If you are using Ubuntu LTS, you can use packages we are developing for Galaxy dependencies on Bio-linux: https://launchpad.net/~nebc/+archive/galaxy This list is currently incomplete, but steadily growing. Perhaps what you need is here already. Best regards, Casey Casey Bergman, Ph.D. Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road, M13 9PT Manchester, UK Tel: +44-(0)161-275-1713 Lab: +44-(0)161-275-5980 Fax: +44-(0)161-275-5082 skype: caseymbergman Email: casey.bergman@manchester.ac.uk Web: http://bergmanlab.smith.man.ac.uk/ Twitter: http://twitter.com/bergmanlab Begin forwarded message:

From: "Bicak, Mesude" <mbicak@ceh.ac.uk> Date: 20 December 2011 18:09:50 GMT To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Cc: "anton@bx.psu.edu" <anton@bx.psu.edu>, "jeremy.goecks@emory.edu" <jeremy.goecks@emory.edu>, "clements@galaxyproject.org" <clements@galaxyproject.org>, "Booth, Timothy G." <tbooth@ceh.ac.uk>, "Gweon, Hyun S." <hyugwe@ceh.ac.uk>, "fiedawn@gmail.com" <fiedawn@gmail.com>, "casey.bergman@manchester.ac.uk" <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.

On 2 Feb 2012, at 20:13, Jennifer Jackson wrote:

Hello,

These types of tools are not rewritten, but are instead wrapped so that they function within the Galaxy framework. Galaxy, dependent tools, and reference datasets and indexes are all installed separately.

For the basic overview, please see: http://getgalaxy.org

A list of Tool dependencies is included in this wiki: http://galaxyproject.org/Admin/Tools/Tool Dependencies

And all of the administrative details can be found linked from here: http://galaxyproject.org/Admin

Hopefully this helps to explain the process, but please let us know if you have more questions,

Best,

Jen Galaxy team

On 2/2/12 7:01 AM, bmoumen@jouy.inra.fr wrote:

...

Dear galaxy team thank you a lot for providing a complete solution for biologists to analyse their data, i have one question about galaxy : i see that there are a lot of tools for example for ngs, and i could not understand or find the tool in galaxy directories, is that means that all the tool are rewritten in python ? eg bowtie, samtools, fastx and ... Or the binaries are located in some folder that i can not see . thanks

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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___________________________________________________________ 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:

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