
>         >
>         >
>         >         Today's Topics:
>         >
>         >            1. Re: shared folders disappeared after update
>         (Tim Booth)
>         >
>         >
>         >
>          ----------------------------------------------------------------------
>         >
>         >         Message: 1
>         >         Date: Mon, 2 Mar 2015 10:21:46 +0000
>         >         From: Tim Booth <tbooth at ceh.ac.uk>
>         >         To: Bio-Linux help and discussion
>         >         <bio-linux at nebclists.nerc.ac.uk>
>         >         Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
>         >         Subject: Re: [Bio-Linux] shared folders disappeared
>         after
>         >         update
>         >         Message-ID:
>         >
>         >
>          <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
>         >         Content-Type: text/plain; charset="UTF-8"
>         >
>         >         Hi Parham,
>         >
>         >         Sorry to hear about this.  Let's check things
>         through one step
>         >         at a
>         >         time, though I'm sure you've done most of this
>         already:
>         >
>         >         1) In the VM, check that all updates applied
>         successfully.
>         >         You can do
>         >         this in the terminal like so:
>         >
>         >         sudo apt-get update
>         >         sudo apt-get dist-upgrade
>         >
>         >         You should see 0 to install and 0 errors.
>         >
>         >         2) Type 'groups' and see if the list includes the
>         word
>         >         'vboxsf'.  If
>         >         not, run:
>         >
>         >         sudo usermod -aG vboxsf $USER
>         >
>         >         3) Shut down the VM
>         >
>         >         4) In the shared folder settings in the VM, remove
>         the shared
>         >         folder
>         >         definition and recreate it from scratch with the
>         options
>         >         'auto-mount'
>         >         and 'make permanent' selected.
>         >
>         >         5) Boot up the VM
>         >
>         >         6) In the VM, open up a terminal and give the
>         command:
>         >
>         >         sudo VBoxControl --nologo sharedfolder list
>         >
>         >         What do you see?
>         >
>         >         7) Also, give the command:
>         >
>         >         ls -l /media
>         >
>         >         Again, what do you see?
>         >
>         >         Cheers,
>         >
>         >         TIM
>         >
>         >         On Fri, 2015-02-27 at 22:00 +0000, Parham
>         Pourbozorgi wrote:
>         >         > Hello all,
>         >         > I have been using biolinux 8 on VMware player
>         7.1.0
>         >         build-2496824.
>         >         > Yesterday after a biolinux (or may be Ubuntu)
>         update the
>         >         shared
>         >         > folders between VMware and my host (Windows 8.1)
>         disappeared
>         >         and no
>         >         > matter how many of the online tips I tried and how
>         many
>         >         times I
>         >         > re-installed the biolinux I couldn't figure out a
>         solution.
>         >         I was
>         >         > wondering if you know the cause and you can give
>         any advise.
>         >         >
>         >         >
>         >         > I must add that biolinux is a fantastic job and I
>         really
>         >         appreciate
>         >         > the effort, thanks!
>         >         >
>         >         >
>         >         >
>         >         > Cheers,
>         >         > Parham
>         >
>         >         --
>         >         Tim Booth <tbooth at ceh.ac.uk>
>         >         NERC Environmental Bioinformatics Centre
>         >
>         >         Centre for Ecology and Hydrology
>         >         Maclean Bldg, Benson Lane
>         >         Crowmarsh Gifford
>         >         Wallingford, England
>         >         OX10 8BB
>         >
>         >         http://environmentalomics.org/bio-linux
>         >         +44 1491 69 2297
>         >
>         >
>         >
>         >         ------------------------------
>         >
>         >         Subject: Digest Footer
>         >
>         >         _______________________________________________
>         >         Bio-Linux mailing list
>         >         Bio-Linux at nebclists.nerc.ac.uk
>         >
>          http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         >
>         >
>         >         ------------------------------
>         >
>         >         End of Bio-Linux Digest, Vol 78, Issue 1
>         >         ****************************************
>         >
>         >
>         
>         --
>         Tim Booth <tbooth at ceh.ac.uk>
>         NERC Environmental Bioinformatics Centre
>         
>         Centre for Ecology and Hydrology
>         Maclean Bldg, Benson Lane
>         Crowmarsh Gifford
>         Wallingford, England
>         OX10 8BB
>         
>         http://environmentalomics.org/bio-linux
>         +44 1491 69 2297
>         
>         
>         
>         ------------------------------
>         
>         Subject: Digest Footer
>         
>         _______________________________________________
>         Bio-Linux mailing list
>         Bio-Linux at nebclists.nerc.ac.uk
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         
>         
>         ------------------------------
>         
>         End of Bio-Linux Digest, Vol 78, Issue 2
>         ****************************************
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From papo0009 at gapps.umu.se  Wed Mar  4 08:39:23 2015
From: papo0009 at gapps.umu.se (Parham Pourbozorgi)
Date: Wed, 4 Mar 2015 14:39:23 +0100
Subject: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 4
In-Reply-To: <mailman.1.1425470402.31884.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1425470402.31884.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <CAHhAhSjGj5g78R3DUbwbU8UrX39nDJyJ=YLSrPDoEXOv5XUXSA@mail.gmail.com>

Hi Tim,
Good that you are confirming you couldn't set it up neither because I tried
so many different online tips.
I am moving to Vbox since it is working fine there.  Thanks for all the
help any how.

Cheers,
Parham

On Wed, Mar 4, 2015 at 1:00 PM, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:

> Send Bio-Linux mailing list submissions to
>         bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
>         bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
>         bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
>    1. VMWare shared folders (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Mar 2015 18:51:25 +0000
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Subject: [Bio-Linux] VMWare shared folders
> Message-ID: <1425408685.9751.22.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Parham,
>
> In the last day I've gone through and retried the setup on a fresh test
> installation using VMWare Desktop (which I think uses exactly the same
> drivers as the player) and indeed I was unable to get it working.
>
> So I'm sorry my original answers were totally useless and I think you
> are right that support has been discontinued.  I came to this page:
>
> https://github.com/rasa/vmware-tools-patches
>
> Which suggested that by installing the 3.16.x kernel package
> "linux-image-virtual-lts-utopic" and applying the patches from that page
> I should be able to get the necessary kernel module compiled, but I've
> had no luck.
>
> Did the articles you read suggest an alternative?  I'd imagine that
> sharing the folders in Windows then connecting to them using either
> gvfs-mount or mount.cifs would work, but as all the traffic will need to
> go through the networking layer it won't be as fast as using shared
> folders.
>
> Cheers,
>
> TIM
>
> On Tue, 2015-03-03 at 12:41 +0000, Parham Pourbozorgi wrote:
> > Hi Tim,
> > No worries thanks any way.
> > I tried the commands and here is the output again:
> >
> >
> > sudo mount -t vmhgfs .host:/ /mnt/shared
> > Error: cannot mount filesystem: No such device
> >
> >
> > I assumed vmware-config-tools.pl should be ran with default values. It
> > seems it's not working with VMware. I don't have any problem with
> > VirtualBox. I just prefer VM because it runs biolinux faster than
> > VirtualBox. At least a year ago that was my experience so then I
> > switched to VM. I must add that several places I read that VM has
> > removed this shared folder option from newer version. Could that be
> > the reason?
> >
> >
> >
> >
> > Cheers,
> > Parham
> >
> >
> >
> > Kind regards,
> > Parham Pourbozorogi
> >
> >
> > PhD student,
> > Dept. of medical biochemistry and biophysics,
> > Ume? Unviersity,
> > Ume? - Sweden
> >
> > On Tue, Mar 3, 2015 at 1:00 PM,
> > <bio-linux-request at nebclists.nerc.ac.uk> wrote:
> >         Send Bio-Linux mailing list submissions to
> >                 bio-linux at nebclists.nerc.ac.uk
> >
> >         To subscribe or unsubscribe via the World Wide Web, visit
> >                 http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >         or, via email, send a message with subject or body 'help' to
> >                 bio-linux-request at nebclists.nerc.ac.uk
> >
> >         You can reach the person managing the list at
> >                 bio-linux-owner at nebclists.nerc.ac.uk
> >
> >         When replying, please edit your Subject line so it is more
> >         specific
> >         than "Re: Contents of Bio-Linux digest..."
> >
> >
> >         Today's Topics:
> >
> >            1. Re: Bio-Linux Digest, Vol 78, Issue 1 (Parham
> >         Pourbozorgi)
> >            2. VMWare player shared folders (Tim Booth)
> >
> >
> >
>  ----------------------------------------------------------------------
> >
> >         Message: 1
> >         Date: Mon, 2 Mar 2015 15:43:45 +0100
> >         From: Parham Pourbozorgi <papo0009 at gapps.umu.se>
> >         To: bio-linux at nebclists.nerc.ac.uk
> >         Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 1
> >         Message-ID:
> >                 <CAHhAhSjuPFw54R8YMY+jVCZim7aVkFXL41-mj1fjEoUDq
> >         +PUsg at mail.gmail.com>
> >         Content-Type: text/plain; charset="utf-8"
> >
> >         Hi,
> >         Thanks for looking into it. I tried the steps, it seems there
> >         is no vboxsf
> >         available. This is the output:
> >         sudo usermod -aG vboxsf $USER
> >         usermod: group 'vboxsf' does not exist
> >
> >         I must add that I installed VMware's tools with default
> >         values, in case
> >         they had to be changed.
> >
> >         Cheers,
> >         Parham
> >
> >         Kind regards,
> >         Parham Pourbozorogi
> >
> >         PhD student,
> >         Dept. of medical biochemistry and biophysics,
> >         Ume? Unviersity,
> >         Ume? - Sweden
> >
> >         On Mon, Mar 2, 2015 at 1:00 PM,
> >         <bio-linux-request at nebclists.nerc.ac.uk>
> >         wrote:
> >
> >         > Send Bio-Linux mailing list submissions to
> >         >         bio-linux at nebclists.nerc.ac.uk
> >         >
> >         > To subscribe or unsubscribe via the World Wide Web, visit
> >         >
> >          http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >         > or, via email, send a message with subject or body 'help' to
> >         >         bio-linux-request at nebclists.nerc.ac.uk
> >         >
> >         > You can reach the person managing the list at
> >         >         bio-linux-owner at nebclists.nerc.ac.uk
> >         >
> >         > When replying, please edit your Subject line so it is more
> >         specific
> >         > than "Re: Contents of Bio-Linux digest..."
> >         >
> >         >
> >         > Today's Topics:
> >         >
> >         >    1. Re: shared folders disappeared after update (Tim
> >         Booth)
> >         >
> >         >
> >         >
> >
>  ----------------------------------------------------------------------
> >         >
> >         > Message: 1
> >         > Date: Mon, 2 Mar 2015 10:21:46 +0000
> >         > From: Tim Booth <tbooth at ceh.ac.uk>
> >         > To: Bio-Linux help and discussion
> >         <bio-linux at nebclists.nerc.ac.uk>
> >         > Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
> >         > Subject: Re: [Bio-Linux] shared folders disappeared after
> >         update
> >         > Message-ID:
> >         >
> >          <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
> >         > Content-Type: text/plain; charset="UTF-8"
> >         >
> >         > Hi Parham,
> >         >
> >         > Sorry to hear about this.  Let's check things through one
> >         step at a
> >         > time, though I'm sure you've done most of this already:
> >         >
> >         > 1) In the VM, check that all updates applied successfully.
> >         You can do
> >         > this in the terminal like so:
> >         >
> >         > sudo apt-get update
> >         > sudo apt-get dist-upgrade
> >         >
> >         > You should see 0 to install and 0 errors.
> >         >
> >         > 2) Type 'groups' and see if the list includes the word
> >         'vboxsf'.  If
> >         > not, run:
> >         >
> >         > sudo usermod -aG vboxsf $USER
> >         >
> >         > 3) Shut down the VM
> >         >
> >         > 4) In the shared folder settings in the VM, remove the
> >         shared folder
> >         > definition and recreate it from scratch with the options
> >         'auto-mount'
> >         > and 'make permanent' selected.
> >         >
> >         > 5) Boot up the VM
> >         >
> >         > 6) In the VM, open up a terminal and give the command:
> >         >
> >         > sudo VBoxControl --nologo sharedfolder list
> >         >
> >         > What do you see?
> >         >
> >         > 7) Also, give the command:
> >         >
> >         > ls -l /media
> >         >
> >         > Again, what do you see?
> >         >
> >         > Cheers,
> >         >
> >         > TIM
> >         >
> >         > On Fri, 2015-02-27 at 22:00 +0000, Parham Pourbozorgi wrote:
> >         > > Hello all,
> >         > > I have been using biolinux 8 on VMware player 7.1.0
> >         build-2496824.
> >         > > Yesterday after a biolinux (or may be Ubuntu) update the
> >         shared
> >         > > folders between VMware and my host (Windows 8.1)
> >         disappeared and no
> >         > > matter how many of the online tips I tried and how many
> >         times I
> >         > > re-installed the biolinux I couldn't figure out a
> >         solution. I was
> >         > > wondering if you know the cause and you can give any
> >         advise.
> >         > >
> >         > >
> >         > > I must add that biolinux is a fantastic job and I really
> >         appreciate
> >         > > the effort, thanks!
> >         > >
> >         > >
> >         > >
> >         > > Cheers,
> >         > > Parham
> >         >
> >         > --
> >         > Tim Booth <tbooth at ceh.ac.uk>
> >         > NERC Environmental Bioinformatics Centre
> >         >
> >         > Centre for Ecology and Hydrology
> >         > Maclean Bldg, Benson Lane
> >         > Crowmarsh Gifford
> >         > Wallingford, England
> >         > OX10 8BB
> >         >
> >         > http://environmentalomics.org/bio-linux
> >         > +44 1491 69 2297
> >         >
> >         >
> >         >
> >         > ------------------------------
> >         >
> >         > Subject: Digest Footer
> >         >
> >         > _______________________________________________
> >         > Bio-Linux mailing list
> >         > Bio-Linux at nebclists.nerc.ac.uk
> >         > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >         >
> >         >
> >         > ------------------------------
> >         >
> >         > End of Bio-Linux Digest, Vol 78, Issue 1
> >         > ****************************************
> >         >
> >         -------------- next part --------------
> >         An HTML attachment was scrubbed...
> >         URL:
> >         <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150302/bfbf99a3/attachment-0001.html
> >
> >
> >         ------------------------------
> >
> >         Message: 2
> >         Date: Mon, 2 Mar 2015 16:46:53 +0000
> >         From: Tim Booth <tbooth at ceh.ac.uk>
> >         To: Bio-Linux help and discussion
> >         <bio-linux at nebclists.nerc.ac.uk>
> >         Subject: [Bio-Linux] VMWare player shared folders
> >         Message-ID:
> >
> >         <1425314813.29012.158.camel at wllt1771.nerc-wallingford.ac.uk>
> >         Content-Type: text/plain; charset="UTF-8"
> >
> >         Hi Parham,
> >
> >         I do apologise - I didn't read your e-mail properly and sent
> >         instructions for VirtualBox rather than VMWare.  You can
> >         ignore the
> >         vboxsf stuff.
> >
> >         Given you already installed the VMWare drivers, please try
> >         this:
> >
> >         sudo apt-get install linux-headers-generic
> >
> >         sudo vmware-config-tools.pl
> >
> >         sudo mkdir -p /mnt/shared
> >
> >         sudo mount -t vmhgfs .host:/ /mnt/shared
> >
> >         ls /mnt/*
> >
> >         Any joy?  Or else what exact error messages do you get?
> >
> >         Cheers,
> >
> >         TIM
> >
> >         On Mon, 2015-03-02 at 14:43 +0000, Parham Pourbozorgi wrote:
> >         > Hi,
> >         > Thanks for looking into it. I tried the steps, it seems
> >         there is no
> >         > vboxsf available. This is the output:
> >         > sudo usermod -aG vboxsf $USER
> >         > usermod: group 'vboxsf' does not exist
> >         >
> >         >
> >         > I must add that I installed VMware's tools with default
> >         values, in
> >         > case they had to be changed.
> >         >
> >         >
> >         > Cheers,
> >         > Parham
> >         >
> >         > Kind regards,
> >         > Parham Pourbozorogi
> >         >
> >         >
> >         > PhD student,
> >         > Dept. of medical biochemistry and biophysics,
> >         > Ume? Unviersity,
> >         > Ume? - Sweden
> >         >
> >         > On Mon, Mar 2, 2015 at 1:00 PM,
> >         > <bio-linux-request at nebclists.nerc.ac.uk> wrote:
> >         >         Send Bio-Linux mailing list submissions to
> >         >                 bio-linux at nebclists.nerc.ac.uk
> >         >
> >         >         To subscribe or unsubscribe via the World Wide Web,
> >         visit
> >         >
> >          http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >         >         or, via email, send a message with subject or body
> >         'help' to
> >         >                 bio-linux-request at nebclists.nerc.ac.uk
> >         >
> >         >         You can reach the person managing the list at
> >         >                 bio-linux-owner at nebclists.nerc.ac.uk
> >         >
> >         >         When replying, please edit your Subject line so it
> >         is more
> >         >         specific
> >         >         than "Re: Contents of Bio-Linux digest..."
> >         >
> >         >
> >         >         Today's Topics:
> >         >
> >         >            1. Re: shared folders disappeared after update
> >         (Tim Booth)
> >         >
> >         >
> >         >
> >
> ----------------------------------------------------------------------
> >         >
> >         >         Message: 1
> >         >         Date: Mon, 2 Mar 2015 10:21:46 +0000
> >         >         From: Tim Booth <tbooth at ceh.ac.uk>
> >         >         To: Bio-Linux help and discussion
> >         >         <bio-linux at nebclists.nerc.ac.uk>
> >         >         Cc: Parham Pourbozorgi <papo0009 at gapps.umu.se>
> >         >         Subject: Re: [Bio-Linux] shared folders disappeared
> >         after
> >         >         update
> >         >         Message-ID:
> >         >
> >         >
> >          <1425291706.29012.142.camel at wllt1771.nerc-wallingford.ac.uk>
> >         >         Content-Type: text/plain; charset="UTF-8"
> >         >
> >         >         Hi Parham,
> >         >
> >         >         Sorry to hear about this.  Let's check things
> >         through one step
> >         >         at a
> >         >         time, though I'm sure you've done most of this
> >         already:
> >         >
> >         >         1) In the VM, check that all updates applied
> >         successfully.
> >         >         You can do
> >         >         this in the terminal like so:
> >         >
> >         >         sudo apt-get update
> >         >         sudo apt-get dist-upgrade
> >         >
> >         >         You should see 0 to install and 0 errors.
> >         >
> >         >         2) Type 'groups' and see if the list includes the
> >         word
> >         >         'vboxsf'.  If
> >         >         not, run:
> >         >
> >         >         sudo usermod -aG vboxsf $USER
> >         >
> >         >         3) Shut down the VM
> >         >
> >         >         4) In the shared folder settings in the VM, remove
> >         the shared
> >         >         folder
> >         >         definition and recreate it from scratch with the
> >         options
> >         >         'auto-mount'
> >         >         and 'make permanent' selected.
> >         >
> >         >         5) Boot up the VM
> >         >
> >         >         6) In the VM, open up a terminal and give the
> >         command:
> >         >
> >         >         sudo VBoxControl --nologo sharedfolder list
> >         >
> >         >         What do you see?
> >         >
> >         >         7) Also, give the command:
> >         >
> >         >         ls -l /media
> >         >
> >         >         Again, what do you see?
> >         >
> >         >         Cheers,
> >         >
> >         >         TIM
> >         >
> >         >         On Fri, 2015-02-27 at 22:00 +0000, Parham
> >         Pourbozorgi wrote:
> >         >         > Hello all,
> >         >         > I have been using biolinux 8 on VMware player
> >         7.1.0
> >         >         build-2496824.
> >         >         > Yesterday after a biolinux (or may be Ubuntu)
> >         update the
> >         >         shared
> >         >         > folders between VMware and my host (Windows 8.1)
> >         disappeared
> >         >         and no
> >         >         > matter how many of the online tips I tried and how
> >         many
> >         >         times I
> >         >         > re-installed the biolinux I couldn't figure out a
> >         solution.
> >         >         I was
> >         >         > wondering if you know the cause and you can give
> >         any advise.
> >         >         >
> >         >         >
> >         >         > I must add that biolinux is a fantastic job and I
> >         really
> >         >         appreciate
> >         >         > the effort, thanks!
> >         >         >
> >         >         >
> >         >         >
> >         >         > Cheers,
> >         >         > Parham
> >         >
> >         >         --
> >         >         Tim Booth <tbooth at ceh.ac.uk>
> >         >         NERC Environmental Bioinformatics Centre
> >         >
> >         >         Centre for Ecology and Hydrology
> >         >         Maclean Bldg, Benson Lane
> >         >         Crowmarsh Gifford
> >         >         Wallingford, England
> >         >         OX10 8BB
> >         >
> >         >         http://environmentalomics.org/bio-linux
> >         >         +44 1491 69 2297
> >         >
> >         >
> >         >
> >         >         ------------------------------
> >         >
> >         >         Subject: Digest Footer
> >         >
> >         >         _______________________________________________
> >         >         Bio-Linux mailing list
> >         >         Bio-Linux at nebclists.nerc.ac.uk
> >         >
> >          http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >         >
> >         >
> >         >         ------------------------------
> >         >
> >         >         End of Bio-Linux Digest, Vol 78, Issue 1
> >         >         ****************************************
> >         >
> >         >
> >
> >         --
> >         Tim Booth <tbooth at ceh.ac.uk>
> >         NERC Environmental Bioinformatics Centre
> >
> >         Centre for Ecology and Hydrology
> >         Maclean Bldg, Benson Lane
> >         Crowmarsh Gifford
> >         Wallingford, England
> >         OX10 8BB
> >
> >         http://environmentalomics.org/bio-linux
> >         +44 1491 69 2297
> >
> >
> >
> >         ------------------------------
> >
> >         Subject: Digest Footer
> >
> >         _______________________________________________
> >         Bio-Linux mailing list
> >         Bio-Linux at nebclists.nerc.ac.uk
> >         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> >         ------------------------------
> >
> >         End of Bio-Linux Digest, Vol 78, Issue 2
> >         ****************************************
> >
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 4
> ****************************************
>
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From morais at iq.usp.br  Fri Mar  6 08:05:58 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Fri, 6 Mar 2015 10:05:58 -0300
Subject: [Bio-Linux] Qiime 1.9
Message-ID: <CAAzi7nayFwp4OebFNvbvXqrMfyinFA7fGg3Y+NM3Q4oM3aAKqg@mail.gmail.com>

Hi all,

    I would like to know if there is a plan to include the new version of
Qiime 1.9 to the repository. If so, when?

Thanks,
    Carlos
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From tbooth at ceh.ac.uk  Fri Mar  6 09:45:23 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 6 Mar 2015 14:45:23 +0000
Subject: [Bio-Linux] Qiime 1.9
In-Reply-To: <CAAzi7nayFwp4OebFNvbvXqrMfyinFA7fGg3Y+NM3Q4oM3aAKqg@mail.gmail.com>
References: <CAAzi7nayFwp4OebFNvbvXqrMfyinFA7fGg3Y+NM3Q4oM3aAKqg@mail.gmail.com>
Message-ID: <1425653123.9751.124.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

So, the update on QIIME 1.9 is that I'd hoped to have it done by the end
of Feb but I've hit several complications and I'm literally having to
re-write some bits of the QIIME code to make it work properly with the
Bio-Linux tool suite, as well as updating various packages that QIIME
depends on.  QIIME 1.9 looks very much like 1.8 on the surface but under
the hood it's all been rearranged!

The main job was tackling a pair of packages called
"python-burrito-fillings" and "python-skbio" that handle all the links
between QIIME and the tools it uses, but that's done and I'm now on to
final testing for QIIME itself.

Obviously I want to be very careful before pushing the update out,
because once you install the update there is no easy way to downgrade
again.

If I do get it finished and tested today I'll push the update on Monday,
as I have a rule about no major updates on a Friday afternoon, but this
thing may yet have more nasty surprises in store for me so no promises.

Thanks for your patience,

TIM

On Fri, 2015-03-06 at 13:05 +0000, Carlos Morais wrote:
> Hi all,
> 
>     I would like to know if there is a plan to include the new version
> of Qiime 1.9 to the repository. If so, when?
> 
> 
> Thanks,
> 
>     Carlos
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From morais at iq.usp.br  Fri Mar  6 09:57:55 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Fri, 6 Mar 2015 11:57:55 -0300
Subject: [Bio-Linux] Qiime 1.9
In-Reply-To: <1425653123.9751.124.camel@wllt1771.nerc-wallingford.ac.uk>
References: <CAAzi7nayFwp4OebFNvbvXqrMfyinFA7fGg3Y+NM3Q4oM3aAKqg@mail.gmail.com>
 <1425653123.9751.124.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CAAzi7nYSxuas8BkVuqY7iDeVZBxkuWb3z-dN4C_8qHjJu=nMXw@mail.gmail.com>

Thankyou Tim. I know that this process can be tiresome and appreciate the
effort.

Regards,
    Carlos

P.S.: Agree with 'no releases on Friday' politics.

On Fri, Mar 6, 2015 at 11:45 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi,
>
> So, the update on QIIME 1.9 is that I'd hoped to have it done by the end
> of Feb but I've hit several complications and I'm literally having to
> re-write some bits of the QIIME code to make it work properly with the
> Bio-Linux tool suite, as well as updating various packages that QIIME
> depends on.  QIIME 1.9 looks very much like 1.8 on the surface but under
> the hood it's all been rearranged!
>
> The main job was tackling a pair of packages called
> "python-burrito-fillings" and "python-skbio" that handle all the links
> between QIIME and the tools it uses, but that's done and I'm now on to
> final testing for QIIME itself.
>
> Obviously I want to be very careful before pushing the update out,
> because once you install the update there is no easy way to downgrade
> again.
>
> If I do get it finished and tested today I'll push the update on Monday,
> as I have a rule about no major updates on a Friday afternoon, but this
> thing may yet have more nasty surprises in store for me so no promises.
>
> Thanks for your patience,
>
> TIM
>
> On Fri, 2015-03-06 at 13:05 +0000, Carlos Morais wrote:
> > Hi all,
> >
> >     I would like to know if there is a plan to include the new version
> > of Qiime 1.9 to the repository. If so, when?
> >
> >
> > Thanks,
> >
> >     Carlos
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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From paumarc at gmail.com  Mon Mar  9 06:23:21 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Mon, 9 Mar 2015 11:23:21 +0100
Subject: [Bio-Linux] perl libraries for ensembl
Message-ID: <CADFuJLhn7Xn9=LLsNOaz+82pOhL=KkF1Pkv7CpsGLCs2g97ONg@mail.gmail.com>

Good morning

Are ensembl libraries  included at biolinux?

thanks

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
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From tbooth at ceh.ac.uk  Mon Mar  9 07:12:01 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 9 Mar 2015 11:12:01 +0000
Subject: [Bio-Linux] perl libraries for ensembl
In-Reply-To: <CADFuJLhn7Xn9=LLsNOaz+82pOhL=KkF1Pkv7CpsGLCs2g97ONg@mail.gmail.com>
References: <CADFuJLhn7Xn9=LLsNOaz+82pOhL=KkF1Pkv7CpsGLCs2g97ONg@mail.gmail.com>
Message-ID: <1425899521.9751.142.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

Sadly not.  There was a Debian Med/Eagle Genomics project to add ENSEMBL
packages to Debian a few years back, and these would have been inherited
by Bio-Linux, but the effort was never finished.

Hopefully installing the libraries directly from ENSEMBL is not too
problematic.  If you try to do that and run into difficulties then do
ask for help on this list.

The installation instructions for ENSEMBL say you need BioPerl 1.6.1,
and Bio-Linux has 1.6.9.  In theory, packages with only changes in the
last part of the version number should be completely compatible with
earlier versions, so you should at least be able to use the vesrion of
BioPerl that you already have.

Cheers,

TIM

On Mon, 2015-03-09 at 10:23 +0000, Pau Marc Mu?oz Torres wrote:
> Good morning 
>  
> Are ensembl libraries  included at biolinux?
> 
> 
> thanks
> 
> Pau Marc Mu?oz Torres
> 
> skype: pau_marc
> http://www.linkedin.com/in/paumarc
> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From gawbul at gmail.com  Mon Mar  9 08:54:15 2015
From: gawbul at gmail.com (Steve Moss)
Date: Mon, 9 Mar 2015 12:54:15 +0000
Subject: [Bio-Linux] perl libraries for ensembl
Message-ID: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>

Dear Pau,

I created a Docker image to pull and setup the EnsEMBL Perl libraries if
that helps? See here
https://registry.hub.docker.com/u/gawbul/docker-ensembl/.

Kindest regards,

Steve Moss

On 9 March 2015 at 12:00, <bio-linux-request at nebclists.nerc.ac.uk> wrote:

> Date: Mon, 9 Mar 2015 11:23:21 +0100
> From: Pau Marc Mu?oz Torres <paumarc at gmail.com>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] perl libraries for ensembl
> Message-ID:
>         <CADFuJLhn7Xn9=LLsNOaz+82pOhL=
> KkF1Pkv7CpsGLCs2g97ONg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Good morning
>
> Are ensembl libraries  included at biolinux?
>
> thanks
>
> Pau Marc Mu?oz Torres
> skype: pau_marc
> http://www.linkedin.com/in/paumarc
> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
>



-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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From paumarc at gmail.com  Mon Mar  9 10:16:54 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Mon, 9 Mar 2015 15:16:54 +0100
Subject: [Bio-Linux] perl libraries for ensembl
In-Reply-To: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>
References: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>
Message-ID: <CADFuJLhgXRvSix9N3BHsi0fqFXC-DzNAQP4gEdqq9fMPWD2_Ag@mail.gmail.com>

thanks!

p

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/


2015-03-09 13:54 GMT+01:00 Steve Moss <gawbul at gmail.com>:

> Dear Pau,
>
> I created a Docker image to pull and setup the EnsEMBL Perl libraries if
> that helps? See here
> https://registry.hub.docker.com/u/gawbul/docker-ensembl/.
>
> Kindest regards,
>
> Steve Moss
>
> On 9 March 2015 at 12:00, <bio-linux-request at nebclists.nerc.ac.uk> wrote:
>
>> Date: Mon, 9 Mar 2015 11:23:21 +0100
>> From: Pau Marc Mu?oz Torres <paumarc at gmail.com>
>> To: bio-linux at nebclists.nerc.ac.uk
>> Subject: [Bio-Linux] perl libraries for ensembl
>> Message-ID:
>>         <CADFuJLhn7Xn9=LLsNOaz+82pOhL=
>> KkF1Pkv7CpsGLCs2g97ONg at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Good morning
>>
>> Are ensembl libraries  included at biolinux?
>>
>> thanks
>>
>> Pau Marc Mu?oz Torres
>> skype: pau_marc
>> http://www.linkedin.com/in/paumarc
>> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
>>
>
>
>
> --
>
> Steve Moss
> about.me/gawbul
> [image: Steve Moss on about.me]
>   <http://about.me/gawbul>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
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From tbooth at ceh.ac.uk  Tue Mar 10 14:49:33 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 10 Mar 2015 18:49:33 +0000
Subject: [Bio-Linux] QIIME 1.9
Message-ID: <1426013373.4114.75.camel@wllt1771.nerc-wallingford.ac.uk>

Dear All,

It's taken a while, but you can now upgrade to QIIME 1.9 on Bio-Linux 8.
The update should come through in the regular system updater.  If you
had update errors earlier today please try again as I fixed a couple of
things.

If you are still using Bio-Linux 7 and want this new software please
upgrade to Bio-Linux 8.

Important Notes:

1) Consistency of results with new tools

On Bio-Linux, QIIME uses the latest versions of component packages like
RDP-classifier, BWA, CD-HIT, etc. etc.  Also, QIIME will use the free program
vSearch in place of uSearch61.  This means that your results will not be identical
to the results obtained with the official QIIME installation.  You can run:

qiime print_qiime_config_all

to see exactly what you have installed.  If you need consistent results
with older or official versions of QIIME you should set up the software
as per the official instructions on the QIIME website.  If you want to
override just one particular tool, ensure that your path is set so that
the custom version takes precedence.  The standard way to do this
is to just install the alternative under /usr/local/bin.

2) Choice of database for taxonomy identification

When assigning taxonomy to sequences, the default method is uclust for
which you need to specify --id_to_taxonomy_fp and --reference_seqs_fp,
either on the command line or in your .qiime_config.  QIIME now ships
with a release of Greengenes you can use for this,
under /usr/share/qiime/data/gg_13_8_otus.  

If you want a quick classification, specify "rdp" as the assignment
method and the default RDP 16S database will be used.  You can also
specify --id_to_taxonomy_fp and --reference_seqs_fp to be used with the
rdp classifier, but be aware that retraining it on the Greengenes index
uses a fair chunk of RAM.

Finally...

The main delay in releasing the package for Bio-Linux was, as I
previously commented on the mailing list, that I've been busy ensuring
that QIIME can handle all the new tool versions.  Thanks for your
patience while I got this done.  I've tested as much as I can but if you
find bugs please let me know by posting on the
bio-linux at nebclists.nerc.ac.uk address and I'll try to fix them ASAP.
There may well be bugs - this is a very complex beast!

Best,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From lister at liverpool.ac.uk  Thu Mar 12 06:28:19 2015
From: lister at liverpool.ac.uk (Rosin, Angela)
Date: Thu, 12 Mar 2015 10:28:19 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
Message-ID: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>

Hi all,

Pymol runs fine on Biolinux 8 as a desktop session but as soon as soon as you connect and run via x2Go it crashes when you open a pdb file with a segmentation fault. 

Mar 12 09:51:04 wolfson32 kernel: [3532840.217920] python2.7[14279]: segfault at 7fff5788a610 ip 00007f8a0e014932 sp 00007fff576870d0 error 6 in libgallium.so.0.0.0[7f8a0dedc000+1e9000]

It's version 1.7.0 installed via synaptic (not something I've tried to build myself!). Other graphical applications work fine. Has anyone seen something similar and is there a fix apart from "build the latest version and see if it works".

Thanks,

Angela Rosin
Technology Enhanced Learning (TEL) Support Technician/Supervisor
Institute of Learning and Teaching | Faculty of Health and Life Sciences | Life Sciences Building
e: lister at liv.ac.uk t: 0151 795 5139 w: http://www.liv.ac.uk/learning-and-teaching/tel/


From sejal.modha at glasgow.ac.uk  Mon Mar 16 06:26:56 2015
From: sejal.modha at glasgow.ac.uk (Sejal Modha)
Date: Mon, 16 Mar 2015 10:26:56 +0000
Subject: [Bio-Linux] Tablet and x2go crashes the current session
In-Reply-To: <CADFuJLhgXRvSix9N3BHsi0fqFXC-DzNAQP4gEdqq9fMPWD2_Ag@mail.gmail.com>
References: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>
 <CADFuJLhgXRvSix9N3BHsi0fqFXC-DzNAQP4gEdqq9fMPWD2_Ag@mail.gmail.com>
Message-ID: <5506AFF0.5040203@glasgow.ac.uk>

Hi There,

BioLinux users at our centre are unable to run Tablet on the server 
running BioLinux.
x2go session crashes at the user end as soon as they launch the application.

I was wondering if anyone else is facing similar problems or can propose 
a solution to fix it.

Many thanks for your help in advance.

Sej
*Sejal Modha*

Bioinformatician
MRC-University of Glasgow Centre for Virus Research
117 Sir Michael Stoker Building
464 Bearsden Road
Glasgow
G61 1QH
Tel: 0141-330-4019
http://bioinformatics.cvr.ac.uk
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From tony.travis at abdn.ac.uk  Mon Mar 16 06:32:06 2015
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Mon, 16 Mar 2015 10:32:06 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
In-Reply-To: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
References: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
Message-ID: <5506B126.8090507@abdn.ac.uk>

On 12/03/15 10:28, Rosin, Angela wrote:
> Hi all,
>
> Pymol runs fine on Biolinux 8 as a desktop session but as soon as
> soon as you connect and run via x2Go it crashes when you open a pdb
> file with a segmentation fault.
> [...]

Hi, Angela.

Yes, we had similar problems running RStudio on a MATE remote desktop.

Tim discovered that this was caused by the Qt binaries bundled in the
RStudio .deb. A similar fix might work for you:

> cd /usr/lib/rstudio/bin
> mkdir notused
> mv -i libQ* notused/
> mv -i qt.conf notused/

HTH,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.


From tbooth at ceh.ac.uk  Tue Mar 17 09:59:13 2015
From: tbooth at ceh.ac.uk (Booth, Timothy G.)
Date: Tue, 17 Mar 2015 13:59:13 +0000
Subject: [Bio-Linux] Tablet and x2go crashes the current session
In-Reply-To: <5506AFF0.5040203@glasgow.ac.uk>
References: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>
 <CADFuJLhgXRvSix9N3BHsi0fqFXC-DzNAQP4gEdqq9fMPWD2_Ag@mail.gmail.com>,
 <5506AFF0.5040203@glasgow.ac.uk>
Message-ID: <8C33D34D431A974EAEA913101DDA194407E83C9E07@nerckwmbc.ad.nerc.ac.uk>

Hi Sej,

Sorry to hear this.  I've not seen this issue before, and I just tried running Tablet via x2go and it worked fine.  Could you please check the following:

1) Is x2go on the server fully updated?
2) Which client are you connecting from?  Mac, Windows, Linux?  Are you able to try from an alternative OS?
3) Any messages or errors if you start Tablet from the command line?
4) Are you using the regular version of Java:

$ java -version
java version "1.7.0_75"
OpenJDK Runtime Environment (IcedTea 2.5.4) (7u75-2.5.4-1~trusty1)
OpenJDK 64-Bit Server VM (build 24.75-b04, mixed mode)

5) What about other Java applications?  eg. Acacia, Artemis?

Cheers,

TIM

________________________________________
From: Sejal Modha [sejal.modha at glasgow.ac.uk]
Sent: 16 March 2015 10:26
To: Bio-Linux help and discussion
Subject: [Bio-Linux] Tablet and x2go crashes the current session

Hi There,

BioLinux users at our centre are unable to run Tablet on the server running BioLinux.
x2go session crashes at the user end as soon as they launch the application.

I was wondering if anyone else is facing similar problems or can propose a solution to fix it.

Many thanks for your help in advance.

Sej
Sejal Modha

Bioinformatician
MRC-University of Glasgow Centre for Virus Research
117 Sir Michael Stoker Building
464 Bearsden Road
Glasgow
G61 1QH
Tel: 0141-330-4019
http://bioinformatics.cvr.ac.uk

This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.


From sejal.modha at glasgow.ac.uk  Tue Mar 17 10:08:52 2015
From: sejal.modha at glasgow.ac.uk (Sejal Modha)
Date: Tue, 17 Mar 2015 14:08:52 +0000
Subject: [Bio-Linux] Tablet and x2go crashes the current session
In-Reply-To: <8C33D34D431A974EAEA913101DDA194407E83C9E07@nerckwmbc.ad.nerc.ac.uk>
References: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>
 <CADFuJLhgXRvSix9N3BHsi0fqFXC-DzNAQP4gEdqq9fMPWD2_Ag@mail.gmail.com>,
 <5506AFF0.5040203@glasgow.ac.uk>
 <8C33D34D431A974EAEA913101DDA194407E83C9E07@nerckwmbc.ad.nerc.ac.uk>
Message-ID: <55083574.9040005@glasgow.ac.uk>

Hi Tim,

It's a random bug but I had managed to replicate the x2go crash issue 
with Ubuntu, Mac and Windows x2go clients.
x2go server is updated but I am running slightly different version of Java

$ java -version
java version "1.7.0_76"
Java(TM) SE Runtime Environment (build 1.7.0_76-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.76-b04, mixed mode)

However, this was resolved by installing the 
bio-linux-tablet(1.14.04.10) instead of the latest available version 
1.14.10.20

Other Java applications do not have this issue.

Thanks
Sej
On 17/03/15 13:59, Booth, Timothy G. wrote:
> Hi Sej,
>
> Sorry to hear this.  I've not seen this issue before, and I just tried running Tablet via x2go and it worked fine.  Could you please check the following:
>
> 1) Is x2go on the server fully updated?
> 2) Which client are you connecting from?  Mac, Windows, Linux?  Are you able to try from an alternative OS?
> 3) Any messages or errors if you start Tablet from the command line?
> 4) Are you using the regular version of Java:
>
> $ java -version
> java version "1.7.0_75"
> OpenJDK Runtime Environment (IcedTea 2.5.4) (7u75-2.5.4-1~trusty1)
> OpenJDK 64-Bit Server VM (build 24.75-b04, mixed mode)
>
> 5) What about other Java applications?  eg. Acacia, Artemis?
>
> Cheers,
>
> TIM
>
> ________________________________________
> From: Sejal Modha [sejal.modha at glasgow.ac.uk]
> Sent: 16 March 2015 10:26
> To: Bio-Linux help and discussion
> Subject: [Bio-Linux] Tablet and x2go crashes the current session
>
> Hi There,
>
> BioLinux users at our centre are unable to run Tablet on the server running BioLinux.
> x2go session crashes at the user end as soon as they launch the application.
>
> I was wondering if anyone else is facing similar problems or can propose a solution to fix it.
>
> Many thanks for your help in advance.
>
> Sej
> Sejal Modha
>
> Bioinformatician
> MRC-University of Glasgow Centre for Virus Research
> 117 Sir Michael Stoker Building
> 464 Bearsden Road
> Glasgow
> G61 1QH
> Tel: 0141-330-4019
> http://bioinformatics.cvr.ac.uk
>
> This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>


-- 
*Sejal Modha*

Bioinformatician
MRC-University of Glasgow Centre for Virus Research
117 Sir Michael Stoker Building
464 Bearsden Road
Glasgow
G61 1QH
Tel: 0141-330-4019
http://bioinformatics.cvr.ac.uk
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From sejal.modha at glasgow.ac.uk  Tue Mar 17 10:08:52 2015
From: sejal.modha at glasgow.ac.uk (Sejal Modha)
Date: Tue, 17 Mar 2015 14:08:52 +0000
Subject: [Bio-Linux] Tablet and x2go crashes the current session
In-Reply-To: <8C33D34D431A974EAEA913101DDA194407E83C9E07@nerckwmbc.ad.nerc.ac.uk>
References: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>
 <CADFuJLhgXRvSix9N3BHsi0fqFXC-DzNAQP4gEdqq9fMPWD2_Ag@mail.gmail.com>,
 <5506AFF0.5040203@glasgow.ac.uk>
 <8C33D34D431A974EAEA913101DDA194407E83C9E07@nerckwmbc.ad.nerc.ac.uk>
Message-ID: <55083574.9040005@glasgow.ac.uk>

Hi Tim,

It's a random bug but I had managed to replicate the x2go crash issue 
with Ubuntu, Mac and Windows x2go clients.
x2go server is updated but I am running slightly different version of Java

$ java -version
java version "1.7.0_76"
Java(TM) SE Runtime Environment (build 1.7.0_76-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.76-b04, mixed mode)

However, this was resolved by installing the 
bio-linux-tablet(1.14.04.10) instead of the latest available version 
1.14.10.20

Other Java applications do not have this issue.

Thanks
Sej
On 17/03/15 13:59, Booth, Timothy G. wrote:
> Hi Sej,
>
> Sorry to hear this.  I've not seen this issue before, and I just tried running Tablet via x2go and it worked fine.  Could you please check the following:
>
> 1) Is x2go on the server fully updated?
> 2) Which client are you connecting from?  Mac, Windows, Linux?  Are you able to try from an alternative OS?
> 3) Any messages or errors if you start Tablet from the command line?
> 4) Are you using the regular version of Java:
>
> $ java -version
> java version "1.7.0_75"
> OpenJDK Runtime Environment (IcedTea 2.5.4) (7u75-2.5.4-1~trusty1)
> OpenJDK 64-Bit Server VM (build 24.75-b04, mixed mode)
>
> 5) What about other Java applications?  eg. Acacia, Artemis?
>
> Cheers,
>
> TIM
>
> ________________________________________
> From: Sejal Modha [sejal.modha at glasgow.ac.uk]
> Sent: 16 March 2015 10:26
> To: Bio-Linux help and discussion
> Subject: [Bio-Linux] Tablet and x2go crashes the current session
>
> Hi There,
>
> BioLinux users at our centre are unable to run Tablet on the server running BioLinux.
> x2go session crashes at the user end as soon as they launch the application.
>
> I was wondering if anyone else is facing similar problems or can propose a solution to fix it.
>
> Many thanks for your help in advance.
>
> Sej
> Sejal Modha
>
> Bioinformatician
> MRC-University of Glasgow Centre for Virus Research
> 117 Sir Michael Stoker Building
> 464 Bearsden Road
> Glasgow
> G61 1QH
> Tel: 0141-330-4019
> http://bioinformatics.cvr.ac.uk
>
> This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>


-- 
*Sejal Modha*

Bioinformatician
MRC-University of Glasgow Centre for Virus Research
117 Sir Michael Stoker Building
464 Bearsden Road
Glasgow
G61 1QH
Tel: 0141-330-4019
http://bioinformatics.cvr.ac.uk
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From tony.travis at minke-informatics.co.uk  Thu Mar 12 07:58:05 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 12 Mar 2015 11:58:05 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
In-Reply-To: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
References: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
Message-ID: <55017F4D.7080102@minke-informatics.co.uk>

On 12/03/15 10:28, Rosin, Angela wrote:
> Hi all,
> 
> Pymol runs fine on Biolinux 8 as a desktop session but as soon as
> soon as you connect and run via x2Go it crashes when you open a pdb
> file with a segmentation fault.
> [...]

Hi, Angela.

Yes, we had similar problems running RStudio on a MATE remote desktop.

Tim discovered that this was caused by the Qt binaries bundled in the
RStudio .deb. A similar fix might work for you:

> cd /usr/lib/rstudio/bin
> mkdir notused
> mv -i libQ* notused/
> mv -i qt.conf notused/

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk


From lister at liverpool.ac.uk  Wed Mar 18 08:48:32 2015
From: lister at liverpool.ac.uk (Rosin, Angela)
Date: Wed, 18 Mar 2015 12:48:32 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
In-Reply-To: <5506B126.8090507@abdn.ac.uk>
References: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
 <5506B126.8090507@abdn.ac.uk>
Message-ID: <B1F4E9B78FFD5F4F88055C0B649FD3B7C7603605@CHEXMBX1.livad.liv.ac.uk>



> -----Original Message-----
> From: Tony Travis [mailto:tony.travis at abdn.ac.uk] 
>
> Hi, Angela.
>
> Yes, we had similar problems running RStudio on a MATE remote desktop.
>
> Tim discovered that this was caused by the Qt binaries bundled in the RStudio .deb. A similar fix might work for you:

I don't think so. I've got a feeling its to do with the graphics library but I can't find anything immediately obvious. The pymol install sits under the python libs.  Thanks for the help.

Ang


From tbooth at ceh.ac.uk  Wed Mar 18 10:39:25 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 18 Mar 2015 14:39:25 +0000
Subject: [Bio-Linux] Tablet and x2go crashes the current session
In-Reply-To: <55083574.9040005@glasgow.ac.uk>
References: <CALKAsdo2rb3v3OjpkL=M1Q7qa09UH7xrPeAKbZ5n-Mzh1QV9pA@mail.gmail.com>
 <CADFuJLhgXRvSix9N3BHsi0fqFXC-DzNAQP4gEdqq9fMPWD2_Ag@mail.gmail.com>
 , <5506AFF0.5040203@glasgow.ac.uk>
 <8C33D34D431A974EAEA913101DDA194407E83C9E07@nerckwmbc.ad.nerc.ac.uk>
 <55083574.9040005@glasgow.ac.uk>
Message-ID: <1426689565.28109.21.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Sej,

OK, I can only vouch for the bio-linux-tablet version running on the
default OpenJava JVM as that's the only one I test.

If there is some feature you need in the new Tablet version then let me
know and I'll try to prioritise updating it.

The issue is probably not with tablet or Java per-se but with the
graphics libraries they use.  The libraries on Ubuntu have been patched
to fix these issues and make them x2go compatible, and the DEB packages
are then compiled to use the system libraries, which is why the official
packages generally work.  If you install Java or Tablet manually you'll
find they come bundled with their own un-patched graphics libraries.

Cheers,

TIM

On Tue, 2015-03-17 at 14:08 +0000, Sejal Modha wrote:
> Hi Tim,
> 
> It's a random bug but I had managed to replicate the x2go crash issue
> with Ubuntu, Mac and Windows x2go clients.
> x2go server is updated but I am running slightly different version of
> Java
> 
> $ java -version
> java version "1.7.0_76"
> Java(TM) SE Runtime Environment (build 1.7.0_76-b13)
> Java HotSpot(TM) 64-Bit Server VM (build 24.76-b04, mixed mode)
> 
> However, this was resolved by installing the
> bio-linux-tablet(1.14.04.10) instead of the latest available version
> 1.14.10.20 
> 
> Other Java applications do not have this issue.
> 
> Thanks
> Sej
> On 17/03/15 13:59, Booth, Timothy G. wrote:
> 
> > Hi Sej,
> > 
> > Sorry to hear this.  I've not seen this issue before, and I just tried running Tablet via x2go and it worked fine.  Could you please check the following:
> > 
> > 1) Is x2go on the server fully updated?
> > 2) Which client are you connecting from?  Mac, Windows, Linux?  Are you able to try from an alternative OS?
> > 3) Any messages or errors if you start Tablet from the command line?
> > 4) Are you using the regular version of Java:
> > 
> > $ java -version
> > java version "1.7.0_75"
> > OpenJDK Runtime Environment (IcedTea 2.5.4) (7u75-2.5.4-1~trusty1)
> > OpenJDK 64-Bit Server VM (build 24.75-b04, mixed mode)
> > 
> > 5) What about other Java applications?  eg. Acacia, Artemis?
> > 
> > Cheers,
> > 
> > TIM
> > 
> > ________________________________________
> > From: Sejal Modha [sejal.modha at glasgow.ac.uk]
> > Sent: 16 March 2015 10:26
> > To: Bio-Linux help and discussion
> > Subject: [Bio-Linux] Tablet and x2go crashes the current session
> > 
> > Hi There,
> > 
> > BioLinux users at our centre are unable to run Tablet on the server running BioLinux.
> > x2go session crashes at the user end as soon as they launch the application.
> > 
> > I was wondering if anyone else is facing similar problems or can propose a solution to fix it.
> > 
> > Many thanks for your help in advance.
> > 
> > Sej
> > Sejal Modha
> > 
> > Bioinformatician
> > MRC-University of Glasgow Centre for Virus Research
> > 117 Sir Michael Stoker Building
> > 464 Bearsden Road
> > Glasgow
> > G61 1QH
> > Tel: 0141-330-4019
> > http://bioinformatics.cvr.ac.uk
> > 
> > This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > 
> 
> 
> -- 
> Sejal Modha
> 
> Bioinformatician
> MRC-University of Glasgow Centre for Virus Research
> 117 Sir Michael Stoker Building
> 464 Bearsden Road
> Glasgow
> G61 1QH
> Tel: 0141-330-4019
> http://bioinformatics.cvr.ac.uk

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From tbooth at ceh.ac.uk  Wed Mar 18 11:11:03 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 18 Mar 2015 15:11:03 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
In-Reply-To: <B1F4E9B78FFD5F4F88055C0B649FD3B7C7603605@CHEXMBX1.livad.liv.ac.uk>
References: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
 <5506B126.8090507@abdn.ac.uk>
 <B1F4E9B78FFD5F4F88055C0B649FD3B7C7603605@CHEXMBX1.livad.liv.ac.uk>
Message-ID: <1426691463.28109.37.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Angela,

When you say "The pymol install sits under the python libs." do you mean
you installed PyMol manually?  Could you please try the version you get
from running "apt-get install pymol" and tell me if that makes any
difference?

Cheers,

TIM

On Wed, 2015-03-18 at 12:48 +0000, Rosin, Angela wrote:
> 
> > -----Original Message-----
> > From: Tony Travis [mailto:tony.travis at abdn.ac.uk] 
> >
> > Hi, Angela.
> >
> > Yes, we had similar problems running RStudio on a MATE remote desktop.
> >
> > Tim discovered that this was caused by the Qt binaries bundled in the RStudio .deb. A similar fix might work for you:
> 
> I don't think so. I've got a feeling its to do with the graphics library but I can't find anything immediately obvious. The pymol install sits under the python libs.  Thanks for the help.
> 
> Ang
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From lister at liverpool.ac.uk  Wed Mar 18 11:36:15 2015
From: lister at liverpool.ac.uk (Rosin, Angela)
Date: Wed, 18 Mar 2015 15:36:15 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
In-Reply-To: <1426691463.28109.37.camel@wllt1771.nerc-wallingford.ac.uk>
References: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
 <5506B126.8090507@abdn.ac.uk>
 <B1F4E9B78FFD5F4F88055C0B649FD3B7C7603605@CHEXMBX1.livad.liv.ac.uk>,
 <1426691463.28109.37.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <AEE84107-F3A4-412C-B9BD-5AF777B991B5@liverpool.ac.uk>

Hi Tim,

No. I used the distribution through apt-get (version 1.7).

Angela Rosin
Technology Enhanced Learning (TEL) Support Technician/Supervisor
Institute of Learning and Teaching | Faculty of Health and Life Sciences | Life Sciences Building
e: lister at liv.ac.uk<mailto:lister at liv.ac.uk> t: 0151 795 5139<tel:0151%20795%205139> w: http://www.liv.ac.uk/learning-and-teaching/tel/

On 18 Mar 2015, at 15:11, Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>> wrote:

Hi Angela,

When you say "The pymol install sits under the python libs." do you mean
you installed PyMol manually?  Could you please try the version you get
from running "apt-get install pymol" and tell me if that makes any
difference?

Cheers,

TIM

On Wed, 2015-03-18 at 12:48 +0000, Rosin, Angela wrote:

-----Original Message-----
From: Tony Travis [mailto:tony.travis at abdn.ac.uk]

Hi, Angela.

Yes, we had similar problems running RStudio on a MATE remote desktop.

Tim discovered that this was caused by the Qt binaries bundled in the RStudio .deb. A similar fix might work for you:

I don't think so. I've got a feeling its to do with the graphics library but I can't find anything immediately obvious. The pymol install sits under the python libs.  Thanks for the help.

Ang
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

--
Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://environmentalomics.org/bio-linux
+44 1491 69 2297

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
-------------- next part --------------
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From tbooth at ceh.ac.uk  Wed Mar 18 13:25:26 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 18 Mar 2015 17:25:26 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
In-Reply-To: <AEE84107-F3A4-412C-B9BD-5AF777B991B5@liverpool.ac.uk>
References: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
 <5506B126.8090507@abdn.ac.uk>
 <B1F4E9B78FFD5F4F88055C0B649FD3B7C7603605@CHEXMBX1.livad.liv.ac.uk>
 , <1426691463.28109.37.camel@wllt1771.nerc-wallingford.ac.uk>
 <AEE84107-F3A4-412C-B9BD-5AF777B991B5@liverpool.ac.uk>
Message-ID: <1426699526.28109.41.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Angela,

I do apologise - I see you already told me that and I didn't read your
first e-mail properly.

I've reproduced the problem and I think I may have a workaround for you,
by setting the environment variable LIBGL_ALWAYS_INDIRECT - eg:

$ env LIBGL_ALWAYS_INDIRECT=1 pymol

Does that help?

Cheers,

TIM

On Wed, 2015-03-18 at 15:36 +0000, Rosin, Angela wrote:
> Hi Tim,
> 
> 
> No. I used the distribution through apt-get (version 1.7). 
> 
> Angela Rosin
> Technology Enhanced Learning (TEL) Support Technician/Supervisor
> Institute of Learning and Teaching | Faculty of Health and Life
> Sciences | Life Sciences Building
> e: lister at liv.ac.uk t: 0151 795
> 5139 w: http://www.liv.ac.uk/learning-and-teaching/tel/
> 
> On 18 Mar 2015, at 15:11, Tim Booth <tbooth at ceh.ac.uk> wrote:
> 
> 
> > Hi Angela,
> > 
> > When you say "The pymol install sits under the python libs." do you
> > mean
> > you installed PyMol manually?  Could you please try the version you
> > get
> > from running "apt-get install pymol" and tell me if that makes any
> > difference?
> > 
> > Cheers,
> > 
> > TIM
> > 
> > On Wed, 2015-03-18 at 12:48 +0000, Rosin, Angela wrote:
> > > 
> > > > -----Original Message-----
> > > > From: Tony Travis [mailto:tony.travis at abdn.ac.uk]
> > > > 
> > > > Hi, Angela.
> > > > 
> > > > Yes, we had similar problems running RStudio on a MATE remote
> > > > desktop.
> > > > 
> > > > Tim discovered that this was caused by the Qt binaries bundled
> > > > in the RStudio .deb. A similar fix might work for you:
> > > 
> > > I don't think so. I've got a feeling its to do with the graphics
> > > library but I can't find anything immediately obvious. The pymol
> > > install sits under the python libs.  Thanks for the help.
> > > 
> > > Ang
> > > _______________________________________________
> > > Bio-Linux mailing list
> > > Bio-Linux at nebclists.nerc.ac.uk
> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > 
> > -- 
> > Tim Booth <tbooth at ceh.ac.uk>
> > NERC Environmental Bioinformatics Centre 
> > 
> > Centre for Ecology and Hydrology
> > Maclean Bldg, Benson Lane
> > Crowmarsh Gifford
> > Wallingford, England
> > OX10 8BB 
> > 
> > http://environmentalomics.org/bio-linux
> > +44 1491 69 2297
> > 
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From thackray at rci.rutgers.edu  Wed Mar 18 22:57:39 2015
From: thackray at rci.rutgers.edu (Josh Thackray)
Date: Wed, 18 Mar 2015 22:57:39 -0400
Subject: [Bio-Linux] MACS update
Message-ID: <550A3B23.8050309@rci.rutgers.edu>

Hi,

I would like to request for an update to MACS. Looks like the current 
package version is 1.4.1 which has a bug where paired end reads are not 
parsed properly from sam/bam files (quite important to me at the 
moment). Also some later versions have some nice additional features 
such as ability to specify output directory.

It would also be nice to see a package for MACS2.

Thanks,

Josh

-- 
Josh Thackray
Laboratory Researcher III
Human Genetics Institute of NJ
Department of Genetics
Rutgers University



From tbooth at ceh.ac.uk  Thu Mar 19 07:43:12 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 19 Mar 2015 11:43:12 +0000
Subject: [Bio-Linux] MACS update
In-Reply-To: <550A3B23.8050309@rci.rutgers.edu>
References: <550A3B23.8050309@rci.rutgers.edu>
Message-ID: <1426765392.11944.7.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Josh,

Thanks for the heads-up.  I've updated the macs14 package to MACS 1.4.2
which I guess addresses the bug.  It's building on the build server just
now.

There is a package for MACS 2:

The macs14 package provides 'macs14' and 'macs' as a synonym
The macs package provides 'macs2'

Confusing, I know, but changing it would break programs and scripts that
expect 'macs' to be MACS 1.4.  I've added this explanation to the macs
manpage in the updated package, and also to the package notes.

Cheers,

TIM

On Thu, 2015-03-19 at 02:57 +0000, Josh Thackray wrote:
> Hi,
> 
> I would like to request for an update to MACS. Looks like the current 
> package version is 1.4.1 which has a bug where paired end reads are not 
> parsed properly from sam/bam files (quite important to me at the 
> moment). Also some later versions have some nice additional features 
> such as ability to specify output directory.
> 
> It would also be nice to see a package for MACS2.
> 
> Thanks,
> 
> Josh
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From lister at liverpool.ac.uk  Thu Mar 19 09:17:34 2015
From: lister at liverpool.ac.uk (Rosin, Angela)
Date: Thu, 19 Mar 2015 13:17:34 +0000
Subject: [Bio-Linux] Running pymol through x2Go. Crashes
In-Reply-To: <1426699526.28109.41.camel@wllt1771.nerc-wallingford.ac.uk>
References: <B1F4E9B78FFD5F4F88055C0B649FD3B7C30C19A5@CHEXMBX1.livad.liv.ac.uk>
 <5506B126.8090507@abdn.ac.uk>
 <B1F4E9B78FFD5F4F88055C0B649FD3B7C7603605@CHEXMBX1.livad.liv.ac.uk> ,
 <1426691463.28109.37.camel@wllt1771.nerc-wallingford.ac.uk>
 <AEE84107-F3A4-412C-B9BD-5AF777B991B5@liverpool.ac.uk>,
 <1426699526.28109.41.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <41F28AC6-29FB-4590-AD1E-D055A2A08119@liverpool.ac.uk>

Thanks Tim. That's fixed it, I'm so grateful you had a look.

Angela Rosin
Technology Enhanced Learning (TEL) Support Technician/Supervisor
Institute of Learning and Teaching | Faculty of Health and Life Sciences | Life Sciences Building
e: lister at liv.ac.uk<mailto:lister at liv.ac.uk> t: 0151 795 5139<tel:0151%20795%205139> w: http://www.liv.ac.uk/learning-and-teaching/tel/

On 18 Mar 2015, at 17:25, Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>> wrote:

Hi Angela,

I do apologise - I see you already told me that and I didn't read your
first e-mail properly.

I've reproduced the problem and I think I may have a workaround for you,
by setting the environment variable LIBGL_ALWAYS_INDIRECT - eg:

$ env LIBGL_ALWAYS_INDIRECT=1 pymol

Does that help?

Cheers,

TIM

On Wed, 2015-03-18 at 15:36 +0000, Rosin, Angela wrote:
Hi Tim,


No. I used the distribution through apt-get (version 1.7).

Angela Rosin
Technology Enhanced Learning (TEL) Support Technician/Supervisor
Institute of Learning and Teaching | Faculty of Health and Life
Sciences | Life Sciences Building
e: lister at liv.ac.uk<mailto:lister at liv.ac.uk> t: 0151 795
5139 w: http://www.liv.ac.uk/learning-and-teaching/tel/

On 18 Mar 2015, at 15:11, Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>> wrote:


Hi Angela,

When you say "The pymol install sits under the python libs." do you
mean
you installed PyMol manually?  Could you please try the version you
get
from running "apt-get install pymol" and tell me if that makes any
difference?

Cheers,

TIM

On Wed, 2015-03-18 at 12:48 +0000, Rosin, Angela wrote:

-----Original Message-----
From: Tony Travis [mailto:tony.travis at abdn.ac.uk]

Hi, Angela.

Yes, we had similar problems running RStudio on a MATE remote
desktop.

Tim discovered that this was caused by the Qt binaries bundled
in the RStudio .deb. A similar fix might work for you:

I don't think so. I've got a feeling its to do with the graphics
library but I can't find anything immediately obvious. The pymol
install sits under the python libs.  Thanks for the help.

Ang
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

--
Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://environmentalomics.org/bio-linux
+44 1491 69 2297

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


--
Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://environmentalomics.org/bio-linux
+44 1491 69 2297

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
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From stefano.campanaro at gmail.com  Fri Mar 27 12:54:58 2015
From: stefano.campanaro at gmail.com (Stefano Campanaro)
Date: Fri, 27 Mar 2015 17:54:58 +0100
Subject: [Bio-Linux] is it possible to install biolinux on a dell server
 with 64Gb RAM and 16 cores?
Message-ID: <CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ@mail.gmail.com>

Hi,
I would install biolinux on a recently acquired DELL server with 64Gb RAM
and 16 cores. I would have some suggestions from users that are using bio
linux on servers with similar characteristics.
Thank you
Sincerely
-- 
Stefano
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From tony.travis at minke-informatics.co.uk  Fri Mar 27 13:19:43 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Fri, 27 Mar 2015 17:19:43 +0000
Subject: [Bio-Linux] is it possible to install biolinux on a dell server
 with 64Gb RAM and 16 cores?
In-Reply-To: <CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ@mail.gmail.com>
References: <CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ@mail.gmail.com>
Message-ID: <5515912F.2030803@minke-informatics.co.uk>

On 27/03/15 16:54, Stefano Campanaro wrote:
> Hi,
> I would install biolinux on a recently acquired DELL server with 64Gb
> RAM and 16 cores. I would have some suggestions from users that are
> using bio linux on servers with similar characteristics.

Hi, Stefano.

I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
8-core Opteron 6128 CPU's and 128GiB RAM in each at the University of
Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to boot
from RAID6 if it's not degraded.

I've also set up Bio-Linux terminal servers many times in the past, for
example at the Wellcome Trust Centre for Cell Biology in Edinburgh, and
I helped my friends at Assam Agricultural University set up Bio-Linux 8
servers there for a training course we held recently.

Bio-Linux 8 works very well as an "x2go" or SSH terminal server, thanks
to the efforts that Tim and his team at EOS have put into Bio-Linux 8.

I've got 10 at SATA2 drives in each of our three Bio-Linux servers here:

6 at 2TB:
	RAID1 /boot
	RAID6 /, swap, /usr/local, /home, work

2 at 4TB:
	JBOD /backup1
	JBOD /backup2

2 at 4TB:
	JBOD /archive
	JBOD /scratch

Let me know if there is anything I can do to help?

If you boot your server from a Bio-Linux USB-stick and let me in through
your firewall I can install it for you remotely. I've done this several
times already for disaster recovery on an EU FP-6 project.

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk


From M.D.Sharma at exeter.ac.uk  Fri Mar 27 13:17:56 2015
From: M.D.Sharma at exeter.ac.uk (Sharma, M D)
Date: Fri, 27 Mar 2015 17:17:56 +0000
Subject: [Bio-Linux] is it possible to install biolinux on a dell server
 with 64Gb RAM and 16 cores?
In-Reply-To: <CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ@mail.gmail.com>
References: <CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ@mail.gmail.com>
Message-ID: <vackbrvwh29b5de7j29erggg.1427476673744@email.android.com>

Absolutely... I have it as you described and also with 64 cores and 512 GB of RAM..

Sent from my HTC

On 27 Mar 2015 16:55, Stefano Campanaro <stefano.campanaro at gmail.com> wrote:
Hi,
I would install biolinux on a recently acquired DELL server with 64Gb RAM and 16 cores. I would have some suggestions from users that are using bio linux on servers with similar characteristics.
Thank you
Sincerely
--
Stefano
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From mkmodi at aau.ac.in  Mon Mar 30 06:38:04 2015
From: mkmodi at aau.ac.in (Mahendra Modi)
Date: Mon, 30 Mar 2015 16:08:04 +0530
Subject: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 16
In-Reply-To: <mailman.1.1427544001.19080.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1427544001.19080.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <CAPUhUGx419u3XA2mC2R+LgaSKBDTkVBc9UiqBHvn=oxQTkhrUg@mail.gmail.com>

Hi,

We are running 3(three) servers with Bio-linux 8 and one of the me is a
Dell r520 with 2 8core Xeon processors and 128GiB RAM. Tony Travis from
Aberdeen University helped us in customisation of the servers. We use these
servers for NGS data analysis and Simulation studies using Gromacs.

Mahendra



On Sat, Mar 28, 2015 at 5:30 PM, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:

> Send Bio-Linux mailing list submissions to
>         bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
>         bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
>         bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
>    1. is it possible to install biolinux on a dell server with 64Gb
>       RAM and 16 cores? (Stefano Campanaro)
>    2. Re: is it possible to install biolinux on a dell server with
>       64Gb RAM and 16 cores? (Tony Travis)
>    3. Re: is it possible to install biolinux on a dell server with
>       64Gb RAM and 16 cores? (Sharma, M D)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 27 Mar 2015 17:54:58 +0100
> From: Stefano Campanaro <stefano.campanaro at gmail.com>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] is it possible to install biolinux on a dell
>         server with 64Gb RAM and 16 cores?
> Message-ID:
>         <
> CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I would install biolinux on a recently acquired DELL server with 64Gb RAM
> and 16 cores. I would have some suggestions from users that are using bio
> linux on servers with similar characteristics.
> Thank you
> Sincerely
> --
> Stefano
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/2dbe225a/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Fri, 27 Mar 2015 17:19:43 +0000
> From: Tony Travis <tony.travis at minke-informatics.co.uk>
> To: <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
>         server with 64Gb RAM and 16 cores?
> Message-ID: <5515912F.2030803 at minke-informatics.co.uk>
> Content-Type: text/plain; charset="windows-1252"
>
> On 27/03/15 16:54, Stefano Campanaro wrote:
> > Hi,
> > I would install biolinux on a recently acquired DELL server with 64Gb
> > RAM and 16 cores. I would have some suggestions from users that are
> > using bio linux on servers with similar characteristics.
>
> Hi, Stefano.
>
> I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
> 8-core Opteron 6128 CPU's and 128GiB RAM in each at the University of
> Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
> from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to boot
> from RAID6 if it's not degraded.
>
> I've also set up Bio-Linux terminal servers many times in the past, for
> example at the Wellcome Trust Centre for Cell Biology in Edinburgh, and
> I helped my friends at Assam Agricultural University set up Bio-Linux 8
> servers there for a training course we held recently.
>
> Bio-Linux 8 works very well as an "x2go" or SSH terminal server, thanks
> to the efforts that Tim and his team at EOS have put into Bio-Linux 8.
>
> I've got 10 at SATA2 drives in each of our three Bio-Linux servers here:
>
> 6 at 2TB:
>         RAID1 /boot
>         RAID6 /, swap, /usr/local, /home, work
>
> 2 at 4TB:
>         JBOD /backup1
>         JBOD /backup2
>
> 2 at 4TB:
>         JBOD /archive
>         JBOD /scratch
>
> Let me know if there is anything I can do to help?
>
> If you boot your server from a Bio-Linux USB-stick and let me in through
> your firewall I can install it for you remotely. I've done this several
> times already for disaster recovery on an EU FP-6 project.
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 27 Mar 2015 17:17:56 +0000
> From: "Sharma, M D" <M.D.Sharma at exeter.ac.uk>
> To: Stefano Campanaro <stefano.campanaro at gmail.com>, "Bio-Linux help
>         and discussion" <bio-linux at nebclists.nerc.ac.uk>,
>         "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
>         server with 64Gb RAM and 16 cores?
> Message-ID: <vackbrvwh29b5de7j29erggg.1427476673744 at email.android.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Absolutely... I have it as you described and also with 64 cores and 512 GB
> of RAM..
>
> Sent from my HTC
>
> On 27 Mar 2015 16:55, Stefano Campanaro <stefano.campanaro at gmail.com>
> wrote:
> Hi,
> I would install biolinux on a recently acquired DELL server with 64Gb RAM
> and 16 cores. I would have some suggestions from users that are using bio
> linux on servers with similar characteristics.
> Thank you
> Sincerely
> --
> Stefano
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/3695ba87/attachment-0001.html
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 16
> *****************************************
>



-- 
________________________
Prof. Mahendra K Modi
Head, Agril Biotechnology & Coordinator, DIC
Assam Agricultural University
Jorhat 785013, India
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From robtyx at yahoo.com  Mon Mar 30 07:25:18 2015
From: robtyx at yahoo.com (Robert Tyx)
Date: Mon, 30 Mar 2015 04:25:18 -0700
Subject: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 17
In-Reply-To: <mailman.1.1427713201.28071.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <1427714718.45474.YahooMailAndroidMobile@web140803.mail.bf1.yahoo.com>

Hi,?

In contrast to Mohendra, I have not been able to get BL8 to install successfully on a Dell R720. There's probably a way to get it to work (special drivers or something) but I don't know. It gets a kernel panic pretty quickly every time. For what it's worth, vanilla Ubuntu 14.04 LTS workstation does not install either, but the server version works fine. BL 7 works fine on this system also...

Sent from Yahoo Mail on Android

From:"bio-linux-request at nebclists.nerc.ac.uk" <bio-linux-request at nebclists.nerc.ac.uk>
Date:Mon, Mar 30, 2015 at 7:00 AM
Subject:Bio-Linux Digest, Vol 78, Issue 17

Send Bio-Linux mailing list submissions to
??? bio-linux at nebclists.nerc.ac.uk

To subscribe or unsubscribe via the World Wide Web, visit
??? http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
or, via email, send a message with subject or body 'help' to
??? bio-linux-request at nebclists.nerc.ac.uk

You can reach the person managing the list at
??? bio-linux-owner at nebclists.nerc.ac.uk

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Bio-Linux digest..."


Today's Topics:

? 1. Re: Bio-Linux Digest, Vol 78, Issue 16 (Mahendra Modi)


----------------------------------------------------------------------

Message: 1
Date: Mon, 30 Mar 2015 16:08:04 +0530
From: Mahendra Modi <mkmodi at aau.ac.in>
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 16
Message-ID:
??? <CAPUhUGx419u3XA2mC2R+LgaSKBDTkVBc9UiqBHvn=oxQTkhrUg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi,

We are running 3(three) servers with Bio-linux 8 and one of the me is a
Dell r520 with 2 8core Xeon processors and 128GiB RAM. Tony Travis from
Aberdeen University helped us in customisation of the servers. We use these
servers for NGS data analysis and Simulation studies using Gromacs.

Mahendra



On Sat, Mar 28, 2015 at 5:30 PM, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:

> Send Bio-Linux mailing list submissions to
>? ? ? ? bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
>? ? ? ? http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
>? ? ? ? bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
>? ? ? ? bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
>? ? 1. is it possible to install biolinux on a dell server with 64Gb
>? ? ? RAM and 16 cores? (Stefano Campanaro)
>? ? 2. Re: is it possible to install biolinux on a dell server with
>? ? ? 64Gb RAM and 16 cores? (Tony Travis)
>? ? 3. Re: is it possible to install biolinux on a dell server with
>? ? ? 64Gb RAM and 16 cores? (Sharma, M D)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 27 Mar 2015 17:54:58 +0100
> From: Stefano Campanaro <stefano.campanaro at gmail.com>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] is it possible to install biolinux on a dell
>? ? ? ? server with 64Gb RAM and 16 cores?
> Message-ID:
>? ? ? ? <
> CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I would install biolinux on a recently acquired DELL server with 64Gb RAM
> and 16 cores. I would have some suggestions from users that are using bio
> linux on servers with similar characteristics.
> Thank you
> Sincerely
> --
> Stefano
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/2dbe225a/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Fri, 27 Mar 2015 17:19:43 +0000
> From: Tony Travis <tony.travis at minke-informatics.co.uk>
> To: <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
>? ? ? ? server with 64Gb RAM and 16 cores?
> Message-ID: <5515912F.2030803 at minke-informatics.co.uk>
> Content-Type: text/plain; charset="windows-1252"
>
> On 27/03/15 16:54, Stefano Campanaro wrote:
> > Hi,
> > I would install biolinux on a recently acquired DELL server with 64Gb
> > RAM and 16 cores. I would have some suggestions from users that are
> > using bio linux on servers with similar characteristics.
>
> Hi, Stefano.
>
> I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
> 8-core Opteron 6128 CPU's and 128GiB RAM in each at the University of
> Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
> from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to boot
> from RAID6 if it's not degraded.
>
> I've also set up Bio-Linux terminal servers many times in the past, for
> example at the Wellcome Trust Centre for Cell Biology in Edinburgh, and
> I helped my friends at Assam Agricultural University set up Bio-Linux 8
> servers there for a training course we held recently.
>
> Bio-Linux 8 works very well as an "x2go" or SSH terminal server, thanks
> to the efforts that Tim and his team at EOS have put into Bio-Linux 8.
>
> I've got 10 at SATA2 drives in each of our three Bio-Linux servers here:
>
> 6 at 2TB:
>? ? ? ? RAID1 /boot
>? ? ? ? RAID6 /, swap, /usr/local, /home, work
>
> 2 at 4TB:
>? ? ? ? JBOD /backup1
>? ? ? ? JBOD /backup2
>
> 2 at 4TB:
>? ? ? ? JBOD /archive
>? ? ? ? JBOD /scratch
>
> Let me know if there is anything I can do to help?
>
> If you boot your server from a Bio-Linux USB-stick and let me in through
> your firewall I can install it for you remotely. I've done this several
> times already for disaster recovery on an EU FP-6 project.
>
>? Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548? ? ? ? ? ? ? ? ? ? http://minke-informatics.co.uk
> mob. +44(0)7985 078324? ? ? ? mailto:tony.travis at minke-informatics.co.uk
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 27 Mar 2015 17:17:56 +0000
> From: "Sharma, M D" <M.D.Sharma at exeter.ac.uk>
> To: Stefano Campanaro <stefano.campanaro at gmail.com>, "Bio-Linux help
>? ? ? ? and discussion" <bio-linux at nebclists.nerc.ac.uk>,
>? ? ? ? "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
>? ? ? ? server with 64Gb RAM and 16 cores?
> Message-ID: <vackbrvwh29b5de7j29erggg.1427476673744 at email.android.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Absolutely... I have it as you described and also with 64 cores and 512 GB
> of RAM..
>
> Sent from my HTC
>
> On 27 Mar 2015 16:55, Stefano Campanaro <stefano.campanaro at gmail.com>
> wrote:
> Hi,
> I would install biolinux on a recently acquired DELL server with 64Gb RAM
> and 16 cores. I would have some suggestions from users that are using bio
> linux on servers with similar characteristics.
> Thank you
> Sincerely
> --
> Stefano
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/3695ba87/attachment-0001.html
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 16
> *****************************************
>



-- 
________________________
Prof. Mahendra K Modi
Head, Agril Biotechnology & Coordinator, DIC
Assam Agricultural University
Jorhat 785013, India
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------------------------------

Subject: Digest Footer

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


------------------------------

End of Bio-Linux Digest, Vol 78, Issue 17
*****************************************

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From tbooth at ceh.ac.uk  Mon Mar 30 08:18:05 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 30 Mar 2015 13:18:05 +0100
Subject: [Bio-Linux] Bio-Linux on Dell R720
In-Reply-To: <1427714718.45474.YahooMailAndroidMobile@web140803.mail.bf1.yahoo.com>
References: <1427714718.45474.YahooMailAndroidMobile@web140803.mail.bf1.yahoo.com>
Message-ID: <1427717885.12632.5.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Robert,

Strange that you should find the server version of 14.04 works but the
desktop doesn't, because the kernel and drivers are identical.  The
server installer just puts on a different selection of packages.  Is it
possible that the Unity desktop, which uses the 3D capabilities of the
graphics card, is triggering the crash, do you think?

So does this mean you are running vanilla 14.04 from the server
installation and installing just the Bio-Linux packages you need, or did
you try using my upgrade script to add all the Bio-Linux stuff in one
go?

Cheers,

TIM

On Mon, 2015-03-30 at 12:25 +0100, Robert Tyx wrote:
> Hi, 
> In contrast to Mohendra, I have not been able to get BL8 to install
> successfully on a Dell R720. There's probably a way to get it to work
> (special drivers or something) but I don't know. It gets a kernel
> panic pretty quickly every time. For what it's worth, vanilla Ubuntu
> 14.04 LTS workstation does not install either, but the server version
> works fine. BL 7 works fine on this system also...
> 
> 
> 
> Sent from Yahoo Mail on Android
> 
> 
> ______________________________________________________________________
> From:"bio-linux-request at nebclists.nerc.ac.uk"
> <bio-linux-request at nebclists.nerc.ac.uk>
> Date:Mon, Mar 30, 2015 at 7:00 AM
> Subject:Bio-Linux Digest, Vol 78, Issue 17
> 
> 
> Send Bio-Linux mailing list submissions to
>     bio-linux at nebclists.nerc.ac.uk
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>     http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
>     bio-linux-request at nebclists.nerc.ac.uk
> 
> You can reach the person managing the list at
>     bio-linux-owner at nebclists.nerc.ac.uk
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Bio-Linux Digest, Vol 78, Issue 16 (Mahendra Modi)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 30 Mar 2015 16:08:04 +0530
> From: Mahendra Modi <mkmodi at aau.ac.in>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 16
> Message-ID:
>     <CAPUhUGx419u3XA2mC2R
> +LgaSKBDTkVBc9UiqBHvn=oxQTkhrUg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi,
> 
> We are running 3(three) servers with Bio-linux 8 and one of the me is
> a
> Dell r520 with 2 8core Xeon processors and 128GiB RAM. Tony Travis
> from
> Aberdeen University helped us in customisation of the servers. We use
> these
> servers for NGS data analysis and Simulation studies using Gromacs.
> 
> Mahendra
> 
> 
> 
> On Sat, Mar 28, 2015 at 5:30 PM,
> <bio-linux-request at nebclists.nerc.ac.uk>
> wrote:
> 
> > Send Bio-Linux mailing list submissions to
> >        bio-linux at nebclists.nerc.ac.uk
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >        http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > or, via email, send a message with subject or body 'help' to
> >        bio-linux-request at nebclists.nerc.ac.uk
> >
> > You can reach the person managing the list at
> >        bio-linux-owner at nebclists.nerc.ac.uk
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bio-Linux digest..."
> >
> >
> > Today's Topics:
> >
> >    1. is it possible to install biolinux on a dell server with 64Gb
> >      RAM and 16 cores? (Stefano Campanaro)
> >    2. Re: is it possible to install biolinux on a dell server with
> >      64Gb RAM and 16 cores? (Tony Travis)
> >    3. Re: is it possible to install biolinux on a dell server with
> >      64Gb RAM and 16 cores? (Sharma, M D)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 27 Mar 2015 17:54:58 +0100
> > From: Stefano Campanaro <stefano.campanaro at gmail.com>
> > To: bio-linux at nebclists.nerc.ac.uk
> > Subject: [Bio-Linux] is it possible to install biolinux on a dell
> >        server with 64Gb RAM and 16 cores?
> > Message-ID:
> >        <
> > CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> > I would install biolinux on a recently acquired DELL server with
> 64Gb RAM
> > and 16 cores. I would have some suggestions from users that are
> using bio
> > linux on servers with similar characteristics.
> > Thank you
> > Sincerely
> > --
> > Stefano
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/2dbe225a/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 27 Mar 2015 17:19:43 +0000
> > From: Tony Travis <tony.travis at minke-informatics.co.uk>
> > To: <bio-linux at nebclists.nerc.ac.uk>
> > Subject: Re: [Bio-Linux] is it possible to install biolinux on a
> dell
> >        server with 64Gb RAM and 16 cores?
> > Message-ID: <5515912F.2030803 at minke-informatics.co.uk>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > On 27/03/15 16:54, Stefano Campanaro wrote:
> > > Hi,
> > > I would install biolinux on a recently acquired DELL server with
> 64Gb
> > > RAM and 16 cores. I would have some suggestions from users that
> are
> > > using bio linux on servers with similar characteristics.
> >
> > Hi, Stefano.
> >
> > I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
> > 8-core Opteron 6128 CPU's and 128GiB RAM in each at the University
> of
> > Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
> > from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to
> boot
> > from RAID6 if it's not degraded.
> >
> > I've also set up Bio-Linux terminal servers many times in the past,
> for
> > example at the Wellcome Trust Centre for Cell Biology in Edinburgh,
> and
> > I helped my friends at Assam Agricultural University set up
> Bio-Linux 8
> > servers there for a training course we held recently.
> >
> > Bio-Linux 8 works very well as an "x2go" or SSH terminal server,
> thanks
> > to the efforts that Tim and his team at EOS have put into Bio-Linux
> 8.
> >
> > I've got 10 at SATA2 drives in each of our three Bio-Linux servers
> here:
> >
> > 6 at 2TB:
> >        RAID1 /boot
> >        RAID6 /, swap, /usr/local, /home, work
> >
> > 2 at 4TB:
> >        JBOD /backup1
> >        JBOD /backup2
> >
> > 2 at 4TB:
> >        JBOD /archive
> >        JBOD /scratch
> >
> > Let me know if there is anything I can do to help?
> >
> > If you boot your server from a Bio-Linux USB-stick and let me in
> through
> > your firewall I can install it for you remotely. I've done this
> several
> > times already for disaster recovery on an EU FP-6 project.
> >
> >  Tony.
> >
> > --
> > Minke Informatics Limited, Registered in Scotland - Company No.
> SC419028
> > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland
> (UK)
> > tel. +44(0)19755 63548
> http://minke-informatics.co.uk
> > mob. +44(0)7985 078324
> mailto:tony.travis at minke-informatics.co.uk
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Fri, 27 Mar 2015 17:17:56 +0000
> > From: "Sharma, M D" <M.D.Sharma at exeter.ac.uk>
> > To: Stefano Campanaro <stefano.campanaro at gmail.com>, "Bio-Linux help
> >        and discussion" <bio-linux at nebclists.nerc.ac.uk>,
> >        "bio-linux at nebclists.nerc.ac.uk"
> <bio-linux at nebclists.nerc.ac.uk>
> > Subject: Re: [Bio-Linux] is it possible to install biolinux on a
> dell
> >        server with 64Gb RAM and 16 cores?
> > Message-ID:
> <vackbrvwh29b5de7j29erggg.1427476673744 at email.android.com>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Absolutely... I have it as you described and also with 64 cores and
> 512 GB
> > of RAM..
> >
> > Sent from my HTC
> >
> > On 27 Mar 2015 16:55, Stefano Campanaro
> <stefano.campanaro at gmail.com>
> > wrote:
> > Hi,
> > I would install biolinux on a recently acquired DELL server with
> 64Gb RAM
> > and 16 cores. I would have some suggestions from users that are
> using bio
> > linux on servers with similar characteristics.
> > Thank you
> > Sincerely
> > --
> > Stefano
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/3695ba87/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> > ------------------------------
> >
> > End of Bio-Linux Digest, Vol 78, Issue 16
> > *****************************************
> >
> 
> 
> 
> -- 
> ________________________
> Prof. Mahendra K Modi
> Head, Agril Biotechnology & Coordinator, DIC
> Assam Agricultural University
> Jorhat 785013, India
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> <http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150330/ced686e3/attachment-0001.html>
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> 
> ------------------------------
> 
> End of Bio-Linux Digest, Vol 78, Issue 17
> *****************************************
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297



From mkmodi at aau.ac.in  Mon Mar 30 08:26:53 2015
From: mkmodi at aau.ac.in (Mahendra Modi)
Date: Mon, 30 Mar 2015 17:56:53 +0530
Subject: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 18
In-Reply-To: <mailman.37.1427717876.2858.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.37.1427717876.2858.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <CAPUhUGxsPEr6URG3E-1LMaF4XxhMzobyUeZowqemDEHNg2qQGg@mail.gmail.com>

Hi Robert,

You will need to set nomodeset immediately after you see the splash screen
as the graphics chip is not sufficient to run unity desktop. Once you may
edit grub to include nomodeset and choose to run the mate terminal instead
of ubuntu. I think thats what I did to get my system going.

Mahendra

On Mon, Mar 30, 2015 at 5:47 PM, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:

> Send Bio-Linux mailing list submissions to
>         bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
>         bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
>         bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
>    1. Re: Bio-Linux Digest, Vol 78, Issue 17 (Robert Tyx)
>    2. Re: Bio-Linux on Dell R720 (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Mar 2015 04:25:18 -0700
> From: Robert Tyx <robtyx at yahoo.com>
> To: "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 17
> Message-ID:
>         <
> 1427714718.45474.YahooMailAndroidMobile at web140803.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,?
>
> In contrast to Mohendra, I have not been able to get BL8 to install
> successfully on a Dell R720. There's probably a way to get it to work
> (special drivers or something) but I don't know. It gets a kernel panic
> pretty quickly every time. For what it's worth, vanilla Ubuntu 14.04 LTS
> workstation does not install either, but the server version works fine. BL
> 7 works fine on this system also...
>
> Sent from Yahoo Mail on Android
>
> From:"bio-linux-request at nebclists.nerc.ac.uk" <
> bio-linux-request at nebclists.nerc.ac.uk>
> Date:Mon, Mar 30, 2015 at 7:00 AM
> Subject:Bio-Linux Digest, Vol 78, Issue 17
>
> Send Bio-Linux mailing list submissions to
> ??? bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
> ??? http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
> ??? bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
> ??? bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
> ? 1. Re: Bio-Linux Digest, Vol 78, Issue 16 (Mahendra Modi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Mar 2015 16:08:04 +0530
> From: Mahendra Modi <mkmodi at aau.ac.in>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 16
> Message-ID:
> ??? <CAPUhUGx419u3XA2mC2R+LgaSKBDTkVBc9UiqBHvn=oxQTkhrUg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> We are running 3(three) servers with Bio-linux 8 and one of the me is a
> Dell r520 with 2 8core Xeon processors and 128GiB RAM. Tony Travis from
> Aberdeen University helped us in customisation of the servers. We use these
> servers for NGS data analysis and Simulation studies using Gromacs.
>
> Mahendra
>
>
>
> On Sat, Mar 28, 2015 at 5:30 PM, <bio-linux-request at nebclists.nerc.ac.uk>
> wrote:
>
> > Send Bio-Linux mailing list submissions to
> >? ? ? ? bio-linux at nebclists.nerc.ac.uk
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >? ? ? ? http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > or, via email, send a message with subject or body 'help' to
> >? ? ? ? bio-linux-request at nebclists.nerc.ac.uk
> >
> > You can reach the person managing the list at
> >? ? ? ? bio-linux-owner at nebclists.nerc.ac.uk
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bio-Linux digest..."
> >
> >
> > Today's Topics:
> >
> >? ? 1. is it possible to install biolinux on a dell server with 64Gb
> >? ? ? RAM and 16 cores? (Stefano Campanaro)
> >? ? 2. Re: is it possible to install biolinux on a dell server with
> >? ? ? 64Gb RAM and 16 cores? (Tony Travis)
> >? ? 3. Re: is it possible to install biolinux on a dell server with
> >? ? ? 64Gb RAM and 16 cores? (Sharma, M D)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 27 Mar 2015 17:54:58 +0100
> > From: Stefano Campanaro <stefano.campanaro at gmail.com>
> > To: bio-linux at nebclists.nerc.ac.uk
> > Subject: [Bio-Linux] is it possible to install biolinux on a dell
> >? ? ? ? server with 64Gb RAM and 16 cores?
> > Message-ID:
> >? ? ? ? <
> > CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> > I would install biolinux on a recently acquired DELL server with 64Gb RAM
> > and 16 cores. I would have some suggestions from users that are using bio
> > linux on servers with similar characteristics.
> > Thank you
> > Sincerely
> > --
> > Stefano
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/2dbe225a/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 27 Mar 2015 17:19:43 +0000
> > From: Tony Travis <tony.travis at minke-informatics.co.uk>
> > To: <bio-linux at nebclists.nerc.ac.uk>
> > Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
> >? ? ? ? server with 64Gb RAM and 16 cores?
> > Message-ID: <5515912F.2030803 at minke-informatics.co.uk>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > On 27/03/15 16:54, Stefano Campanaro wrote:
> > > Hi,
> > > I would install biolinux on a recently acquired DELL server with 64Gb
> > > RAM and 16 cores. I would have some suggestions from users that are
> > > using bio linux on servers with similar characteristics.
> >
> > Hi, Stefano.
> >
> > I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
> > 8-core Opteron 6128 CPU's and 128GiB RAM in each at the University of
> > Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
> > from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to boot
> > from RAID6 if it's not degraded.
> >
> > I've also set up Bio-Linux terminal servers many times in the past, for
> > example at the Wellcome Trust Centre for Cell Biology in Edinburgh, and
> > I helped my friends at Assam Agricultural University set up Bio-Linux 8
> > servers there for a training course we held recently.
> >
> > Bio-Linux 8 works very well as an "x2go" or SSH terminal server, thanks
> > to the efforts that Tim and his team at EOS have put into Bio-Linux 8.
> >
> > I've got 10 at SATA2 drives in each of our three Bio-Linux servers here:
> >
> > 6 at 2TB:
> >? ? ? ? RAID1 /boot
> >? ? ? ? RAID6 /, swap, /usr/local, /home, work
> >
> > 2 at 4TB:
> >? ? ? ? JBOD /backup1
> >? ? ? ? JBOD /backup2
> >
> > 2 at 4TB:
> >? ? ? ? JBOD /archive
> >? ? ? ? JBOD /scratch
> >
> > Let me know if there is anything I can do to help?
> >
> > If you boot your server from a Bio-Linux USB-stick and let me in through
> > your firewall I can install it for you remotely. I've done this several
> > times already for disaster recovery on an EU FP-6 project.
> >
> >? Tony.
> >
> > --
> > Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> > tel. +44(0)19755 63548? ? ? ? ? ? ? ? ? ? http://minke-informatics.co.uk
> > mob. +44(0)7985 078324? ? ? ? mailto:tony.travis at minke-informatics.co.uk
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Fri, 27 Mar 2015 17:17:56 +0000
> > From: "Sharma, M D" <M.D.Sharma at exeter.ac.uk>
> > To: Stefano Campanaro <stefano.campanaro at gmail.com>, "Bio-Linux help
> >? ? ? ? and discussion" <bio-linux at nebclists.nerc.ac.uk>,
> >? ? ? ? "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> > Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
> >? ? ? ? server with 64Gb RAM and 16 cores?
> > Message-ID: <vackbrvwh29b5de7j29erggg.1427476673744 at email.android.com>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Absolutely... I have it as you described and also with 64 cores and 512
> GB
> > of RAM..
> >
> > Sent from my HTC
> >
> > On 27 Mar 2015 16:55, Stefano Campanaro <stefano.campanaro at gmail.com>
> > wrote:
> > Hi,
> > I would install biolinux on a recently acquired DELL server with 64Gb RAM
> > and 16 cores. I would have some suggestions from users that are using bio
> > linux on servers with similar characteristics.
> > Thank you
> > Sincerely
> > --
> > Stefano
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/3695ba87/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> > ------------------------------
> >
> > End of Bio-Linux Digest, Vol 78, Issue 16
> > *****************************************
> >
>
>
>
> --
> ________________________
> Prof. Mahendra K Modi
> Head, Agril Biotechnology & Coordinator, DIC
> Assam Agricultural University
> Jorhat 785013, India
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150330/ced686e3/attachment-0001.html
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 17
> *****************************************
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150330/0771194a/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Mon, 30 Mar 2015 13:18:05 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] Bio-Linux on Dell R720
> Message-ID: <1427717885.12632.5.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Robert,
>
> Strange that you should find the server version of 14.04 works but the
> desktop doesn't, because the kernel and drivers are identical.  The
> server installer just puts on a different selection of packages.  Is it
> possible that the Unity desktop, which uses the 3D capabilities of the
> graphics card, is triggering the crash, do you think?
>
> So does this mean you are running vanilla 14.04 from the server
> installation and installing just the Bio-Linux packages you need, or did
> you try using my upgrade script to add all the Bio-Linux stuff in one
> go?
>
> Cheers,
>
> TIM
>
> On Mon, 2015-03-30 at 12:25 +0100, Robert Tyx wrote:
> > Hi,
> > In contrast to Mohendra, I have not been able to get BL8 to install
> > successfully on a Dell R720. There's probably a way to get it to work
> > (special drivers or something) but I don't know. It gets a kernel
> > panic pretty quickly every time. For what it's worth, vanilla Ubuntu
> > 14.04 LTS workstation does not install either, but the server version
> > works fine. BL 7 works fine on this system also...
> >
> >
> >
> > Sent from Yahoo Mail on Android
> >
> >
> > ______________________________________________________________________
> > From:"bio-linux-request at nebclists.nerc.ac.uk"
> > <bio-linux-request at nebclists.nerc.ac.uk>
> > Date:Mon, Mar 30, 2015 at 7:00 AM
> > Subject:Bio-Linux Digest, Vol 78, Issue 17
> >
> >
> > Send Bio-Linux mailing list submissions to
> >     bio-linux at nebclists.nerc.ac.uk
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >     http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > or, via email, send a message with subject or body 'help' to
> >     bio-linux-request at nebclists.nerc.ac.uk
> >
> > You can reach the person managing the list at
> >     bio-linux-owner at nebclists.nerc.ac.uk
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bio-Linux digest..."
> >
> >
> > Today's Topics:
> >
> >   1. Re: Bio-Linux Digest, Vol 78, Issue 16 (Mahendra Modi)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 30 Mar 2015 16:08:04 +0530
> > From: Mahendra Modi <mkmodi at aau.ac.in>
> > To: bio-linux at nebclists.nerc.ac.uk
> > Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 16
> > Message-ID:
> >     <CAPUhUGx419u3XA2mC2R
> > +LgaSKBDTkVBc9UiqBHvn=oxQTkhrUg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > We are running 3(three) servers with Bio-linux 8 and one of the me is
> > a
> > Dell r520 with 2 8core Xeon processors and 128GiB RAM. Tony Travis
> > from
> > Aberdeen University helped us in customisation of the servers. We use
> > these
> > servers for NGS data analysis and Simulation studies using Gromacs.
> >
> > Mahendra
> >
> >
> >
> > On Sat, Mar 28, 2015 at 5:30 PM,
> > <bio-linux-request at nebclists.nerc.ac.uk>
> > wrote:
> >
> > > Send Bio-Linux mailing list submissions to
> > >        bio-linux at nebclists.nerc.ac.uk
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > >        http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > > or, via email, send a message with subject or body 'help' to
> > >        bio-linux-request at nebclists.nerc.ac.uk
> > >
> > > You can reach the person managing the list at
> > >        bio-linux-owner at nebclists.nerc.ac.uk
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of Bio-Linux digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. is it possible to install biolinux on a dell server with 64Gb
> > >      RAM and 16 cores? (Stefano Campanaro)
> > >    2. Re: is it possible to install biolinux on a dell server with
> > >      64Gb RAM and 16 cores? (Tony Travis)
> > >    3. Re: is it possible to install biolinux on a dell server with
> > >      64Gb RAM and 16 cores? (Sharma, M D)
> > >
> > >
> > >
> > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Fri, 27 Mar 2015 17:54:58 +0100
> > > From: Stefano Campanaro <stefano.campanaro at gmail.com>
> > > To: bio-linux at nebclists.nerc.ac.uk
> > > Subject: [Bio-Linux] is it possible to install biolinux on a dell
> > >        server with 64Gb RAM and 16 cores?
> > > Message-ID:
> > >        <
> > > CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ at mail.gmail.com>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Hi,
> > > I would install biolinux on a recently acquired DELL server with
> > 64Gb RAM
> > > and 16 cores. I would have some suggestions from users that are
> > using bio
> > > linux on servers with similar characteristics.
> > > Thank you
> > > Sincerely
> > > --
> > > Stefano
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> > >
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/2dbe225a/attachment-0001.html
> > > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Fri, 27 Mar 2015 17:19:43 +0000
> > > From: Tony Travis <tony.travis at minke-informatics.co.uk>
> > > To: <bio-linux at nebclists.nerc.ac.uk>
> > > Subject: Re: [Bio-Linux] is it possible to install biolinux on a
> > dell
> > >        server with 64Gb RAM and 16 cores?
> > > Message-ID: <5515912F.2030803 at minke-informatics.co.uk>
> > > Content-Type: text/plain; charset="windows-1252"
> > >
> > > On 27/03/15 16:54, Stefano Campanaro wrote:
> > > > Hi,
> > > > I would install biolinux on a recently acquired DELL server with
> > 64Gb
> > > > RAM and 16 cores. I would have some suggestions from users that
> > are
> > > > using bio linux on servers with similar characteristics.
> > >
> > > Hi, Stefano.
> > >
> > > I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
> > > 8-core Opteron 6128 CPU's and 128GiB RAM in each at the University
> > of
> > > Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
> > > from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to
> > boot
> > > from RAID6 if it's not degraded.
> > >
> > > I've also set up Bio-Linux terminal servers many times in the past,
> > for
> > > example at the Wellcome Trust Centre for Cell Biology in Edinburgh,
> > and
> > > I helped my friends at Assam Agricultural University set up
> > Bio-Linux 8
> > > servers there for a training course we held recently.
> > >
> > > Bio-Linux 8 works very well as an "x2go" or SSH terminal server,
> > thanks
> > > to the efforts that Tim and his team at EOS have put into Bio-Linux
> > 8.
> > >
> > > I've got 10 at SATA2 drives in each of our three Bio-Linux servers
> > here:
> > >
> > > 6 at 2TB:
> > >        RAID1 /boot
> > >        RAID6 /, swap, /usr/local, /home, work
> > >
> > > 2 at 4TB:
> > >        JBOD /backup1
> > >        JBOD /backup2
> > >
> > > 2 at 4TB:
> > >        JBOD /archive
> > >        JBOD /scratch
> > >
> > > Let me know if there is anything I can do to help?
> > >
> > > If you boot your server from a Bio-Linux USB-stick and let me in
> > through
> > > your firewall I can install it for you remotely. I've done this
> > several
> > > times already for disaster recovery on an EU FP-6 project.
> > >
> > >  Tony.
> > >
> > > --
> > > Minke Informatics Limited, Registered in Scotland - Company No.
> > SC419028
> > > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland
> > (UK)
> > > tel. +44(0)19755 63548
> > http://minke-informatics.co.uk
> > > mob. +44(0)7985 078324
> > mailto:tony.travis at minke-informatics.co.uk
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Fri, 27 Mar 2015 17:17:56 +0000
> > > From: "Sharma, M D" <M.D.Sharma at exeter.ac.uk>
> > > To: Stefano Campanaro <stefano.campanaro at gmail.com>, "Bio-Linux help
> > >        and discussion" <bio-linux at nebclists.nerc.ac.uk>,
> > >        "bio-linux at nebclists.nerc.ac.uk"
> > <bio-linux at nebclists.nerc.ac.uk>
> > > Subject: Re: [Bio-Linux] is it possible to install biolinux on a
> > dell
> > >        server with 64Gb RAM and 16 cores?
> > > Message-ID:
> > <vackbrvwh29b5de7j29erggg.1427476673744 at email.android.com>
> > > Content-Type: text/plain; charset="us-ascii"
> > >
> > > Absolutely... I have it as you described and also with 64 cores and
> > 512 GB
> > > of RAM..
> > >
> > > Sent from my HTC
> > >
> > > On 27 Mar 2015 16:55, Stefano Campanaro
> > <stefano.campanaro at gmail.com>
> > > wrote:
> > > Hi,
> > > I would install biolinux on a recently acquired DELL server with
> > 64Gb RAM
> > > and 16 cores. I would have some suggestions from users that are
> > using bio
> > > linux on servers with similar characteristics.
> > > Thank you
> > > Sincerely
> > > --
> > > Stefano
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> > >
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/3695ba87/attachment-0001.html
> > > >
> > >
> > > ------------------------------
> > >
> > > Subject: Digest Footer
> > >
> > > _______________________________________________
> > > Bio-Linux mailing list
> > > Bio-Linux at nebclists.nerc.ac.uk
> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > >
> > >
> > > ------------------------------
> > >
> > > End of Bio-Linux Digest, Vol 78, Issue 16
> > > *****************************************
> > >
> >
> >
> >
> > --
> > ________________________
> > Prof. Mahendra K Modi
> > Head, Agril Biotechnology & Coordinator, DIC
> > Assam Agricultural University
> > Jorhat 785013, India
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> > <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150330/ced686e3/attachment-0001.html
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> > ------------------------------
> >
> > End of Bio-Linux Digest, Vol 78, Issue 17
> > *****************************************
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 18
> *****************************************
>



-- 
________________________
Prof. Mahendra K Modi
Head, Agril Biotechnology & Coordinator, DIC
Assam Agricultural University
Jorhat 785013, India
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From tony.travis at minke-informatics.co.uk  Mon Mar 30 09:00:19 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Mon, 30 Mar 2015 14:00:19 +0100
Subject: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 18
In-Reply-To: <CAPUhUGxsPEr6URG3E-1LMaF4XxhMzobyUeZowqemDEHNg2qQGg@mail.gmail.com>
References: <mailman.37.1427717876.2858.bio-linux@nebclists.nerc.ac.uk>
 <CAPUhUGxsPEr6URG3E-1LMaF4XxhMzobyUeZowqemDEHNg2qQGg@mail.gmail.com>
Message-ID: <551948E3.3090401@minke-informatics.co.uk>

On 30/03/15 13:26, Mahendra Modi wrote:
> Hi Robert,
> 
> You will need to set nomodeset immediately after you see the splash
> screen as the graphics chip is not sufficient to run unity desktop. Once
> you may edit grub to include nomodeset and choose to run the mate
> terminal instead of ubuntu. I think thats what I did to get my system going.

Hi, Mahendra.

Yes, it is ;-)

This is how we did it on "wildcat" and we did the same on "Aryabhatta":

> rwt017 at wildcat:/etc/default$ diff grub.orig grub
> 7c7
> < GRUB_HIDDEN_TIMEOUT=0
> ---
>> #GRUB_HIDDEN_TIMEOUT=0
> 11,12c11,12
> < GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
> < GRUB_CMDLINE_LINUX=""
> ---
>> GRUB_CMDLINE_LINUX_DEFAULT="bootdegraded=yes nomodeset"
>> GRUB_CMDLINE_LINUX="bootdegraded=yes nomodeset"

Bye,

  Tony.

-- 
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis




From robtyx at yahoo.com  Mon Mar 30 10:55:38 2015
From: robtyx at yahoo.com (Robert Tyx)
Date: Mon, 30 Mar 2015 14:55:38 +0000 (UTC)
Subject: [Bio-Linux] BL8 on Server - Poweredge R720
In-Reply-To: <mailman.42.1427718864.2858.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.42.1427718864.2858.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <871548838.1519399.1427727338629.JavaMail.yahoo@mail.yahoo.com>

Great! Thanks for the tip Mahendra. I'll be trying it soon...
and I apologize for the Re: Contents of Bio-Linux digest... totally forgot the subject needed to be changed.

~Robert

      From: "bio-linux-request at nebclists.nerc.ac.uk" <bio-linux-request at nebclists.nerc.ac.uk>
 To: bio-linux at nebclists.nerc.ac.uk 
 Sent: Monday, March 30, 2015 8:34 AM
 Subject: Bio-Linux Digest, Vol 78, Issue 19
   
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? 1. Re: Bio-Linux Digest, Vol 78, Issue 18 (Mahendra Modi)


----------------------------------------------------------------------

Message: 1
Date: Mon, 30 Mar 2015 17:56:53 +0530
From: Mahendra Modi <mkmodi at aau.ac.in>
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 18
Message-ID:
??? <CAPUhUGxsPEr6URG3E-1LMaF4XxhMzobyUeZowqemDEHNg2qQGg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Robert,

You will need to set nomodeset immediately after you see the splash screen
as the graphics chip is not sufficient to run unity desktop. Once you may
edit grub to include nomodeset and choose to run the mate terminal instead
of ubuntu. I think thats what I did to get my system going.

Mahendra

  
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