On Fri, Sep 20, 2013 at 11:10 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Wed, Sep 18, 2013 at 11:47 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
I also tried running the command that returns error code 64 on the same system that runs the automated tests, and it downloaded the correct file for that operating system and architecture. So I'm not sure why it's failing when run through buildbot, but I'll look into it and get back to you.
I've added a trello card to track progress on this issue:
https://trello.com/c/9ERDMc7j/1079-toolshed-investigate-cause-of-shell-comma...
--Dave B.
Hi Dave,
Something seems to have changed again on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/4ae1bac976f3
Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion blast+ package 2.2.26+ Error /bin/sh: 2: [[: not found /bin/sh: 3: [[: not found /bin/sh: 4: [[: not found /bin/sh: 6: [[: not found /bin/sh: 7: [[: not found tar: option requires an argument -- 'f' Try `tar --help' or `tar --usage' for more information.
Is the test cluster really missing /bin/sh? Can you check that and post the full installation log please?
I really would like to push an update to ncbi_blast_plus to the main Tool Shed with an updated README file (using RST) and the new citation information - plus of course handling the binary dependency via the new package:
http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
Once this is done there is a backlog of updates I want to tackle following our productive BoF meeting at GCC2013: http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyBlast
Thanks,
Peter
A related bug for Greg (I think), despite this strange no /bin/sh error, this repository is not listed on the Test Tool Shed under "Latest revision: installation errors".
Regards,
Peter
Aside from the oddities reported via the Test Tool Shed testing, feedback for the package_blast_plus_2_2_26 dependency has been positive, so I have just updated the BLAST+ wrappers on the main Tool Shed to use it (v0.0.20): http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/70e7dcbf6573 Fingers crossed this works 'in the wild', and that the curious missing /bin/sh issue on the test machines can be solved. Regards, Peter