Hello Nate,
> On May 14, 2013, at 10:58 AM, John Chilton wrote:
>
> > Hey Nate,
> >
> > On Tue, May 14, 2013 at 8:40 AM, Nate Coraor wrote:
> >> Hi John,
> >>
> >> A few of us in the lab here at Penn State actually discussed automatic
> >> creation of virtualenvs for dependency installations
Done.
On the topic of the freeze, if Dannon's change requiring all metadata
to be "set externally" is going to be included I would suggest someone
looking at build_command_line in runners/__init__.py.
https://bitbucket.org/galaxy/galaxy-central/src/237209336f0337ea9f47df39548df3c11900f182/lib/gal
John,
Could you create a pull request with your changes from the branch in github?
I'll accept them and then commit my additions and changes. Today is the
"freeze" so I'd like to get this in to the next release.
Thanks,
---nate
On May 17, 2013, at 11:21 AM, John Chilton wrote:
> Hey All,
>
Hey All,
There was a long conversation about this topic in IRC yesterday (among
people who don't actually use the tool shed all that frequently), I
have posted it to the new unofficial Galaxy Google+ group if anyone
would like to read and chime in.
https://plus.google.com/111860405027053012444/po
Hey Nate,
On Tue, May 14, 2013 at 8:40 AM, Nate Coraor wrote:
> Hi John,
>
> A few of us in the lab here at Penn State actually discussed automatic
> creation of virtualenvs for dependency installations a couple weeks ago.
> This was in the context of Bjoern's request for supporting compile-ti
Greg created the following card, and I'm working on a few changes to your
commit:
https://trello.com/card/toolshed-consider-enhancing-tool-dependency-definition-framework-per-john-chilton-s-pull-request/506338ce32ae458f6d15e4b3/848
Thanks,
--nate
On May 14, 2013, at 1:45 PM, Nate Coraor wrote:
On May 14, 2013, at 10:58 AM, John Chilton wrote:
> Hey Nate,
>
> On Tue, May 14, 2013 at 8:40 AM, Nate Coraor wrote:
>> Hi John,
>>
>> A few of us in the lab here at Penn State actually discussed automatic
>> creation of virtualenvs for dependency installations a couple weeks ago.
>> This w
Hi John,
A few of us in the lab here at Penn State actually discussed automatic creation
of virtualenvs for dependency installations a couple weeks ago. This was in
the context of Bjoern's request for supporting compile-time dependencies. I
think it's a great idea, but there's a limitation th
The proliferation of individual python package install definitions has
continued and it has spread to some MSI managed tools. I worry about
the tedium I will have to endure in the future if that becomes an
established best practice :) so I have implemented the python version
of what I had described
On Tue, Apr 16, 2013 at 2:46 PM, John Chilton wrote:
> Stepping back a little, is the right way to address Python
> dependencies?
Looks like I missed this thread, hence:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014169.html
> I was a big advocate for inter-repository dependencies,
Stepping back a little, is the right way to address Python
dependencies? I was a big advocate for inter-repository dependencies,
but I think taking it to the level of individual python packages might
be going too far - my thought was they were needed for big 100Mb
programs and stuff like that. At t
Hi Greg.
> >
> >> If numpy is not required for compiling matplotlib components (i.e.,
> >> matplotlib components just use numpy after installation),
> >> then you should be able to make this work using a complex repository
> >> dependency for numpy in your tool_dependencies.xml definition for
Hi Björn,
On Apr 15, 2013, at 6:31 PM, Björn Grüning wrote:
> Hi Greg,
>
>> If numpy is not required for compiling matplotlib components (i.e.,
>> matplotlib components just use numpy after installation),
>> then you should be able to make this work using a complex repository
>> dependency fo
Hi Greg,
> If numpy is not required for compiling matplotlib components (i.e.,
> matplotlib components just use numpy after installation),
> then you should be able to make this work using a complex repository
> dependency for numpy in your tool_dependencies.xml definition for matplotlib.
>
Hi,
is there a general rule to handle dependencies inside of
tool_dependencies.xml?
Lets assume I write a matplotlib orphan tool_dependencies.xml file.
matplotlib depends on numpy. Numpy has already a orphan definition.
Is there a way to include numpy as dependency inside the
matplotlib-definit
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