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,
Folder contained: env.sh

Missing mira under $MIRA4,
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:


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.


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