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?
One way to catch this kind of error would be if the nightly Tool Shed tests included attempting to install package repositories (e.g. the new "Tool dependency definition") explicitly.
(I think I've suggested this before - but it is worth reiterating)
Oh that would be so nice! +1 for me. And by the way, notifications about new orphan tool dependencies also do not happen. I think that would be very useful for a few developers that are waiting for numpy, blast+ and so on.
Logged on Trello, please subscribe and vote: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-pac... Peter