On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
<bjoern.gruen...@gmail.com> wrote:
> On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
>> Maybe I should retitle this thread...
>>
>> On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock <p.j.a.c...@googlemail.com> 
>> wrote:
>> >
>> > Thank you - installing the NumPy package now works for me,
>> > http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
>> >
>> > I'm moving on to something odd with matplotlib instead...
>> >
>> > Peter
>>
>> There are currently two revisions to the main Tool Shed
>> package for numpy,
>> http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
>>
>> Rev 0: c75482be1d3a - needs not-yet-released features
>> Rev 1: 74c21f9bdc39 - simplified
>>
>> I'm trying to install a package dependent on this via
>> matplotlib - but installing the matplotlib package fails:
>> http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2
>>
>> This is something odd, why does it think it needs to install
>> the rev 0 c75482be1d3a version of package_numpy_1_7?
>> See screenshot, except here:
>>
>> Repository dependencies - installation of these additional
>> repositories is required
>> Name  Revision        Owner   Installation status
>> package_freetype_2_4  8761091302c4    iuc     Installed
>> package_numpy_1_7     74c21f9bdc39    iuc     Installed
>> package_numpy_1_7     c75482be1d3a    iuc     Uninstalled
>>
>> Yes, the matplotlib tool_dependencies.xml does list the
>> original revision:
>>
>>     <package name="numpy" version="1.7.1">
>>        <repository changeset_revision="c75482be1d3a"
>> name="package_numpy_1_7" owner="iuc"
>> prior_installation_required="True"
>> toolshed="http://toolshed.g2.bx.psu.edu"; />
>>     </package>
>>     <package name="freetype" version="2.4.11">
>>         <repository changeset_revision="8761091302c4"
>> name="package_freetype_2_4" owner="iuc"
>> prior_installation_required="True"
>> toolshed="http://toolshed.g2.bx.psu.edu"; />
>>     </package>
>>
>> But I thought as a "Tool dependency definition" only the
>> tip revision is ever used?
>
> That is also what I understood, regardless of the revision there is only
> one install able revision. But I guess the TS is generating the path to
> numpy from the <package> tag and that points to an old non existing
> version.

Hmm. Something for Greg to look at then.

>> After attempting to install this, the status is "Installed, missing
>> repository dependencies" and this oddity about wanting two
>> revisions of NumPy persists.
>>
>> The actual failure appears to be in compiling matplotlib itself...
>> I don't think it is finding the NumPy installation.
>>
>> Is it possible to view the INSTALLATION.log from within the
>> Galaxy Admin web interface?
>
> Yes you should see all installed files/folder and the INSTALLATION.log
> in your web browser.

Can you give me a little more information on how to see
this from within Galaxy?

1. Open my Galaxy instance and log in,
2. Click on "Admin" from top menu
3. Click on "Manage installed tool shed repositories" on left
4. Select repository of interest

At this point the repository drop down menus I see are
"Get updates" and "Delete or inactivate". I must be looking
in the wrong place?

>
> I can reproduce it here and it fails because of numpy.

OK, that's good - it sounds like the rival revision problem
is what is going wrong.

>
> One fix to get it working is to upload again biopython.

Good plan - as discussed here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016001.html

Thank you,

Peter
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