The two options I normally use for that are the "Repository dependency definitions" and "Tool dependency definitions" links under the "Valid Galaxy Utilities" heading in the left panel, which provide an overview of all dependencies of the relevant type. --Dave B. On Mon 21 Apr 2014 09:39:51 AM EDT, Peter Cock wrote:
Thanks Dave,
On a slight tangent, is there a way in the ToolShed to see what other repositories use a given repository as a dependency?
e.g. From http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 it there any way to see what uses samtools 0.1.19?
Cheers,
Peter
On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation.
--Dave B.
On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote:
Hi all,
This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration?
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19
Regards,
Peter
On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> wrote:
Hi all,
I'm working on a new wrapper for "samtools depad" (which I have been using with MIRA v4 output), now on the Test ToolShed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
The unit tests work for me locally and via TravisCI.
The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency ("status Error") event though the samtools package is listed as a successful installation. Odd...
Any thoughts?
Thanks,
Peter
--
Automated tool test results
Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3
Installation errors Tool dependencies Type Name Version samtools package 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error.
Successful installations Repository dependencies/- installation of these additional repositories is required/
Tool shed Name Owner Changeset revision testtoolshed.g2.bx.psu.edu <http://testtoolshed.g2.bx.psu.edu> package_samtools_0_1_19 iuc 36aa94676939
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