From thackray at rci.rutgers.edu  Wed Dec  3 12:20:54 2014
From: thackray at rci.rutgers.edu (Josh Thackray)
Date: Wed, 03 Dec 2014 12:20:54 -0500
Subject: [Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2
Message-ID: <547F4676.50005@rci.rutgers.edu>

Hi,

I am running biolinux 8 and am trying to use Tophat (version 2.0.9) but 
this is incompatible with the version of bowtie2 (2.2.3) installed on 
the system by default. It looks like this issue was resolved in tophat 
version 2.0.12. It looks like the issue has to do with a change in the 
structure of the bowtie2 package where the aligner changed names from 
"bowtie2-align" to just "bowtie2". How can I update my tophat to this 
version?

Thanks,

Josh

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



From tbooth at ceh.ac.uk  Mon Dec  8 04:55:44 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 8 Dec 2014 09:55:44 +0000
Subject: [Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2
In-Reply-To: <547F4676.50005@rci.rutgers.edu>
References: <547F4676.50005@rci.rutgers.edu>
Message-ID: <1418032544.26424.160.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Josh,

I was looking at updating all the "Tuxedo Tools" packages at the end of
last week but due to some library interdependencies it's taking longer
than I expected.  I don't want to risk making things worse by rushing
untested updates onto the main package repository.

However, if you still need a package for TopHat 2.0.13 then I've put one
here:

http://nebc.nerc.ac.uk/downloads/bl8_only/tophat_2.0.13-0biolinux1_amd64.deb

If you download that and install it 
(sudo dpkg -i tophat_2.0.13-0biolinux1_amd64.deb) then I'm hoping it
will fix your problem.

Cheers,

TIM

On Wed, 2014-12-03 at 17:20 +0000, Josh Thackray wrote:
> Hi,
> 
> I am running biolinux 8 and am trying to use Tophat (version 2.0.9) but 
> this is incompatible with the version of bowtie2 (2.2.3) installed on 
> the system by default. It looks like this issue was resolved in tophat 
> version 2.0.12. It looks like the issue has to do with a change in the 
> structure of the bowtie2 package where the aligner changed names from 
> "bowtie2-align" to just "bowtie2". How can I update my tophat to this 
> version?
> 
> 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://nebc.nerc.ac.uk
+44 1491 69 2705


From tbooth at ceh.ac.uk  Mon Dec  8 05:53:06 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 8 Dec 2014 10:53:06 +0000
Subject: [Bio-Linux] Some last minute places available on Bio-Linux course
 next week in Bangor, North Wales
Message-ID: <1418035986.26424.167.camel@wllt1771.nerc-wallingford.ac.uk>

Hi All,

It's very short notice but I'm just sending this around in case anyone
on this list is interested, or knows anyone who might be interested.

I'm running an introduction to Bio-Linux course in Bangor next week and
after advertising it locally there are still places left.  See details
below for the on-line signup link and location/timings.

In preparing this course I'm updating the tutorial materials and these
will appear on the website shortly after the course.  I'm also hoping to
run one or two more courses in the London area early in 2015 and will
post details to this list when I have them.

Cheers,

TIM

-------- Forwarded Message --------
From: James McDonald <j.mcdonald at bangor.ac.uk>
To: Emma Ransom-Jones <e.ransom-jones at bangor.ac.uk>, Banner - All
research postgraduates students in biol <biol-gr-all-list at bangor.ac.uk>,
Banner - All research postgraduates students in senr
<senr-gr-all-list at bangor.ac.uk>, Staff-College of Natural Sciences
<cns-allstaff at bangor.ac.uk>, Banner - All research postgraduates
students in sos <sos-gr-all-list at bangor.ac.uk>
CC: "Booth, Timothy G." <tbooth at ceh.ac.uk>, James McDonald
<j.mcdonald at bangor.ac.uk>
Subject: Introduction to Bio-Linux 8
Date: Fri, 5 Dec 2014 14:09:24 +0000

Dear all, 


We still have some places available on this course if anyone would like
to attend:


A one-day training course titled "Introduction to Bio-Linux 8? will be
running on Wednesday 17th December in the Deiniol Library (AD_035). This
course is limited to 25 places with a ?20 registration fee to include
lunch, refreshments, 8GB Bio-Linux USB stick and printed course
booklet. 


For more information and to register please visit the
website http://mmeg-2014.bangor.ac.uk/BioLinux8course.php.en


The registration deadline is Midnight on Wednesday 10th December.
Best wishes,


James


-- 

Dr. James McDonald

Lecturer in Environmental Microbiology 
SBS Director of Graduate Studies                  
Bangor University,
Brambell Building,
Deiniol Road, Bangor, 
Gwynedd, LL57 2UW, UK.   

E-mail: j.mcdonald at bangor.ac.uk
Tel: +44(0)1248 383077  
Fax: +44(0)1248 370731
Website: http://jamesmcdonaldlab.com/ 

 

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Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio,
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This email and any attachments may contain confidential material and is
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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://nebc.nerc.ac.uk
+44 1491 69 2705


From hwh at email.arizona.edu  Mon Dec  8 11:21:45 2014
From: hwh at email.arizona.edu (Hans-Werner Herrmann)
Date: Mon, 08 Dec 2014 09:21:45 -0700
Subject: [Bio-Linux] BioLinux 8.0 cannot connect to windows file server
In-Reply-To: <5475FD20.1050100@abdn.ac.uk>
References: <5475EE7C.6070704@u.arizona.edu> <5475FD20.1050100@abdn.ac.uk>
Message-ID: <5485D019.8080504@email.arizona.edu>

Thanks! That worked. File server is mounted now.

H-W

Hans-Werner Herrmann, PhD
School of Plant Sciences
Joint Appointments with School of Natural Resources and the Environment &
Department of Soil, Water and Environmental Sciences
University of Arizona
Email: hwh at u.arizona.edu
Phone: (520)621-6674
Cell:  (520)780-1440

On 11/26/2014 9:17 AM, Tony Travis wrote:
> On 26/11/14 15:15, Hans-Werner Herrmann wrote:
>> I am running a server with BioLinux 8.0 and am trying to access our
>> Windows file server through "Connect to server..." every time I enter
>> smb://  I get a message saying "This file server type is not recognized"
>> and the Connect botton is grayed out. Can you help with this?
> Hi, Hans-Werner.
>
> I can connect to Windows using Nautilus "connect to server" OK, but the
> server is NOT in an NT domain. I suspect that your problem is the
> Windows server you are trying to access is using NT domain security and
> it won't let you in unless your Bio-Linux machine joins the NT domain.
>
> You could, instead, use cifs to connect and this might be a better
> solution because it means the files are accessible to any program.
>
> I put a line like this in /etc/fstab:
>
>> //windows-server      /share  cifs    noauto,credentials=filename     0       0
> Where:
>
>    //windows-server is DNS name of your Windows server
>    /share is the name of the Windows share you want to access
>    cifs is the filesystem type
>    noauto means don't automatically mount it when booting Linux
>    credentials is a file containing the Windows login credentials
>
> Please note that the credentials file MUST be well protected(!).
>
> You can debug the connection using "smbclient" - Try:
>
>    smbclient -L servername
>
> [Just press enter when asked for a password]
>
> HTH,
>
>    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.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux



From hwh at email.arizona.edu  Mon Dec  8 13:42:19 2014
From: hwh at email.arizona.edu (Hans-Werner Herrmann)
Date: Mon, 08 Dec 2014 11:42:19 -0700
Subject: [Bio-Linux] BioLinux 8 update times out
Message-ID: <5485F10B.2070108@email.arizona.edu>

Hi,

When I try to update BioLinux8 I get the following message: Could not 
get update details, timeout was reached. Suggestions to fix this are 
very appreciated. Thanks.

H-W

-- 
Hans-Werner Herrmann, PhD
School of Plant Sciences
Joint Appointments with School of Natural Resources and the Environment &
Department of Soil, Water and Environmental Sciences
University of Arizona
Email: hwh at u.arizona.edu
Phone: (520)621-6674
Cell:  (520)780-1440



From tbooth at ceh.ac.uk  Mon Dec  8 13:52:11 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 8 Dec 2014 18:52:11 +0000
Subject: [Bio-Linux] BioLinux 8 update times out
In-Reply-To: <5485F10B.2070108@email.arizona.edu>
References: <5485F10B.2070108@email.arizona.edu>
Message-ID: <1418064731.26424.191.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Hans-Werner,

All the servers that need to be running are running, so maybe it is a
temporary network glitch.  Or, did you change anything at your end since
the last successful update?  Are you using an HTTP proxy that might be
an issue?

If you do this on the command line:

sudo apt-get update

Do you see any more informative messages?

Cheers,

TIM

On Mon, 2014-12-08 at 18:42 +0000, Hans-Werner Herrmann wrote:
> Hi,
> 
> When I try to update BioLinux8 I get the following message: Could not 
> get update details, timeout was reached. Suggestions to fix this are 
> very appreciated. Thanks.
> 
> H-W
> 

-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705


From thackray at rci.rutgers.edu  Mon Dec  8 14:19:35 2014
From: thackray at rci.rutgers.edu (Josh Thackray)
Date: Mon, 08 Dec 2014 14:19:35 -0500
Subject: [Bio-Linux]  biolinux 8, Tophat incompatible with Bowtie2
In-Reply-To: <mailman.1.1418040002.28888.bio-linux@nebclists.nerc.ac.uk>
References: <mailman.1.1418040002.28888.bio-linux@nebclists.nerc.ac.uk>
Message-ID: <5485F9C7.9090800@rci.rutgers.edu>

Hi Tim,

Sounds great, please post to the list when you have the package ready. 
In the meantime, I figured out a workaround to the problem:

 1. The installed version of tophat looks for the bowtie2 executable
    using the name "bowtie2-align" which only exists for older versions
    of bowtie2. In newer versions of bowtie2, the aligner is renamed
    just "bowtie2". The solution here is to create a symbolic link
    "bowtie2-align" in /usr/bin that points to the "bowtie2" wrapper script.
 2. The other change necessary is a little worse to implement. For this
    we actually need to hack the tophat python script as detailed in
    this post:
    https://groups.google.com/d/msg/tuxedo-tools-users/vG5Rn0IgxoA/plOE89Yi55kJ.
    Its only a one line addition to get tophat to get the sam header
    from bowtie2 properly, specifically adding the -x argument.

These two changes got tophat working (mostly) properly with bowtie2 with 
the default installed versions.

The thing that was weird for me was that running tophat with -p > 3 
would cause my entire system to become completely unresponsive. I have a 
system with two quad-core processors so I tried running with "-p 8", and 
the system would freeze (mouse and keyboard did nothing). Running tophat 
with -p in {1, 2, 3} worked very well, and saw appropriate speedups, but 
using any -p >= 4, the system would freeze. Any ideas on this? This 
issue seems quite weird to me. I have a post about it over on biostars 
(https://www.biostars.org/p/122639/)

Thanks,

Josh

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

On 12/8/2014 7:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:
> Hi Josh,
>
> I was looking at updating all the "Tuxedo Tools" packages at the end of
> last week but due to some library interdependencies it's taking longer
> than I expected.  I don't want to risk making things worse by rushing
> untested updates onto the main package repository.
>
> However, if you still need a package for TopHat 2.0.13 then I've put one
> here:
>
> http://nebc.nerc.ac.uk/downloads/bl8_only/tophat_2.0.13-0biolinux1_amd64.deb
>
> If you download that and install it
> (sudo dpkg -i tophat_2.0.13-0biolinux1_amd64.deb) then I'm hoping it
> will fix your problem.
>
> Cheers,
>
> TIM
>
> On Wed, 2014-12-03 at 17:20 +0000, Josh Thackray wrote:
>> Hi,
>>
>> I am running biolinux 8 and am trying to use Tophat (version 2.0.9) but
>> this is incompatible with the version of bowtie2 (2.2.3) installed on
>> the system by default. It looks like this issue was resolved in tophat
>> version 2.0.12. It looks like the issue has to do with a change in the
>> structure of the bowtie2 package where the aligner changed names from
>> "bowtie2-align" to just "bowtie2". How can I update my tophat to this
>> version?
>>
>> Thanks,
>>
>> Josh
>>

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From hwh at email.arizona.edu  Mon Dec  8 14:27:42 2014
From: hwh at email.arizona.edu (Hans-Werner Herrmann)
Date: Mon, 08 Dec 2014 12:27:42 -0700
Subject: [Bio-Linux] BioLinux 8 update times out
In-Reply-To: <1418064731.26424.191.camel@wllt1771.nerc-wallingford.ac.uk>
References: <5485F10B.2070108@email.arizona.edu>
 <1418064731.26424.191.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <5485FBAE.4020405@email.arizona.edu>

With command line download and install no problem. Thanks.

H-W

Hans-Werner Herrmann, PhD
School of Plant Sciences
Joint Appointments with School of Natural Resources and the Environment &
Department of Soil, Water and Environmental Sciences
University of Arizona
Email: hwh at u.arizona.edu
Phone: (520)621-6674
Cell:  (520)780-1440

On 12/8/2014 11:52 AM, Tim Booth wrote:
> Hi Hans-Werner,
>
> All the servers that need to be running are running, so maybe it is a
> temporary network glitch.  Or, did you change anything at your end since
> the last successful update?  Are you using an HTTP proxy that might be
> an issue?
>
> If you do this on the command line:
>
> sudo apt-get update
>
> Do you see any more informative messages?
>
> Cheers,
>
> TIM
>
> On Mon, 2014-12-08 at 18:42 +0000, Hans-Werner Herrmann wrote:
>> Hi,
>>
>> When I try to update BioLinux8 I get the following message: Could not
>> get update details, timeout was reached. Suggestions to fix this are
>> very appreciated. Thanks.
>>
>> H-W
>>



From kissaj at miamioh.edu  Mon Dec  8 18:19:27 2014
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Mon, 8 Dec 2014 18:19:27 -0500
Subject: [Bio-Linux] IPS tools
Message-ID: <407C074F-2631-4E79-A4E3-AD30DDB4ADDD@miamioh.edu>

Hi,

   Anyone know of a tool, or tools that can help visualize the output of an IPS output (version 5)?

Thanks,
____________________________
Andor J Kiss
eMAIL: kissaj at MiamiOH.edu

From tbooth at ceh.ac.uk  Fri Dec 12 12:24:27 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 12 Dec 2014 17:24:27 +0000
Subject: [Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2
In-Reply-To: <5485F9C7.9090800@rci.rutgers.edu>
References: <mailman.1.1418040002.28888.bio-linux@nebclists.nerc.ac.uk>
 <5485F9C7.9090800@rci.rutgers.edu>
Message-ID: <1418405067.26424.277.camel@wllt1771.nerc-wallingford.ac.uk>

Hi All,

I've now updated tophat, bowtie, bowtie2 and cufflinks on Bio-Linux.
The new packages will be installed via the update manager as usual.

This time I tested Tophat as described here:
http://ccb.jhu.edu/software/tophat/tutorial.shtml#test

With the old packages if I run this it says there is no bowtie2.  Now it
finds and uses it, so I'm taking this to mean it all works, but if you
find there are still issues please let me know.

Regarding TopHat freezing with -p >= 4, I'm really not sure.  Sometimes
if you increase the threads too much in a data-centric application you
can overwhelm the IO bus which freezes things up badly unless you have a
server-grade machine with SCSI disks.  Any chance things have improved
with the new packages?

Cheers,

TIM

On Mon, 2014-12-08 at 19:19 +0000, Josh Thackray wrote:
> Hi Tim,
> 
> Sounds great, please post to the list when you have the package ready.
> In the meantime, I figured out a workaround to the problem:
>      1. The installed version of tophat looks for the bowtie2
>         executable using the name "bowtie2-align" which only exists
>         for older versions of bowtie2. In newer versions of bowtie2,
>         the aligner is renamed just "bowtie2". The solution here is to
>         create a symbolic link "bowtie2-align" in /usr/bin that points
>         to the "bowtie2" wrapper script.
>      2. The other change necessary is a little worse to implement. For
>         this we actually need to hack the tophat python script as
>         detailed in this post:
>         https://groups.google.com/d/msg/tuxedo-tools-users/vG5Rn0IgxoA/plOE89Yi55kJ. Its only a one line addition to get tophat to get the sam header from bowtie2 properly, specifically adding the -x argument.
> 
> These two changes got tophat working (mostly) properly with bowtie2
> with the default installed versions.
> 
> 
> The thing that was weird for me was that running tophat with -p > 3
> would cause my entire system to become completely unresponsive. I have
> a system with two quad-core processors so I tried running with "-p 8",
> and the system would freeze (mouse and keyboard did nothing). Running
> tophat with -p in {1, 2, 3} worked very well, and saw appropriate
> speedups, but using any -p >= 4, the system would freeze. Any ideas on
> this? This issue seems quite weird to me. I have a post about it over
> on biostars (https://www.biostars.org/p/122639/)
> 
> 
> Thanks,
> 
> 
> Josh
> 
> 
> Josh Thackray
> Laboratory Researcher III
> Human Genetics Institute of NJ
> Department of Genetics
> Rutgers University
> On 12/8/2014 7:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:
> 
> > Hi Josh,
> > 
> > I was looking at updating all the "Tuxedo Tools" packages at the end of
> > last week but due to some library interdependencies it's taking longer
> > than I expected.  I don't want to risk making things worse by rushing
> > untested updates onto the main package repository.
> > 
> > However, if you still need a package for TopHat 2.0.13 then I've put one
> > here:
> > 
> > http://nebc.nerc.ac.uk/downloads/bl8_only/tophat_2.0.13-0biolinux1_amd64.deb
> > 
> > If you download that and install it 
> > (sudo dpkg -i tophat_2.0.13-0biolinux1_amd64.deb) then I'm hoping it
> > will fix your problem.
> > 
> > Cheers,
> > 
> > TIM
> > 
> > On Wed, 2014-12-03 at 17:20 +0000, Josh Thackray wrote:
> > > Hi,
> > > 
> > > I am running biolinux 8 and am trying to use Tophat (version 2.0.9) but 
> > > this is incompatible with the version of bowtie2 (2.2.3) installed on 
> > > the system by default. It looks like this issue was resolved in tophat 
> > > version 2.0.12. It looks like the issue has to do with a change in the 
> > > structure of the bowtie2 package where the aligner changed names from 
> > > "bowtie2-align" to just "bowtie2". How can I update my tophat to this 
> > > version?
> > > 
> > > 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://nebc.nerc.ac.uk
+44 1491 69 2705


From gawbul at gmail.com  Sat Dec 13 19:13:53 2014
From: gawbul at gmail.com (Steve Moss)
Date: Sun, 14 Dec 2014 00:13:53 +0000
Subject: [Bio-Linux] BioLinux8 Dockerfile
Message-ID: <CALKAsdpNrx1SqqRS=qgE=cGi5p-ARMbtW9CV4uNwrsUgFETiRg@mail.gmail.com>

Dear Tim,

I was hoping to start working on a basic BioLinux8 Docker image. I've setup
a repository here https://github.com/gawbul/DockerBioLinux8, and have
started some of the initial work locally; unpacking and utilising some
steps from the BL8 setup script. I'm aware that some packages have
graphical interfaces, and depend on xserver*, gnome* or unity* packages
etc; I was hoping you might have an idea which could be pinned to prevent
them being installed or otherwise give advice on this? Perhaps checking out
CloudBioLinux would be useful do you think, as I am assuming they did
something similar?

Cheers,

Steve
-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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From tbooth at ceh.ac.uk  Sun Dec 14 09:40:07 2014
From: tbooth at ceh.ac.uk (Booth, Timothy G.)
Date: Sun, 14 Dec 2014 14:40:07 +0000
Subject: [Bio-Linux] BioLinux8 Dockerfile
In-Reply-To: <CALKAsdpNrx1SqqRS=qgE=cGi5p-ARMbtW9CV4uNwrsUgFETiRg@mail.gmail.com>
References: <CALKAsdpNrx1SqqRS=qgE=cGi5p-ARMbtW9CV4uNwrsUgFETiRg@mail.gmail.com>
Message-ID: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk>

Hi Steve,

Good to hear from you again.  I know you are no longer in London but are you still working with the QMUL guys on this?  I know Docker is a big thing to them.

I'm looking forward to seeing how this works out.  Lots of people are talking about Docker but it's hard for me to see how it leads to making things that real biologists want to use - almost certainly a failure of my own imagination!

To answer your question, I'd suggest the following approach - take a fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and X libs packages.  Lots of packages that depend on them will be removed.  Then you can diff the master package list from the upgrade script and the packages you have left on the system to get your blacklist.  I'm sure there are other approaches but this is the one that springs to mind.

(Actually, a really quick way could be to blacklist all the packages that contain a .desktop file, but this won't be as accurate as the other method).

Cheers,

TIM

________________________________________
From: Steve Moss [gawbul at gmail.com]
Sent: 14 December 2014 00:13
To: Bio-Linux help and discussion
Subject: [Bio-Linux] BioLinux8 Dockerfile

Dear Tim,

I was hoping to start working on a basic BioLinux8 Docker image. I've setup a repository here https://github.com/gawbul/DockerBioLinux8, and have started some of the initial work locally; unpacking and utilising some steps from the BL8 setup script. I'm aware that some packages have graphical interfaces, and depend on xserver*, gnome* or unity* packages etc; I was hoping you might have an idea which could be pinned to prevent them being installed or otherwise give advice on this? Perhaps checking out CloudBioLinux would be useful do you think, as I am assuming they did something similar?

Cheers,

Steve
--
<http://about.me/gawbul>

Steve Moss
about.me/gawbul





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 tony.travis at abdn.ac.uk  Mon Dec 15 07:24:01 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Mon, 15 Dec 2014 12:24:01 +0000
Subject: [Bio-Linux] BioLinux8 Dockerfile
In-Reply-To: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk>
References: <CALKAsdpNrx1SqqRS=qgE=cGi5p-ARMbtW9CV4uNwrsUgFETiRg@mail.gmail.com>
 <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk>
Message-ID: <548ED2E1.4050301@abdn.ac.uk>

On 14/12/14 14:40, Booth, Timothy G. wrote:
> [...]
> To answer your question, I'd suggest the following approach - take a
> fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and
> X libs packages.  Lots of packages that depend on them will be
> removed.  Then you can diff the master package list from the upgrade
> script and the packages you have left on the system to get your
> blacklist.  I'm sure there are other approaches but this is the one
> that springs to mind.

Hi, Tim and Steve.

I think you're missing the point about Docker if you're trying to create
a Bio-Linux container. Docker is a lightweight container that relies on
the host OS to provide kernel services and system daemons.

Bio-Linux is more appropriate as a host OS for Docker. I don't really
see the point of trying to run a full Bio-linux in a Docker container
because the overhead will be such that you might as well be using a VM.

Docker is most useful for providing an OS independent environment for
applications like e.g. GATK that have specific version dependencies that
are quite difficult to reconcile with versions of programs that are
installed on a particular host. Docker provides portability of an
application between host and OS's by encapsulating these dependencies.

Having said that, I'm currently trying to use Bio-Linux in a user-level
"fakechroot" under 'Scientific' Linux (CentOS 6.3) on our HPC cluster
because our out-sourced IT support company think Docker is too serious a
security threat to be used on a 'production' server. I've pointed out
that both AWS and Rackspace are offering Docker instances on their own
cloud services 'securely'. I'm experimenting with Docker on my own PC.

[I've CC'ed this to Brad to get his take on using Docker for Bio-Linux]

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 gawbul at gmail.com  Tue Dec 16 07:22:13 2014
From: gawbul at gmail.com (Steve Moss)
Date: Tue, 16 Dec 2014 12:22:13 +0000
Subject: [Bio-Linux] BioLinux8 Dockerfile (Tony Travis)
Message-ID: <CALKAsdprY7pMUqEZ032ieZkbbb8hNhNj3+9Eg1r4sJYQ++neJw@mail.gmail.com>

Dear Tony,

I'm not wanting to create a full Bio-Linux installation in a container. As
you say, that would be contrary to the purpose of containers. I'm more
interested in creating a cut-down Bio-Linux-eqsue Docker image that has all
the relevant command line tools installed for undertaking bioinformatics
analyses, and access to the Bio-Linux 8 repos for installing additional
tools as necessary.

Another way of doing this would be to simply use the ubuntu base image, add
the Bio-Linux 8 repos, pin any GUI packages in apt with -1 priority, and
install all command line packages as part of the Dockerfile configuration.
Just trying to think of the easiest way to approach it.

I've followed Brad's work closely, so be interested to hear his take on
this too.

Cheers,

Steve

On 16 December 2014 at 12:00, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:
>
> Message: 1
> Date: Mon, 15 Dec 2014 12:24:01 +0000
> From: Tony Travis <tony.travis at abdn.ac.uk>
> To: <bio-linux at nebclists.nerc.ac.uk>
> Cc: Brad Chapman <chapmanb at 50mail.com>
> Subject: Re: [Bio-Linux] BioLinux8 Dockerfile
> Message-ID: <548ED2E1.4050301 at abdn.ac.uk>
> Content-Type: text/plain; charset="windows-1252"
>
> On 14/12/14 14:40, Booth, Timothy G. wrote:
> > [...]
> > To answer your question, I'd suggest the following approach - take a
> > fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and
> > X libs packages.  Lots of packages that depend on them will be
> > removed.  Then you can diff the master package list from the upgrade
> > script and the packages you have left on the system to get your
> > blacklist.  I'm sure there are other approaches but this is the one
> > that springs to mind.
>
> Hi, Tim and Steve.
>
> I think you're missing the point about Docker if you're trying to create
> a Bio-Linux container. Docker is a lightweight container that relies on
> the host OS to provide kernel services and system daemons.
>
> Bio-Linux is more appropriate as a host OS for Docker. I don't really
> see the point of trying to run a full Bio-linux in a Docker container
> because the overhead will be such that you might as well be using a VM.
>
> Docker is most useful for providing an OS independent environment for
> applications like e.g. GATK that have specific version dependencies that
> are quite difficult to reconcile with versions of programs that are
> installed on a particular host. Docker provides portability of an
> application between host and OS's by encapsulating these dependencies.
>
> Having said that, I'm currently trying to use Bio-Linux in a user-level
> "fakechroot" under 'Scientific' Linux (CentOS 6.3) on our HPC cluster
> because our out-sourced IT support company think Docker is too serious a
> security threat to be used on a 'production' server. I've pointed out
> that both AWS and Rackspace are offering Docker instances on their own
> cloud services 'securely'. I'm experimenting with Docker on my own PC.
>
> [I've CC'ed this to Brad to get his take on using Docker for Bio-Linux]
>
> Bye,
>
>   Tony.
>

-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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From chapmanb at 50mail.com  Tue Dec 16 09:32:23 2014
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 16 Dec 2014 09:32:23 -0500
Subject: [Bio-Linux] BioLinux8 Dockerfile (Tony Travis)
In-Reply-To: <CALKAsdprY7pMUqEZ032ieZkbbb8hNhNj3+9Eg1r4sJYQ++neJw@mail.gmail.com>
References: <CALKAsdprY7pMUqEZ032ieZkbbb8hNhNj3+9Eg1r4sJYQ++neJw@mail.gmail.com>
Message-ID: <86lhm7d5s8.fsf@fastmail.fm>


Steve and Tony;
I agree with this approach. This is essentially what we are doing with
CloudBioLinux inside bcbio: providing a big ol' container with a lot of
useful tools related to next-gen sequencing:

https://github.com/chapmanb/bcbio-nextgen/blob/master/Dockerfile

This uses both Bio-Linux and other installers like Homebrew cobbled
together with CloudBioLinux.

There is definitely an issue of size as you add more tools but if you
want to run them together it's easier to manage and distribute a single
instance rather than trying to chain multiple images. So somewhere in
between a single tool and all the tools in the world is the right place
to be. It would be cool to see what you can come up with for a Bio-Linux
distribution,
Brad

> Dear Tony,
>
> I'm not wanting to create a full Bio-Linux installation in a container. As
> you say, that would be contrary to the purpose of containers. I'm more
> interested in creating a cut-down Bio-Linux-eqsue Docker image that has all
> the relevant command line tools installed for undertaking bioinformatics
> analyses, and access to the Bio-Linux 8 repos for installing additional
> tools as necessary.
>
> Another way of doing this would be to simply use the ubuntu base image, add
> the Bio-Linux 8 repos, pin any GUI packages in apt with -1 priority, and
> install all command line packages as part of the Dockerfile configuration.
> Just trying to think of the easiest way to approach it.
>
> I've followed Brad's work closely, so be interested to hear his take on
> this too.
>
> Cheers,
>
> Steve
>
> On 16 December 2014 at 12:00, <bio-linux-request at nebclists.nerc.ac.uk>
> wrote:
>>
>> Message: 1
>> Date: Mon, 15 Dec 2014 12:24:01 +0000
>> From: Tony Travis <tony.travis at abdn.ac.uk>
>> To: <bio-linux at nebclists.nerc.ac.uk>
>> Cc: Brad Chapman <chapmanb at 50mail.com>
>> Subject: Re: [Bio-Linux] BioLinux8 Dockerfile
>> Message-ID: <548ED2E1.4050301 at abdn.ac.uk>
>> Content-Type: text/plain; charset="windows-1252"
>>
>> On 14/12/14 14:40, Booth, Timothy G. wrote:
>> > [...]
>> > To answer your question, I'd suggest the following approach - take a
>> > fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and
>> > X libs packages.  Lots of packages that depend on them will be
>> > removed.  Then you can diff the master package list from the upgrade
>> > script and the packages you have left on the system to get your
>> > blacklist.  I'm sure there are other approaches but this is the one
>> > that springs to mind.
>>
>> Hi, Tim and Steve.
>>
>> I think you're missing the point about Docker if you're trying to create
>> a Bio-Linux container. Docker is a lightweight container that relies on
>> the host OS to provide kernel services and system daemons.
>>
>> Bio-Linux is more appropriate as a host OS for Docker. I don't really
>> see the point of trying to run a full Bio-linux in a Docker container
>> because the overhead will be such that you might as well be using a VM.
>>
>> Docker is most useful for providing an OS independent environment for
>> applications like e.g. GATK that have specific version dependencies that
>> are quite difficult to reconcile with versions of programs that are
>> installed on a particular host. Docker provides portability of an
>> application between host and OS's by encapsulating these dependencies.
>>
>> Having said that, I'm currently trying to use Bio-Linux in a user-level
>> "fakechroot" under 'Scientific' Linux (CentOS 6.3) on our HPC cluster
>> because our out-sourced IT support company think Docker is too serious a
>> security threat to be used on a 'production' server. I've pointed out
>> that both AWS and Rackspace are offering Docker instances on their own
>> cloud services 'securely'. I'm experimenting with Docker on my own PC.
>>
>> [I've CC'ed this to Brad to get his take on using Docker for Bio-Linux]
>>
>> Bye,
>>
>>   Tony.
>>
>
> -- 
>
> Steve Moss
> about.me/gawbul
> [image: Steve Moss on about.me]
>   <http://about.me/gawbul>


From thackray at rci.rutgers.edu  Wed Dec 17 13:23:29 2014
From: thackray at rci.rutgers.edu (Josh Thackray)
Date: Wed, 17 Dec 2014 13:23:29 -0500
Subject: [Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2
In-Reply-To: <1418405067.26424.277.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1418405067.26424.277.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <5491CA21.4030609@rci.rutgers.edu>

Hi Tim,

Thanks for updating the packages! I updated using the package manager, 
however bowtie (version 1.1.1) seems to now be broken. Upon further 
investigation, it looks like only the debug binaries get installed. 
Invoking bowtie with the --debug option gives me the help message, while 
invoking bowtie with no options gives an error (No such file or directory).

Thanks,

Josh


From gawbul at gmail.com  Fri Dec 19 07:19:08 2014
From: gawbul at gmail.com (Steve Moss)
Date: Fri, 19 Dec 2014 12:19:08 +0000
Subject: [Bio-Linux] BioLinux8 Dockerfile (Tony Travis)
In-Reply-To: <86lhm7d5s8.fsf@fastmail.fm>
References: <CALKAsdprY7pMUqEZ032ieZkbbb8hNhNj3+9Eg1r4sJYQ++neJw@mail.gmail.com>
 <86lhm7d5s8.fsf@fastmail.fm>
Message-ID: <CALKAsdpjHriO=YViEkBu3x26pxW=-kCX_+nnbPd-_NpaQBU6Pw@mail.gmail.com>

Dear Brad,

Thanks for the input, and glad you agree. Yes, I've been following your
work on bcbio-nextgen. It looks great!

Will keep working away at a minimal Bio-Linux container, and give updates
on my progress here.

Cheers,

Steve

On 16 December 2014 at 14:32, Brad Chapman <chapmanb at 50mail.com> wrote:
>
>
> Steve and Tony;
> I agree with this approach. This is essentially what we are doing with
> CloudBioLinux inside bcbio: providing a big ol' container with a lot of
> useful tools related to next-gen sequencing:
>
> https://github.com/chapmanb/bcbio-nextgen/blob/master/Dockerfile
>
> This uses both Bio-Linux and other installers like Homebrew cobbled
> together with CloudBioLinux.
>
> There is definitely an issue of size as you add more tools but if you
> want to run them together it's easier to manage and distribute a single
> instance rather than trying to chain multiple images. So somewhere in
> between a single tool and all the tools in the world is the right place
> to be. It would be cool to see what you can come up with for a Bio-Linux
> distribution,
> Brad
>
> > Dear Tony,
> >
> > I'm not wanting to create a full Bio-Linux installation in a container.
> As
> > you say, that would be contrary to the purpose of containers. I'm more
> > interested in creating a cut-down Bio-Linux-eqsue Docker image that has
> all
> > the relevant command line tools installed for undertaking bioinformatics
> > analyses, and access to the Bio-Linux 8 repos for installing additional
> > tools as necessary.
> >
> > Another way of doing this would be to simply use the ubuntu base image,
> add
> > the Bio-Linux 8 repos, pin any GUI packages in apt with -1 priority, and
> > install all command line packages as part of the Dockerfile
> configuration.
> > Just trying to think of the easiest way to approach it.
> >
> > I've followed Brad's work closely, so be interested to hear his take on
> > this too.
> >
> > Cheers,
> >
> > Steve
> >
> > On 16 December 2014 at 12:00, <bio-linux-request at nebclists.nerc.ac.uk>
> > wrote:
> >>
> >> Message: 1
> >> Date: Mon, 15 Dec 2014 12:24:01 +0000
> >> From: Tony Travis <tony.travis at abdn.ac.uk>
> >> To: <bio-linux at nebclists.nerc.ac.uk>
> >> Cc: Brad Chapman <chapmanb at 50mail.com>
> >> Subject: Re: [Bio-Linux] BioLinux8 Dockerfile
> >> Message-ID: <548ED2E1.4050301 at abdn.ac.uk>
> >> Content-Type: text/plain; charset="windows-1252"
> >>
> >> On 14/12/14 14:40, Booth, Timothy G. wrote:
> >> > [...]
> >> > To answer your question, I'd suggest the following approach - take a
> >> > fresh Bio-Linux VM (ie. the .ova download) then remove the Gnome and
> >> > X libs packages.  Lots of packages that depend on them will be
> >> > removed.  Then you can diff the master package list from the upgrade
> >> > script and the packages you have left on the system to get your
> >> > blacklist.  I'm sure there are other approaches but this is the one
> >> > that springs to mind.
> >>
> >> Hi, Tim and Steve.
> >>
> >> I think you're missing the point about Docker if you're trying to create
> >> a Bio-Linux container. Docker is a lightweight container that relies on
> >> the host OS to provide kernel services and system daemons.
> >>
> >> Bio-Linux is more appropriate as a host OS for Docker. I don't really
> >> see the point of trying to run a full Bio-linux in a Docker container
> >> because the overhead will be such that you might as well be using a VM.
> >>
> >> Docker is most useful for providing an OS independent environment for
> >> applications like e.g. GATK that have specific version dependencies that
> >> are quite difficult to reconcile with versions of programs that are
> >> installed on a particular host. Docker provides portability of an
> >> application between host and OS's by encapsulating these dependencies.
> >>
> >> Having said that, I'm currently trying to use Bio-Linux in a user-level
> >> "fakechroot" under 'Scientific' Linux (CentOS 6.3) on our HPC cluster
> >> because our out-sourced IT support company think Docker is too serious a
> >> security threat to be used on a 'production' server. I've pointed out
> >> that both AWS and Rackspace are offering Docker instances on their own
> >> cloud services 'securely'. I'm experimenting with Docker on my own PC.
> >>
> >> [I've CC'ed this to Brad to get his take on using Docker for Bio-Linux]
> >>
> >> Bye,
> >>
> >>   Tony.
> >>
> >
> > --
> >
> > Steve Moss
> > about.me/gawbul
> > [image: Steve Moss on about.me]
> >   <http://about.me/gawbul>
>


-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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From tbooth at ceh.ac.uk  Fri Dec 19 08:49:52 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 19 Dec 2014 13:49:52 +0000
Subject: [Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2
In-Reply-To: <5491CA21.4030609@rci.rutgers.edu>
References: <1418405067.26424.277.camel@wllt1771.nerc-wallingford.ac.uk>
 <5491CA21.4030609@rci.rutgers.edu>
Message-ID: <1418996992.5938.60.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Josh,

Sorry about that, I got so distracted trying to compile the tools
against the right version of the SeqAn that I didn't realise I was
missing essential binaries in the package.

New version up now - how's that looking?

Cheers,

TIM

On Wed, 2014-12-17 at 18:23 +0000, Josh Thackray wrote:
> Hi Tim,
> 
> Thanks for updating the packages! I updated using the package manager, 
> however bowtie (version 1.1.1) seems to now be broken. Upon further 
> investigation, it looks like only the debug binaries get installed. 
> Invoking bowtie with the --debug option gives me the help message, while 
> invoking bowtie with no options gives an error (No such file or directory).
> 
> Thanks,
> 
> Josh
> _______________________________________________
> 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://nebc.nerc.ac.uk
+44 1491 69 2705


From gawbul at gmail.com  Sun Dec 21 04:10:57 2014
From: gawbul at gmail.com (Steve Moss)
Date: Sun, 21 Dec 2014 09:10:57 +0000
Subject: [Bio-Linux] BioLinux8 Dockerfile (Tony Travis)
Message-ID: <CALKAsdqLD2AJRG8_sxYGswd-vg-z_-THLvn7hTjU2a_Jvqa8ig@mail.gmail.com>

Dear All,

I've been playing around with the Dockerfile for the Bio-Linux8 Docker
image (https://github.com/gawbul/docker-bio-linux8). I managed to get it to
install all the Bio-Linux packages, as per Tim's upgrade script, with the
exception of a few graphical packages. The image size is around 6Gb,
however.

I'm trying to think of the best way to do this now? Should I just provide a
base image with Bio-Linux repositories configured so users can install what
they want? Or should I install a few commonly used packages? The question
is then, what are the most commonly used/required packages?

Tim, I was trying to think if there would be any metrics on the number of
installs of bioinformatics packages from a given repository that might be
able to help with this? Otherwise, I guess it would be a case of people
giving a list of the packages they need/use on a regular basis?

Cheers,

Steve
-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]

<http://about.me/gawbul>
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From thackray at rci.rutgers.edu  Fri Dec 19 11:34:38 2014
From: thackray at rci.rutgers.edu (Josh Thackray)
Date: Fri, 19 Dec 2014 11:34:38 -0500
Subject: [Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2
In-Reply-To: <1418996992.5938.60.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1418996992.5938.60.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <5494539E.2040704@rci.rutgers.edu>

Hi Tim,

No worries, it happens to the best of us. The updated package looks good 
to me! Thanks for all the hard work!

Josh

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