On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Feb 3, 2014, at 7:01 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Returning to the MIRA4 problem, I got a meaningful test failure which I fixed (I hadn't set an environment variable in the install script), but I now get only partial test output:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler ...
That's all fine, but where are the test results for mira_bait which I would expect to pass?
It looks lie the mira_bait tests results are being populated, but the tests are failing, not passing. This doesn't look like an issue with the Tool Shed's install and test framework.
Confirmed - the Tool Shed issue where only partial test output was shown is fixed (did you work out why the test output was missing?).
I was hoping to see a passing test, but I can now see a failing test (still something not quite right with my dependency installation script - I'll look at this next week hopefully).
Hi Greg, I added a little more debug information to the mirabait test, which confirms a problem in the tool_dependencies.xml file: Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/mirabait' Folder contained: env.sh i.e. $MIRA4 was set to $INSTALL_DIR which is the folder /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/ and (surprisingly) it only contains one file, env.sh Greg: Could you confirm that on the server? i.e. what does this give? $ ls -l /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/ ... Upon downloading mira_4.0_linux-gnu_x86_64_static.tar.bz2 and decompressing it, the tool shed should have changed into the main folder mira_4.0_linux-gnu_x86_64_static and then moved the contents of the bin folder into the $INSTALL_DIR, <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2</action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> i.e. Move files mira, mirabait, miraconvert and miramem into $INSTALL_DIR I am somewhat puzzled - other tools like the BLAST+ installers use a very similar setup and work fine (although there I used $PATH instead). Thanks, Peter