Galaxy Tool Shed packages for Biopython

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Galaxy Tool Shed packages for Biopython

Peter Cock
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

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Re: Galaxy Tool Shed packages for Biopython

Peter Cock
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock <[hidden email]> 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/1d118ab296e9e4d432a913a2ad8d13c680c32a90
https://github.com/biopython/galaxy_packages/blob/1d118ab296e9e4d432a913a2ad8d13c680c32a90/README.rst

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
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Re: Galaxy Tool Shed packages for Biopython

Peter Cock
In reply to this post by Peter Cock
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock <[hidden email]> 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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Re: Galaxy Tool Shed packages for Biopython

Björn Grüning-3
Thanks Peter!

+1 for including that into the Biopython release process

Cheers,
Bjoern

> On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock <[hidden email]> 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
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/

___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/