From tony.travis at minke-informatics.co.uk  Tue Feb  3 15:06:12 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 3 Feb 2015 20:06:12 +0000
Subject: [Bio-linux-dev] bash compatibility
Message-ID: <54D12A34.8070607@minke-informatics.co.uk>

Hi, Tim.

There is a problem with bash compatibility in Bio-Linux 8 because "zsh"
does NOT source /etc/profile by default. Here's a patch to do it:

--- old/zprofile	2013-08-02 22:29:03.000000000 +0530
+++ zprofile	2015-02-04 01:14:06.747837184 +0530
@@ -5,3 +5,6 @@
 # shells invoked with the -l flag.)
 #
 # Global Order: zshenv, zprofile, zshrc, zlogin
+
+# for compatibility with "bash"
+emulate sh -c 'source /etc/profile'

In particular, "profile" fragments installed by packages (or manually)
are never sourced from /etc/profile.d by "zsh" and this breaks things
quite badly on our servers. I didn't notice this previously because we
don't use "zsh". However, the servers at Assam Agricultural University
are set up to use "zsh" for the course, so we can follow your tutorial.

We are installing our own GWAS pipeline called "ParSNP" that uses
/etc/profile.d to set the environment in the normal way for "bash".

Bye,

  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 tbooth at ceh.ac.uk  Wed Feb  4 07:10:55 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 4 Feb 2015 12:10:55 +0000
Subject: [Bio-linux-dev] bash compatibility
In-Reply-To: <54D12A34.8070607@minke-informatics.co.uk>
References: <54D12A34.8070607@minke-informatics.co.uk>
Message-ID: <1423051855.23727.31.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Tony,

Perhaps you could weigh in on this discussion?

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=776663

Note the comment from Axel Beckert:

"With respect to shells, I usually find that applications, that need to
inject code into a user's shell to be by and large mis-designed."

I actually agree.  Applications should not rely on the behaviour of the
controlling shell.  My reason for making the wishlist request was to
allow Andreas' proposed blend selection system to function outside of
Bash, and that's an issue related to default preferences rather than a
requirement for functionality.

Cheers,

TIM

On Tue, 2015-02-03 at 20:06 +0000, Tony Travis wrote:
> Hi, Tim.
> 
> There is a problem with bash compatibility in Bio-Linux 8 because "zsh"
> does NOT source /etc/profile by default. Here's a patch to do it:
> 
> --- old/zprofile	2013-08-02 22:29:03.000000000 +0530
> +++ zprofile	2015-02-04 01:14:06.747837184 +0530
> @@ -5,3 +5,6 @@
>  # shells invoked with the -l flag.)
>  #
>  # Global Order: zshenv, zprofile, zshrc, zlogin
> +
> +# for compatibility with "bash"
> +emulate sh -c 'source /etc/profile'
> 
> In particular, "profile" fragments installed by packages (or manually)
> are never sourced from /etc/profile.d by "zsh" and this breaks things
> quite badly on our servers. I didn't notice this previously because we
> don't use "zsh". However, the servers at Assam Agricultural University
> are set up to use "zsh" for the course, so we can follow your tutorial.
> 
> We are installing our own GWAS pipeline called "ParSNP" that uses
> /etc/profile.d to set the environment in the normal way for "bash".
> 
> Bye,
> 
>   Tony.
> 

-- 
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 tony.travis at abdn.ac.uk  Wed Feb  4 07:42:01 2015
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Wed, 4 Feb 2015 12:42:01 +0000
Subject: [Bio-linux-dev] bash compatibility
In-Reply-To: <1423051855.23727.31.camel@wllt1771.nerc-wallingford.ac.uk>
References: <54D12A34.8070607@minke-informatics.co.uk>
 <1423051855.23727.31.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <54D21399.5090602@abdn.ac.uk>

On 04/02/15 12:10, Tim Booth wrote:
> Hi Tony,
>
> Perhaps you could weigh in on this discussion?
>
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=776663
>
> Note the comment from Axel Beckert:
>
> "With respect to shells, I usually find that applications, that need to
> inject code into a user's shell to be by and large mis-designed."

Hi, Tim.

I will, but not just now...

> I actually agree.  Applications should not rely on the behaviour of the
> controlling shell.  My reason for making the wishlist request was to
> allow Andreas' proposed blend selection system to function outside of
> Bash, and that's an issue related to default preferences rather than a
> requirement for functionality.

I believe that the environment should be set up at login, not each time
a shell is executed. For 'conventional' shells (e.g. sh and bash), that
means /etc/profile. Adding profile 'fragments' in /etc/profile.d comes
from Red-Hat and (before that) BSD. I think it is a useful convention
and use it a lot. One consequence, though, is that GUI terminal windows
then have to be run as a login shell. However, shells spawned from the
terminal window do not source /etc/profile and /etc/profile.d/*.

What bothers me about this is that the vast majority of people using
Debian/Ubuntu do NOT use "zsh". I want to be able to allow our users to
change their shell from "zsh" to "bash" without breaking anything. The
convention of putting config fragments in <service>.d/* is widespread
and useful. However, mirroring /etc/profile.d as /etc/zprofile.d does
not help. It just makes things worse. Winning hearts and minds to use
Bio-Linux is more difficult if you tell people they can't use "bash".

For our course in Assam  in two weeks, we will use "zsh", but with my
patch on the servers so it will source /etc/profile and, indirectly,
/etc/profile.d/*. However, some of the more experienced participants
already use "bash" as I do.

Thanks for the heads-up about the debate :-)

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


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  Wed Feb  4 13:16:09 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 4 Feb 2015 18:16:09 +0000
Subject: [Bio-linux-dev] bash compatibility
In-Reply-To: <54D21399.5090602@abdn.ac.uk>
References: <54D12A34.8070607@minke-informatics.co.uk>
 <1423051855.23727.31.camel@wllt1771.nerc-wallingford.ac.uk>
 <54D21399.5090602@abdn.ac.uk>
Message-ID: <1423073769.23727.79.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Tony,

> Winning hearts and minds to use
> Bio-Linux is more difficult if you tell people they can't use "bash".

For the millionth time, Bash is fully supported in Bio-Linux, which you
know full well because you use it yourself.  But no it isn't the default
and no I'm not going to make it the default and no I'm not going to
re-write all my documentation to reference Bash.  What you choose to
teach is up to you.

The only person dictating shell compatibility here is you, by having
some nasty mis-designed software that depends on the user's selection of
login shell and then when it doesn't work you say it's the system's
fault.  It's not, and if you tried to submit the software to Debian as a
package they'd rightly tell you the package was buggy.  I will not be
adding your "fix" to Bio-Linux.  Fix your software!

TIM


From tony.travis at abdn.ac.uk  Wed Feb  4 15:01:24 2015
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Wed, 4 Feb 2015 20:01:24 +0000
Subject: [Bio-linux-dev] bash compatibility
In-Reply-To: <1423073769.23727.79.camel@wllt1771.nerc-wallingford.ac.uk>
References: <54D12A34.8070607@minke-informatics.co.uk>
 <1423051855.23727.31.camel@wllt1771.nerc-wallingford.ac.uk>
 <54D21399.5090602@abdn.ac.uk>
 <1423073769.23727.79.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <54D27A94.3050603@abdn.ac.uk>

On 04/02/15 18:16, Tim Booth wrote:
> Hi Tony,
>
>> Winning hearts and minds to use
>> Bio-Linux is more difficult if you tell people they can't use "bash".
>
> For the millionth time, Bash is fully supported in Bio-Linux, which you
> know full well because you use it yourself.  But no it isn't the default
> and no I'm not going to make it the default and no I'm not going to
> re-write all my documentation to reference Bash.  What you choose to
> teach is up to you.

Hi, Tim.

Ouch! - That's me told.

Clearly, I wasn't listening the 999,999 times you told me before :-)

However, as I said, we are going to teach "zsh" for the course in Assam
precisely because we want to make use of your comprehensive tutorial.

> The only person dictating shell compatibility here is you, by having
> some nasty mis-designed software that depends on the user's selection of
> login shell and then when it doesn't work you say it's the system's
> fault.  It's not, and if you tried to submit the software to Debian as a
> package they'd rightly tell you the package was buggy.  I will not be
> adding your "fix" to Bio-Linux.  Fix your software!

I just requested that we do something that other "zsh" users do to
increase compatibility of "zsh" with the widely-used /etc/profile.d
directory for "bash". I'm sorry if you think I'm dictating everyone
should use "bash" because I'm not. I'm seeking a way of using either
"zsh" or "bash" with the same global configuration environment and I
don't think I'm alone in seeking that. I think I might be forgiven for
thinking that you agreed with me from your Debian bug report:

> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Debian Bug Tracking System <submit at bugs.debian.org>
> Subject: zsh-common: Wish for /etc/zsh/zprofile.d or equivalent
> Date: Fri, 30 Jan 2015 18:25:21 +0000
>
> Package: zsh-common
> Version: 5.0.2-3ubuntu6
> Severity: wishlist
>
> This is a request on behalf of Bio-Linux and the Debian Med developers.
> The attached file shows the zshrc used on Bio-Linux, and the part we'd really
> like to see in the standard zsh-common package is support for a zprofile.d configuration
> directory to mirror /etc/profile.d which is read by BASH and allows
> packages to drop config fragments into the shell profile.
>
> In Bio-Linux this is hooked from zshrc but actually a modified zprofile
> probably makes more sense.
>
> This is pretty trivial to implement, as far as I can see.  What do you think?
>
> Cheers,
>
> TIM

Thanks for all the work you've done updating your tutorial!

  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


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 jimmy.g.griffin at gmail.com  Tue Feb 17 00:01:16 2015
From: jimmy.g.griffin at gmail.com (Jimmy Griffin)
Date: Tue, 17 Feb 2015 00:01:16 -0500
Subject: [Bio-linux-dev] Scheduler included into BioLinux 7+
Message-ID: <CAFRHGrie3yqSDXqZ6k_vK=xtAD0a1cN_8Wcgjc=HBH5eOp2zYg@mail.gmail.com>

Hello,

Would there be any chance a scheduler be included into the current or
future releases of Bio-Linux?

-- 
Jimmy Griffin

The information contained in this email may be confidential and/or legally
privileged. It has been sent for the sole use of the intended recipient(s).
If the reader of this message is not an intended recipient, you are hereby
notified that any unauthorized review, use, disclosure, dissemination,
distribution, or copying of this communication, or any of its content, is
strictly prohibited. If you have received this communication in error,
please contact the sender by reply email and destroy all copies of the
original message. Thank you.
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From tbooth at ceh.ac.uk  Tue Feb 17 04:11:12 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 17 Feb 2015 09:11:12 +0000
Subject: [Bio-linux-dev] Scheduler included into BioLinux 7+
In-Reply-To: <CAFRHGrie3yqSDXqZ6k_vK=xtAD0a1cN_8Wcgjc=HBH5eOp2zYg@mail.gmail.com>
References: <CAFRHGrie3yqSDXqZ6k_vK=xtAD0a1cN_8Wcgjc=HBH5eOp2zYg@mail.gmail.com>
Message-ID: <1424164272.12415.44.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Jimmy,

I'm not exactly sure what you mean by "a scheduler".  Do you mean
something like SLURM or Condor?

Cheers,

TIM

On Tue, 2015-02-17 at 05:01 +0000, Jimmy Griffin wrote:
> Hello,
> 
> 
> Would there be any chance a scheduler be included into the current or
> future releases of Bio-Linux?
> 
> 
> -- 
> Jimmy Griffin
> 
> The information contained in this email may be confidential and/or
> legally 
> privileged. It has been sent for the sole use of the intended
> recipient(s). 
> If the reader of this message is not an intended recipient, you are
> hereby 
> notified that any unauthorized review, use, disclosure,
> dissemination, 
> distribution, or copying of this communication, or any of its content,
> is 
> strictly prohibited. If you have received this communication in
> error, 
> please contact the sender by reply email and destroy all copies of
> the 
> original message. Thank you.
> 
> 

-- 
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 jimmy.g.griffin at gmail.com  Tue Feb 17 09:13:09 2015
From: jimmy.g.griffin at gmail.com (Jimmy Griffin)
Date: Tue, 17 Feb 2015 14:13:09 +0000
Subject: [Bio-linux-dev] Bio-Linux-dev Digest, Vol 46, Issue 4
References: <mailman.3.1424174402.7233.bio-linux-dev@nebclists.nerc.ac.uk>
Message-ID: <CAFRHGrh_2jYbivFTR4eWV8jH23oQALNCzYi2rBdFF-Q0sG=Pkw@mail.gmail.com>

Yes, something like SGE, Torque, or Slurm?

On Tue, Feb 17, 2015, 7:00 AM null <
bio-linux-dev-request at nebclists.nerc.ac.uk> wrote:

> Send Bio-Linux-dev mailing list submissions to
>         bio-linux-dev at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> or, via email, send a message with subject or body 'help' to
>         bio-linux-dev-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
>         bio-linux-dev-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux-dev digest..."
>
>
> Today's Topics:
>
>    1. Scheduler included into BioLinux 7+ (Jimmy Griffin)
>    2. Re: Scheduler included into BioLinux 7+ (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 17 Feb 2015 00:01:16 -0500
> From: Jimmy Griffin <jimmy.g.griffin at gmail.com>
> To: bio-linux-dev at nebclists.nerc.ac.uk
> Subject: [Bio-linux-dev] Scheduler included into BioLinux 7+
> Message-ID:
>         <CAFRHGrie3yqSDXqZ6k_vK=xtAD0a1cN_8Wcgjc=HBH5eOp2zYg@
> mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> Would there be any chance a scheduler be included into the current or
> future releases of Bio-Linux?
>
> --
> Jimmy Griffin
>
> The information contained in this email may be confidential and/or legally
> privileged. It has been sent for the sole use of the intended recipient(s).
> If the reader of this message is not an intended recipient, you are hereby
> notified that any unauthorized review, use, disclosure, dissemination,
> distribution, or copying of this communication, or any of its content, is
> strictly prohibited. If you have received this communication in error,
> please contact the sender by reply email and destroy all copies of the
> original message. Thank you.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://nebclists.nerc.ac.uk/pipermail/bio-linux-dev/
> attachments/20150217/03eed583/attachment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 17 Feb 2015 09:11:12 +0000
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux technical discussion
>         <bio-linux-dev at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-linux-dev] Scheduler included into BioLinux 7+
> Message-ID:
>         <1424164272.12415.44.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Jimmy,
>
> I'm not exactly sure what you mean by "a scheduler".  Do you mean
> something like SLURM or Condor?
>
> Cheers,
>
> TIM
>
> On Tue, 2015-02-17 at 05:01 +0000, Jimmy Griffin wrote:
> > Hello,
> >
> >
> > Would there be any chance a scheduler be included into the current or
> > future releases of Bio-Linux?
> >
> >
> > --
> > Jimmy Griffin
> >
> > The information contained in this email may be confidential and/or
> > legally
> > privileged. It has been sent for the sole use of the intended
> > recipient(s).
> > If the reader of this message is not an intended recipient, you are
> > hereby
> > notified that any unauthorized review, use, disclosure,
> > dissemination,
> > distribution, or copying of this communication, or any of its content,
> > is
> > strictly prohibited. If you have received this communication in
> > error,
> > please contact the sender by reply email and destroy all copies of
> > the
> > original message. Thank you.
> >
> >
>
> --
> 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-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>
>
> ------------------------------
>
> End of Bio-Linux-dev Digest, Vol 46, Issue 4
> ********************************************
>
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From tbooth at ceh.ac.uk  Tue Feb 17 14:03:01 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 17 Feb 2015 19:03:01 +0000
Subject: [Bio-linux-dev] scheduler on Bio-Linux
In-Reply-To: <CAFRHGrh_2jYbivFTR4eWV8jH23oQALNCzYi2rBdFF-Q0sG=Pkw@mail.gmail.com>
References: <mailman.3.1424174402.7233.bio-linux-dev@nebclists.nerc.ac.uk>
 <CAFRHGrh_2jYbivFTR4eWV8jH23oQALNCzYi2rBdFF-Q0sG=Pkw@mail.gmail.com>
Message-ID: <1424199781.20135.37.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Jimmy,

So if you do:

$ sudo apt-get install gridengine-master torque-server slurm-llnl

In just a few seconds you'll have all three!

But this is not much use.  The problem is that all need to be properly
configured for your computing environment and as people's set-ups and
requirements are different I can't provide a single generic
configuration - you have to read up on your chosen job scheduler and set
it up for your own needs.

If you try to use one of the above and run into problems please do post
questions on the bio-linux users list (not this bio-linux-dev list)
because I know that several Bio-Linux users work on clusters and may be
able to help out.

Cheers,

TIM

On Tue, 2015-02-17 at 14:13 +0000, Jimmy Griffin wrote:
> Yes, something like SGE, Torque, or Slurm?
> 
> 
> On Tue, Feb 17, 2015, 7:00 AM null
> <bio-linux-dev-request at nebclists.nerc.ac.uk> wrote:
>         Send Bio-Linux-dev mailing list submissions to
>                 bio-linux-dev at nebclists.nerc.ac.uk
>         
>         To subscribe or unsubscribe via the World Wide Web, visit
>         
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>         or, via email, send a message with subject or body 'help' to
>                 bio-linux-dev-request at nebclists.nerc.ac.uk
>         
>         You can reach the person managing the list at
>                 bio-linux-dev-owner at nebclists.nerc.ac.uk
>         
>         When replying, please edit your Subject line so it is more
>         specific
>         than "Re: Contents of Bio-Linux-dev digest..."
>         
>         
>         Today's Topics:
>         
>            1. Scheduler included into BioLinux 7+ (Jimmy Griffin)
>            2. Re: Scheduler included into BioLinux 7+ (Tim Booth)
>         
>         
>         ----------------------------------------------------------------------
>         
>         Message: 1
>         Date: Tue, 17 Feb 2015 00:01:16 -0500
>         From: Jimmy Griffin <jimmy.g.griffin at gmail.com>
>         To: bio-linux-dev at nebclists.nerc.ac.uk
>         Subject: [Bio-linux-dev] Scheduler included into BioLinux 7+
>         Message-ID:
>         
>         <CAFRHGrie3yqSDXqZ6k_vK=xtAD0a1cN_8Wcgjc=HBH5eOp2zYg at mail.gmail.com>
>         Content-Type: text/plain; charset="iso-8859-1"
>         
>         Hello,
>         
>         Would there be any chance a scheduler be included into the
>         current or
>         future releases of Bio-Linux?
>         
>         --
>         Jimmy Griffin
>         
>         The information contained in this email may be confidential
>         and/or legally
>         privileged. It has been sent for the sole use of the intended
>         recipient(s).
>         If the reader of this message is not an intended recipient,
>         you are hereby
>         notified that any unauthorized review, use, disclosure,
>         dissemination,
>         distribution, or copying of this communication, or any of its
>         content, is
>         strictly prohibited. If you have received this communication
>         in error,
>         please contact the sender by reply email and destroy all
>         copies of the
>         original message. Thank you.
>         -------------- next part --------------
>         An HTML attachment was scrubbed...
>         URL:
>         <http://nebclists.nerc.ac.uk/pipermail/bio-linux-dev/attachments/20150217/03eed583/attachment-0001.html>
>         
>         ------------------------------
>         
>         Message: 2
>         Date: Tue, 17 Feb 2015 09:11:12 +0000
>         From: Tim Booth <tbooth at ceh.ac.uk>
>         To: Bio-Linux technical discussion
>                 <bio-linux-dev at nebclists.nerc.ac.uk>
>         Subject: Re: [Bio-linux-dev] Scheduler included into BioLinux
>         7+
>         Message-ID:
>         
>         <1424164272.12415.44.camel at wllt1771.nerc-wallingford.ac.uk>
>         Content-Type: text/plain; charset="UTF-8"
>         
>         Hi Jimmy,
>         
>         I'm not exactly sure what you mean by "a scheduler".  Do you
>         mean
>         something like SLURM or Condor?
>         
>         Cheers,
>         
>         TIM
>         
>         On Tue, 2015-02-17 at 05:01 +0000, Jimmy Griffin wrote:
>         > Hello,
>         >
>         >
>         > Would there be any chance a scheduler be included into the
>         current or
>         > future releases of Bio-Linux?
>         >
>         >
>         > --
>         > Jimmy Griffin
>         >
>         > The information contained in this email may be confidential
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>         --
>         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
>         
>         
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>         Subject: Digest Footer
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>         ------------------------------
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>         End of Bio-Linux-dev Digest, Vol 46, Issue 4
>         ********************************************

-- 
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 dr.tony.travis at gmail.com  Wed Feb 18 08:20:28 2015
From: dr.tony.travis at gmail.com (Tony Travis)
Date: Wed, 18 Feb 2015 18:50:28 +0530
Subject: [Bio-linux-dev] nVidia GF108M [GeForce GT 420M] display
Message-ID: <54E4919C.9080709@abdn.ac.uk>

Hi, Tim.

We are having problems getting the display to work correctly after
installing Bio-Linux 8.0.5.1 from the USB-stick. The display works
properly when booted from the stick, but not when booted from the hard
disk. I've checked and the Nouveau drivers are being used on the stick.

Did you make any changes on the stick that we need to make sfter
installing onto the hard disk?

Having a great time running Bio-Linux 8 on 34+ laptops and two servers!

As you can see, some people also want to install it :-)

Thanks,

  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 tbooth at ceh.ac.uk  Wed Feb 18 10:07:52 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 18 Feb 2015 15:07:52 +0000
Subject: [Bio-linux-dev] nVidia GF108M [GeForce GT 420M] display
In-Reply-To: <54E4919C.9080709@abdn.ac.uk>
References: <54E4919C.9080709@abdn.ac.uk>
Message-ID: <1424272072.20135.76.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Tony,

How strange.  I was under the impression that X on the stick was
identical to X after installation and I've certainly not fiddled with
any settings.  Did you opt to install updates from the network during
installation or not?  That's the only thing I can think of that would
change.

I guess the next step is the usual one - start looking through the logs
for clues.

Otherwise, maybe push on and install the binary drivers.  Nasty
closed-source things, I know, but appreciably faster then Nouveau on
modern NVidia cards.

Cheers,

TIM

On Wed, 2015-02-18 at 13:20 +0000, Tony Travis wrote:
> Hi, Tim.
> 
> We are having problems getting the display to work correctly after
> installing Bio-Linux 8.0.5.1 from the USB-stick. The display works
> properly when booted from the stick, but not when booted from the hard
> disk. I've checked and the Nouveau drivers are being used on the stick.
> 
> Did you make any changes on the stick that we need to make sfter
> installing onto the hard disk?
> 
> Having a great time running Bio-Linux 8 on 34+ laptops and two servers!
> 
> As you can see, some people also want to install it :-)
> 
> Thanks,
> 
>   Tony.
> 

-- 
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