Hi Simon, Further to our discussion here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016310.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016316.html Simon wrote:
An example is the NCBI BLAST+ suite, which failed to build on my (EL6) system, because it couldn't run /usr/bin/touch. That's pretty dumb, and pretty simple to solve in isolation - it needs to be running /bin/touch instead.
This was an oddity in the NCBI compile scripts for BLAST 2.2.26+ which can be avoided via a symlink, editing their code, or more simply just downloading their provided binaries. I prefer the later because it is simpler, faster, and should better ensure reproducibility by eliminating things like different compilers and their settings. Unfortunately the new install process to do this from within the Tool Shed is glitching on the Tool Shed's nightly tests: 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.
Nevertheless, the simple binary install is working for me and Bjoern. Could you try the Test Tool Shed package and let us know if that works for you? Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus depends on this, http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 Or, try installing this directly (although it won't get used yet): http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 Given some confirmation then I think I will update the Main Tool Shed http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (which currently tries to compile BLAST) to instead depend on the new package which fetches the binaries. Thanks, Peter