On Mon, Aug 12, 2013 at 2:04 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote:
On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening bjoern.gruening@gmail.com wrote:
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
Hi all,
I'm currently trying out installation of tools from the Tool Shed on a secondary Galaxy server (not our production server nor my development setup). This is running galaxy-dist, current latest stable I believe:
$ sudo -u galaxy hg heads changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user: Dannon Baker dannonbaker@me.com date: Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter
changeset: 10200:fd4113962c32 branch: stable parent: 10198:0a06df7da177 user: Dannon Baker dannonbaker@me.com date: Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter
I'm having some problems, e.g.
Tool shed repository 'package_numpy_1_7' tool dependencies
Name Version Type Status Error atlas 3.10.1 package Error Error installing tool dependency atlas version 3.10.1: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh' lapack 3.4.2 package Error Error installing tool dependency lapack version 3.4.2: [Errno 2] No such file or directory: u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh' numpy 1.7.1 package Error Error installing tool dependency numpy version 1.7.1: Unsupported action type 'template_command' in tool dependency definition.
Is this due to to galaxy-dist being too old for Tool Shed tools whose XML installation scripts use action template_command?
e.g. http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a
Yes.
Is there an easy fix where you could upload an older version of the installation script before you started using the new template_command action?
Sorry, I do not understand the question. To you mean if I could revert the changes and go back to old bash scripts for the time being?
Yes, that is what I meant.
In theory it should be possible. But the aim of my cheetah template patch was to make it easier to write such if else conditions. And create a save fallback to non-atlas users. The next stable release should be out that week, or?
I expect that in the meantime this bug will hit other people as well (and until the Tool Shed testing is improved I'm a little worried there could be other 'broken' packages) :(
If you had a working (minimal non-Altas non-lapack) numpy tool_dependencies.xml pre-dating the template_command action it would seem sensible to upload it now to fix the numpy package on the main Tool Shed.
I would have thought one of the old revisions from the numpy package on the Test Tool Shed would work?
Thanks,
Peter