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.c...@googlemail.com <mailto:p.j.a.c...@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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