Galaxy Tool Shed packages for Biopython
Hi all, I've send this to both the Galaxy and Biopython developers lists, and hope this will make sense to both groups. If you've not heard of Galaxy, start here: http://galaxyproject.org - while the easy to guess Biopython website is at http://biopython.org Brad Chapman and I are both Biopython core developers, and are also both on the "IUC" Galaxy Tool Shed committee because we've been quite involved in wrapping and writing tools for use on Galaxy. Fellow committee member Björn Grüning has done a lot of the hands on work defining package definitions for dependencies within the Galaxy Tool Shed ecosystem - including defining them for Biopython, NumPy, SciPy, MatPlotLib, etc. We're very grateful for his hard work - most of which is now available under the IUC group account: http://toolshed.g2.bx.psu.edu/view/iuc/ http://testtoolshed.g2.bx.psu.edu/view/iuc/ The Biopython packages, however, are under a dedicated "biopython" account on the Galaxy Tool Shed to which currently Bjoern, Brad and I have access to: http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/ This packaging work was initially tracked in Bjoern's own GitHub repository, https://github.com/bgruening/galaxytools/ We (me, Brad and Bjoern) agreed that a Biopython owned repository would be more sensible in the long term, so I have created this and ported Bjoern's commits to it: https://github.com/biopython/galaxy_packages Currently the "Galaxy packagers" team on GitHub which has read and write access to this new repository is just me, Brad and Bjoern. Regards, Peter
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
...
The Biopython packages, however, are under a dedicated "biopython" account on the Galaxy Tool Shed to which currently Bjoern, Brad and I have access to:
http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/
This packaging work was initially tracked in Bjoern's own GitHub repository, https://github.com/bgruening/galaxytools/
We (me, Brad and Bjoern) agreed that a Biopython owned repository would be more sensible in the long term, so I have created this and ported Bjoern's commits to it: https://github.com/biopython/galaxy_packages
Reviewing Bjoern's glimmer3 package I released I was missing the <requirement> tag information in that README, hopefully this is correct now? https://github.com/biopython/galaxy_packages/commit/1d118ab296e9e4d432a913a2... https://github.com/biopython/galaxy_packages/blob/1d118ab296e9e4d432a913a2ad... What I am unclear on is how version information needed in the <requirement> is determined - must it be a perfect match to the tool_dependencies.xml it points at? i.e. matplotlib 1.2 versus 1.2.1, and scipy 0.12 versus 0.12.0 What happens when that gets updated (since the example repository_dependencies.xml implicitly points at the latest version of the tool at upload time)? Thanks, Peter
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I've sent this to both the Galaxy and Biopython developers lists, and hope this will make sense to both groups. If you've not heard of Galaxy, start here: http://galaxyproject.org - while the easy to guess Biopython website is at http://biopython.org
Brad Chapman and I are both Biopython core developers, and are also both on the "IUC" Galaxy Tool Shed committee because we've been quite involved in wrapping and writing tools for use on Galaxy.
Fellow committee member Björn Grüning has done a lot of the hands on work defining package definitions for dependencies within the Galaxy Tool Shed ecosystem - including defining them for Biopython, NumPy, SciPy, MatPlotLib, etc. We're very grateful for his hard work - most of which is now available under the IUC group account:
http://toolshed.g2.bx.psu.edu/view/iuc/ http://testtoolshed.g2.bx.psu.edu/view/iuc/
The Biopython packages, however, are under a dedicated "biopython" account on the Galaxy Tool Shed to which currently Bjoern, Brad and I have access to:
http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/
This packaging work was initially tracked in Bjoern's own GitHub repository, https://github.com/bgruening/galaxytools/
We (me, Brad and Bjoern) agreed that a Biopython owned repository would be more sensible in the long term, so I have created this and ported Bjoern's commits to it: https://github.com/biopython/galaxy_packages
Currently the "Galaxy packagers" team on GitHub which has read and write access to this new repository is just me, Brad and Bjoern.
Regards,
Peter
Earlier today I belatedly setup Galaxy packages for Biopython 1.63, for both the main and test Galaxy ToolSheds: http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/ This could perhaps become part of the Biopython release process in future? Peter
Thanks Peter! +1 for including that into the Biopython release process Cheers, Bjoern
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I've sent this to both the Galaxy and Biopython developers lists, and hope this will make sense to both groups. If you've not heard of Galaxy, start here: http://galaxyproject.org - while the easy to guess Biopython website is at http://biopython.org
Brad Chapman and I are both Biopython core developers, and are also both on the "IUC" Galaxy Tool Shed committee because we've been quite involved in wrapping and writing tools for use on Galaxy.
Fellow committee member Björn Grüning has done a lot of the hands on work defining package definitions for dependencies within the Galaxy Tool Shed ecosystem - including defining them for Biopython, NumPy, SciPy, MatPlotLib, etc. We're very grateful for his hard work - most of which is now available under the IUC group account:
http://toolshed.g2.bx.psu.edu/view/iuc/ http://testtoolshed.g2.bx.psu.edu/view/iuc/
The Biopython packages, however, are under a dedicated "biopython" account on the Galaxy Tool Shed to which currently Bjoern, Brad and I have access to:
http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/
This packaging work was initially tracked in Bjoern's own GitHub repository, https://github.com/bgruening/galaxytools/
We (me, Brad and Bjoern) agreed that a Biopython owned repository would be more sensible in the long term, so I have created this and ported Bjoern's commits to it: https://github.com/biopython/galaxy_packages
Currently the "Galaxy packagers" team on GitHub which has read and write access to this new repository is just me, Brad and Bjoern.
Regards,
Peter Earlier today I belatedly setup Galaxy packages for Biopython 1.63, for both the main and test Galaxy ToolSheds:
http://toolshed.g2.bx.psu.edu/view/biopython/ http://testtoolshed.g2.bx.psu.edu/view/biopython/
This could perhaps become part of the Biopython release process in future?
Peter
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participants (2)
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Björn Grüning -
Peter Cock