Galaxy Server on Bio-Linux
Dear Galaxy Developers, We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research Institute based in Oxford. We develop and distribute Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu distribution that comes with 500+ bioinformatics packages. Within our research group we also provide bioinformatics analysis for NERC-funded researchers, and recently started looking into Galaxy as well. It didn't take us long to discover its power and we would like to enable Bio-Linux users to install, run and maintain the Galaxy server with minimal effort, also with the aim to spread the word on Galaxy in Europe! Recently we took on a project with Dr. Casey Bergman from University of Manchester as the Principal Investigator, to package all the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many pre-requisities are already included with Bio-Linux, we are already some way down this path. New packages that we create will appear in a Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy). We will be happy to hear any comments regarding these efforts and we hope that this will be a useful resource for all Galaxy users. Once the initial packaging is done, we hope to collaborate with Galaxy team in maintaining and improving this resource. Best wishes, Tim, Soon and Mesude -- Dr. Mesude Bicak <mbicak@ceh.ac.uk> Bioinformatician & Bio-Linux Developer NERC Biomolecular Analysis Facility (NBAF) <http://nbaf.nerc.ac.uk> NERC Environmental Bioinformatics Centre (NEBC) <http://nebc.nerc.ac.uk> Molecular Evolution and Bioinformatics Group Centre for Ecology and Hydrology <http://ceh.ac.uk> Maclean Building, Benson Lane Crowmarsh Gifford Wallingford, Oxfordshire OX10 8BB Office Tel: +44 1491 69 2705-- 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.
On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote:
Dear Galaxy Developers,
We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research Institute based in Oxford.
We develop and distribute Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu distribution that comes with 500+ bioinformatics packages. Within our research group we also provide bioinformatics analysis for NERC-funded researchers, and recently started looking into Galaxy as well. It didn't take us long to discover its power and we would like to enable Bio-Linux users to install, run and maintain the Galaxy server with minimal effort, also with the aim to spread the word on Galaxy in Europe!
Recently we took on a project with Dr. Casey Bergman from University of Manchester as the Principal Investigator, to package all the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many pre-requisities are already included with Bio-Linux, we are already some way down this path. New packages that we create will appear in a Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy).
We will be happy to hear any comments regarding these efforts and we hope that this will be a useful resource for all Galaxy users. Once the initial packaging is done, we hope to collaborate with Galaxy team in maintaining and improving this resource.
Best wishes, Tim, Soon and Mesude
Hi Mesude, This is fantastic, thanks for letting us know, and please do post up if there is anything we can help with. Also, if you're not aware, Galaxy's cloud offering is built on CloudBioLinux, which itself is built on Bio-Linux. --nate
-- Dr. Mesude Bicak <mbicak@ceh.ac.uk> Bioinformatician & Bio-Linux Developer
NERC Biomolecular Analysis Facility (NBAF) <http://nbaf.nerc.ac.uk> NERC Environmental Bioinformatics Centre (NEBC) <http://nebc.nerc.ac.uk>
Molecular Evolution and Bioinformatics Group Centre for Ecology and Hydrology <http://ceh.ac.uk> Maclean Building, Benson Lane Crowmarsh Gifford Wallingford, Oxfordshire OX10 8BB
Office Tel: +44 1491 69 2705-- 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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Tue, Jan 3, 2012 at 11:36 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote:
Dear Galaxy Developers,
We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research Institute based in Oxford.
We develop and distribute Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu distribution that comes with 500+ bioinformatics packages. Within our research group we also provide bioinformatics analysis for NERC-funded researchers, and recently started looking into Galaxy as well. It didn't take us long to discover its power and we would like to enable Bio-Linux users to install, run and maintain the Galaxy server with minimal effort, also with the aim to spread the word on Galaxy in Europe!
Recently we took on a project with Dr. Casey Bergman from University of Manchester as the Principal Investigator, to package all the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many pre-requisities are already included with Bio-Linux, we are already some way down this path. New packages that we create will appear in a Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy).
We will be happy to hear any comments regarding these efforts and we hope that this will be a useful resource for all Galaxy users. Once the initial packaging is done, we hope to collaborate with Galaxy team in maintaining and improving this resource.
Best wishes, Tim, Soon and Mesude
Hi Mesude,
This is fantastic, thanks for letting us know, and please do post up if there is anything we can help with. Also, if you're not aware, Galaxy's cloud offering is built on CloudBioLinux, which itself is built on Bio-Linux.
--nate
This is very good news, I'm personally a big fan of avoiding as much as possible installing from source on production systems, as things can get easily out of hand when trying to keep everything updated. Mesude, I recently joined Debian Med (http://www.debian.org/devel/debian-med/ and https://launchpad.net/~debian-med) which the exact same goal of getting as much tools as possible packaged for Debian/Ubuntu. I see Tim Booth is an active member in Debian Med and I was wondering if your group is planning to keep the development of these packages in the git/svn repositories of Debian Med. I wouldn't want to duplicate your efforts. I like very much the use of PPAs while waiting for packages to be officially included in Debian and trickle down to Ubuntu, process that could be somehow slow at times. Just today I was able to upload Tophat's package being developed at Debian Med to the PPA, I'm pretty sure it needs more work, but you might be interested in taking a look. Kind regards, Carlos
Hi Carlos, Yes, I'm an active member of Deb Med but unfortunately not finding time to read the mailing list properly nor to actually run Debian (or even the Ubuntu development release). We've actually factored time into the packaging project to contribute all relevant packaging into the Debian-Med repositories. This has to be done with a bit of care as there are now real differences between standards for Debian Sid and Ubuntu LTS for which we are packaging. My plan is to complete a bunch of packages and then review and commit what we have in a batch later this month. I do have a package for TopHat in my own PPA that I added late last year: https://launchpad.net/~tbooth/+archive/ppa1 I made a couple of tweaks to get the thing to link properly, but again I need to check that these aren't Ubuntu specific before I push any patches back to Alex, who seems to be actively committing changes to Git right now. Cheers, TIM On Wed, 2012-01-04 at 20:22 +0000, Carlos Borroto wrote:
On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote:
Dear Galaxy Developers,
We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research Institute based in Oxford.
We develop and distribute Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu distribution that comes with 500+ bioinformatics packages. Within our research group we also provide bioinformatics analysis for NERC-funded researchers, and recently started looking into Galaxy as well. It didn't take us long to discover its power and we would like to enable Bio-Linux users to install, run and maintain the Galaxy server with minimal effort, also with the aim to spread the word on Galaxy in Europe!
Recently we took on a project with Dr. Casey Bergman from University of Manchester as the Principal Investigator, to package all
We will be happy to hear any comments regarding these efforts and
we hope that this will be a useful resource for all Galaxy users. Once
On Tue, Jan 3, 2012 at 11:36 AM, Nate Coraor <nate@bx.psu.edu> wrote: the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many pre-requisities are already included with Bio-Linux, we are already some way down this path. New packages that we create will appear in a Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy). the initial packaging is done, we hope to collaborate with Galaxy team in maintaining and improving this resource.
Best wishes, Tim, Soon and Mesude
Hi Mesude,
This is fantastic, thanks for letting us know, and please do post up if there is anything we can help with. Also, if you're not aware, Galaxy's cloud offering is built on CloudBioLinux, which itself is built on Bio-Linux.
--nate
This is very good news, I'm personally a big fan of avoiding as much as possible installing from source on production systems, as things can get easily out of hand when trying to keep everything updated.
Mesude, I recently joined Debian Med (http://www.debian.org/devel/debian-med/ and https://launchpad.net/~debian-med) which the exact same goal of getting as much tools as possible packaged for Debian/Ubuntu. I see Tim Booth is an active member in Debian Med and I was wondering if your group is planning to keep the development of these packages in the git/svn repositories of Debian Med. I wouldn't want to duplicate your efforts.
I like very much the use of PPAs while waiting for packages to be officially included in Debian and trickle down to Ubuntu, process that could be somehow slow at times. Just today I was able to upload Tophat's package being developed at Debian Med to the PPA, I'm pretty sure it needs more work, but you might be interested in taking a look.
Kind regards, Carlos
-- Tim Booth <tbooth@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
Dear All, First of all, we wish you all a happy new year! Sending this (see below) again in case it slipped in the rush before X-mas. Best wishes, Tim, Soon and Mesude -- Dr. Mesude Bicak <mbicak@ceh.ac.uk> Bioinformatician & Bio-Linux Developer NERC Biomolecular Analysis Facility (NBAF) <http://nbaf.nerc.ac.uk> NERC Environmental Bioinformatics Centre (NEBC) <http://nebc.nerc.ac.uk> Molecular Evolution and Bioinformatics Group Centre for Ecology and Hydrology <http://ceh.ac.uk> Maclean Building, Benson Lane Crowmarsh Gifford Wallingford, Oxfordshire OX10 8BB Office Tel: +44 1491 69 2705 ________________________________________ From: Bicak, Mesude Sent: 20 December 2011 18:09 To: galaxy-dev@lists.bx.psu.edu Cc: anton@bx.psu.edu; jeremy.goecks@emory.edu; clements@galaxyproject.org; Booth, Timothy G.; Gweon, Hyun S.; fiedawn@gmail.com; casey.bergman@manchester.ac.uk Subject: Galaxy Server on Bio-Linux Dear Galaxy Developers, We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research Institute based in Oxford. We develop and distribute Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu distribution that comes with 500+ bioinformatics packages. Within our research group we also provide bioinformatics analysis for NERC-funded researchers, and recently started looking into Galaxy as well. It didn't take us long to discover its power and we would like to enable Bio-Linux users to install, run and maintain the Galaxy server with minimal effort, also with the aim to spread the word on Galaxy in Europe! Recently we took on a project with Dr. Casey Bergman from University of Manchester as the Principal Investigator, to package all the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many pre-requisities are already included with Bio-Linux, we are already some way down this path. New packages that we create will appear in a Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy). We will be happy to hear any comments regarding these efforts and we hope that this will be a useful resource for all Galaxy users. Once the initial packaging is done, we hope to collaborate with Galaxy team in maintaining and improving this resource. Best wishes, Tim, Soon and Mesude -- Dr. Mesude Bicak <mbicak@ceh.ac.uk> Bioinformatician & Bio-Linux Developer NERC Biomolecular Analysis Facility (NBAF) <http://nbaf.nerc.ac.uk> NERC Environmental Bioinformatics Centre (NEBC) <http://nebc.nerc.ac.uk> Molecular Evolution and Bioinformatics Group Centre for Ecology and Hydrology <http://ceh.ac.uk> Maclean Building, Benson Lane Crowmarsh Gifford Wallingford, Oxfordshire OX10 8BB Office Tel: +44 1491 69 2705 -- 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.
participants (4)
-
Bicak, Mesude -
Carlos Borroto -
Nate Coraor -
Tim Booth