From shou at ceh.ac.uk  Mon Feb 16 09:04:51 2009
From: shou at ceh.ac.uk (Stewart Houten)
Date: Mon, 16 Feb 2009 14:04:51 +0000
Subject: [Bio-Linux] Debian Lenny released
Message-ID: <20090216140451.GA5637@ivpcp068.nerc-oxford.ac.uk>

Dear all,

Just to let everyone running Bio-Linux 4.0 know that the new version
of Debian stable was release over the weekend.  Although the new
stable release "Lenny" replaces "Etch" this will not take automatic
effect on your Bio-Linux machine.  

We would encourage anyone who wishes to upgrade to take the
opportunity to install the new Bio-Linux 5.0.

Regards,
Stewart 
--
Dr Stewart Houten, Bio-Linux Developer
NEBC, CEH, Mansfield Road, Oxford, OX1 3SR
http://nebc.nox.ac.uk/ 



From a.travis at abdn.ac.uk  Tue Feb 17 05:30:16 2009
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 17 Feb 2009 10:30:16 +0000
Subject: [Bio-Linux] zsh
Message-ID: <499A91B8.80302@abdn.ac.uk>

Hello,

Is there any reason why "zsh" is the default shell in Bio-Linux 5.0?

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From shou at ceh.ac.uk  Tue Feb 17 13:03:12 2009
From: shou at ceh.ac.uk (Stewart Houten)
Date: Tue, 17 Feb 2009 18:03:12 +0000
Subject: [Bio-Linux] zsh
In-Reply-To: <499A91B8.80302@abdn.ac.uk>
References: <499A91B8.80302@abdn.ac.uk>
Message-ID: <20090217180312.GA19152@ivpcp068.nerc-oxford.ac.uk>

Hi Tony,

On Feb 17, 2009, Tony Travis <a.travis at abdn.ac.uk> wrote:
>
> Is there any reason why "zsh" is the default shell in Bio-Linux 5.0?

Yes, it was a conscious decision on our part.  The reasoning predates
me but as I recall there was at least one piece of software on
Bio-Linux that had problems running under bash.  I don't remember the
details but I'm sure Tim will when he gets back later this week.

Stewart 



From tbooth at ceh.ac.uk  Wed Feb 18 11:06:14 2009
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 18 Feb 2009 16:06:14 +0000
Subject: [Bio-Linux] zsh
In-Reply-To: <20090217180312.GA19152@ivpcp068.nerc-oxford.ac.uk>
References: <499A91B8.80302@abdn.ac.uk>
	<20090217180312.GA19152@ivpcp068.nerc-oxford.ac.uk>
Message-ID: <1234973174.7741.40.camel@barsukas>

Hi Tony, all,

Nowadays there's probably little to choose between bash and zsh in terms
of features, so as Stewart says the primary motivation is historical
(all our documentation refers to zsh and our existing users are used to
it).  Personally I like the little conveniences in zsh - things like:

ls /m<tab><tab>

cycles through the completion options rather than just displaying them.
And:

echo `pwd`<tab>

replaces `pwd` with the command result in-place.  Also, pressing 'Alt+Q'
lets you push the current command buffer aside and you can add an
RPROMPT as well as a PROMPT etc. etc.

Since we're on the subject I'm going to add a blatant plug.  Since I've
started using Bio-Linux 5 I've collected a variety of tips and tweaks
that make it work better for me.  I'm sticking them on a blog in case
anyone else finds them useful and I'll be aiming to add about one post a
week for the next few months.

http://www.linuxquestions.org/blog/avarus-108601/

I'll be putting up some stuff about Z-shell quite soon.

Cheers,

TIM

On Tue, 2009-02-17 at 18:03 +0000, Stewart Houten wrote:
> Hi Tony,
> 
> On Feb 17, 2009, Tony Travis <a.travis at abdn.ac.uk> wrote:
> >
> > Is there any reason why "zsh" is the default shell in Bio-Linux 5.0?
> 
> Yes, it was a conscious decision on our part.  The reasoning predates
> me but as I recall there was at least one piece of software on
> Bio-Linux that had problems running under bash.  I don't remember the
> details but I'm sure Tim will when he gets back later this week.
> 
> Stewart 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975





From btiwari at ceh.ac.uk  Thu Feb 19 05:13:35 2009
From: btiwari at ceh.ac.uk (Bela Tiwari)
Date: Thu, 19 Feb 2009 10:13:35 +0000
Subject: [Bio-Linux] zsh
Message-ID: <s99d30f6.011@wpo.nerc.ac.uk>

Hello,  

My  memory of why we chose the z-shell is that, at the time, I was most familiar with tcsh and Dan (then the Bio-Linux developer) was most familiar with bash. Z-shell catered for both our syntax habits on the command line. More generally, we thought this would help others - i.e. those used to t or c shell, as well as those who used bash, would be able to use the same syntax as they were used to. 

cheers, 

Bela 




*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> tbooth at ceh.ac.uk 02/18/09 4:06 pm >>>
Hi Tony, all,

Nowadays there's probably little to choose between bash and zsh in terms
of features, so as Stewart says the primary motivation is historical
(all our documentation refers to zsh and our existing users are used to
it).  Personally I like the little conveniences in zsh - things like:

ls /m<tab><tab>

cycles through the completion options rather than just displaying them.
And:

echo `pwd`<tab>

replaces `pwd` with the command result in-place.  Also, pressing 'Alt+Q'
lets you push the current command buffer aside and you can add an
RPROMPT as well as a PROMPT etc. etc.

Since we're on the subject I'm going to add a blatant plug.  Since I've
started using Bio-Linux 5 I've collected a variety of tips and tweaks
that make it work better for me.  I'm sticking them on a blog in case
anyone else finds them useful and I'll be aiming to add about one post a
week for the next few months.

http://www.linuxquestions.org/blog/avarus-108601/ 

I'll be putting up some stuff about Z-shell quite soon.

Cheers,

TIM

On Tue, 2009-02-17 at 18:03 +0000, Stewart Houten wrote:
> Hi Tony,
> 
> On Feb 17, 2009, Tony Travis <a.travis at abdn.ac.uk> wrote:
> >
> > Is there any reason why "zsh" is the default shell in Bio-Linux 5.0?
> 
> Yes, it was a conscious decision on our part.  The reasoning predates
> me but as I recall there was at least one piece of software on
> Bio-Linux that had problems running under bash.  I don't remember the
> details but I'm sure Tim will when he gets back later this week.
> 
> Stewart 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk 
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux 
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Oxford
+44 1865 281 975



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




From a.travis at abdn.ac.uk  Thu Feb 19 05:34:02 2009
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 19 Feb 2009 10:34:02 +0000
Subject: [Bio-Linux] zsh
In-Reply-To: <s99d30f6.011@wpo.nerc.ac.uk>
References: <s99d30f6.011@wpo.nerc.ac.uk>
Message-ID: <499D359A.9060103@abdn.ac.uk>

Bela Tiwari wrote:
> Hello,
> 
> My  memory of why we chose the z-shell is that, at the time, I was
> most familiar with tcsh and Dan (then the Bio-Linux developer) was
> most familiar with bash. Z-shell catered for both our syntax habits
> on the command line. More generally, we thought this would help
> others - i.e. those used to t or c shell, as well as those who used
> bash, would be able to use the same syntax as they were used to.

Hello, Bela and Tim.

I asked the question about "zsh" because "bash" is the standard shell 
used in Ubuntu and, unless there are compelling reasons why you use 
"zsh" instead I would like to use "bash". The Ubuntu documentation, 
which we do use, assumes that the default interactive shell is "bash".

My own experience with BSD and SunOS led me to choose "csh" and later 
"tsh" at the time, mainly for ease of manipulating command line history. 
However, in terms of script portability, I stopped using "csh/tcsh" 
completely when I migrated to Linux :-)

Under Ubuntu 8.04 LTS "bash" adopts a (very) strict POSIX compatibility 
mode when invoked as "sh". This has caused me some problems with (other 
people's!) shell scripts that use "#!/bin/sh", but expect to run "bash".

For NuGO, I'd like to explain why it is necessary for us to change from 
using "bash" to "zsh" when we upgrade our NBX's to Bio-Linux 5.0?

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From btiwari at ceh.ac.uk  Thu Feb 19 05:44:04 2009
From: btiwari at ceh.ac.uk (Bela Tiwari)
Date: Thu, 19 Feb 2009 10:44:04 +0000
Subject: [Bio-Linux] zsh
Message-ID: <s99d3820.050@wpo.nerc.ac.uk>

hi Tony, 

As the discussion is now turning to NUGO/NEBC specific stuff, we'll get back to you off list about this.

cheers, 

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> a.travis at abdn.ac.uk 02/19/09 10:34 am >>>
Bela Tiwari wrote:
> Hello,
> 
> My  memory of why we chose the z-shell is that, at the time, I was
> most familiar with tcsh and Dan (then the Bio-Linux developer) was
> most familiar with bash. Z-shell catered for both our syntax habits
> on the command line. More generally, we thought this would help
> others - i.e. those used to t or c shell, as well as those who used
> bash, would be able to use the same syntax as they were used to.

Hello, Bela and Tim.

I asked the question about "zsh" because "bash" is the standard shell 
used in Ubuntu and, unless there are compelling reasons why you use 
"zsh" instead I would like to use "bash". The Ubuntu documentation, 
which we do use, assumes that the default interactive shell is "bash".

My own experience with BSD and SunOS led me to choose "csh" and later 
"tsh" at the time, mainly for ease of manipulating command line history. 
However, in terms of script portability, I stopped using "csh/tcsh" 
completely when I migrated to Linux :-)

Under Ubuntu 8.04 LTS "bash" adopts a (very) strict POSIX compatibility 
mode when invoked as "sh". This has caused me some problems with (other 
people's!) shell scripts that use "#!/bin/sh", but expect to run "bash".

For NuGO, I'd like to explain why it is necessary for us to change from 
using "bash" to "zsh" when we upgrade our NBX's to Bio-Linux 5.0?

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk 
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt 

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




From bioinformatics.lists at gmail.com  Thu Feb 19 07:25:47 2009
From: bioinformatics.lists at gmail.com (Dan Swan)
Date: Thu, 19 Feb 2009 12:25:47 +0000
Subject: [Bio-Linux] zsh
In-Reply-To: <499D359A.9060103@abdn.ac.uk>
References: <s99d30f6.011@wpo.nerc.ac.uk> <499D359A.9060103@abdn.ac.uk>
Message-ID: <d606310d0902190425i3bb49872g31b5f7a9d0ac4060@mail.gmail.com>

Hello,

> Under Ubuntu 8.04 LTS "bash" adopts a (very) strict POSIX compatibility
> mode when invoked as "sh". This has caused me some problems with (other
> people's!) shell scripts that use "#!/bin/sh", but expect to run "bash".

This is due to Ubuntu replacing /bin/sh with /bin/dash - not bash.  A
widely unpopular move from the forum posts it generated when it
hapepend.

regards,

Dan


-- 
Bioinformatics Support Unit  || http://bsu.ncl.ac.uk/
Institute for Cell and Molecular Biosciences,
Faculty of Medical Sciences, Framlington Place,
Newcastle University, Newcastle, NE2 4HH
Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A - Mon/Wed)
Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26 - Thu/Fri)



From a.travis at abdn.ac.uk  Thu Feb 19 08:58:40 2009
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 19 Feb 2009 13:58:40 +0000
Subject: [Bio-Linux] zsh
In-Reply-To: <d606310d0902190425i3bb49872g31b5f7a9d0ac4060@mail.gmail.com>
References: <s99d30f6.011@wpo.nerc.ac.uk> <499D359A.9060103@abdn.ac.uk>
	<d606310d0902190425i3bb49872g31b5f7a9d0ac4060@mail.gmail.com>
Message-ID: <499D6590.5020303@abdn.ac.uk>

Dan Swan wrote:
> Hello,
> 
>> Under Ubuntu 8.04 LTS "bash" adopts a (very) strict POSIX compatibility
>> mode when invoked as "sh". This has caused me some problems with (other
>> people's!) shell scripts that use "#!/bin/sh", but expect to run "bash".
> 
> This is due to Ubuntu replacing /bin/sh with /bin/dash - not bash.  A
> widely unpopular move from the forum posts it generated when it
> hapepend.

Hello, Dan.

I've learnt something today, because I didn't know about the /bin/bash 
vs. /bin/dash issue in Ubuntu. BTW, what I've learnt today is that I 
don't know everything about Ubuntu ;-)

Actually, I think it's a good thing that scripts using /bin/sh as their 
interpreter conform to POSIX. However, this breaks a few things...

Thanks,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From a.travis at abdn.ac.uk  Thu Feb 19 09:38:16 2009
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 19 Feb 2009 14:38:16 +0000
Subject: [Bio-Linux] zsh
In-Reply-To: <499D6590.5020303@abdn.ac.uk>
References: <s99d30f6.011@wpo.nerc.ac.uk>
	<499D359A.9060103@abdn.ac.uk>	<d606310d0902190425i3bb49872g31b5f7a9d0ac4060@mail.gmail.com>
	<499D6590.5020303@abdn.ac.uk>
Message-ID: <499D6ED8.5000504@abdn.ac.uk>

Tony Travis wrote:
> Dan Swan wrote:
>> Hello,
>>
>>> Under Ubuntu 8.04 LTS "bash" adopts a (very) strict POSIX compatibility
>>> mode when invoked as "sh". This has caused me some problems with (other
>>> people's!) shell scripts that use "#!/bin/sh", but expect to run "bash".
>> This is due to Ubuntu replacing /bin/sh with /bin/dash - not bash.  A
>> widely unpopular move from the forum posts it generated when it
>> hapepend.

Hello, again, Dan.

What I said about "bash" and "sh" is what I read on the "bash" man page:

>        If  bash  is  invoked  with  the name sh, it tries to mimic the startup
>        behavior of historical versions of sh as  closely  as  possible,  while
>        conforming  to the POSIX standard as well.

OK, I completely misunderstood what was happening in scripts that worked 
under Ubuntu 6.06 but are broken under 8.04 because I didn't realise 
that the "sh" POSIX compliance was being imposed by "dash". I thought it 
was the POSIX behaviour of "bash" invoked being as "sh". Now I know it 
wasn't, but the symptoms are the same when scripts break because they 
expect BSD/GNU extensions to POSIX "sh" to be present when they are not.

Thanks for enlightening me,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt