On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster <g...@bx.psu.edu> wrote: >> On Feb 3, 2014, at 7:01 PM, Peter Cock <p.j.a.c...@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/