Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. Thanks! Bjoern
Peter, Björn,
The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved?
--Dave B.
On 8/12/13 11:36:00.000, Bjoern Gruening wrote:
On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening <bjoern.gruening@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.cock@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
5. Click, "Manage tool dependencies" 6. Choose one of the dependencies
There should be a tree like structure to navigate to your INSTALLATION.log file besides your env.sh file.
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
Done.
Thank you,
Peter
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