[Bio-Linux] Bio-Linux Digest, Vol 78, Issue 4

Parham Pourbozorgi papo0009 at gapps.umu.se
Wed Mar 4 08:39:23 EST 2015


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:

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> 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 --------------
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> 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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