On Mon, Feb 17, 2014 at 3:08 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster <g...@bx.psu.edu> wrote: >> Hi Peter, >> >> It looks like you made some changes to your tool dependency >> recipe since the last test run. > > Yeah, the mira de novo test was missing the test-data input files. > But I didn't touch mirabait or the install XML instructions. > >> Dave B and I followed the latest revision of your recipe and manually >> installed it using >> https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2 >> and it looked ok. > > If you mean you installed it via the Tool Shed, and it worked - that's good :) > > (Or did you mean manually by running wget, tar, etc, by hand?) > >> Let's see what the restults of tonight's test run is for this repository >> and if there are still problems after your latest changes we'll track >> them down. > > Sure - fingers crossed,
Hi Greg, Dave, RE: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Same as before, although now both the mirabait and mira de novo tests are attempted: Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait' Folder contained: env.sh Missing mira under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mira' Folder contained: env.sh My Python wrapper checks the $MIRA4 environment variable, which should be the $INSTALL_DIR location which should hold the MIRA binaries (mira, mirabait, etc). According to the Python wrapper, the $MIRA variable was set to: /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/ However, the Python wrapper reports this folder only contains one file, env.sh - which leads me to suspect a glitch in my tool_dependencies.xml and/or the installation framework. Regards, 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/
