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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