Hello Galaxy,
I have been working on adding a tool to my personal instance but I am having an issue with the python interpretter
For some reason it is prepending a defined path to my python command:
python: can't open file '/home/galaxy/galaxy_shed_tools/galaxy-url-???.ca/repos/marcoalbuquerque/add_vaf_and_ccf/586667004174/add_vaf_and_ccf/add_vaf_and_ccf.py': [Errno 2] No such file or directory
Where I have the following command:
<command interpreter="python">
add_vaf_and_ccf.py -d $distance $maf $params $segs $outfile
</command>
This add_vaf_and_ccf.py is currently stored in the associated REPOSITORY_INSTALL_DIR path, but when i tack on the environment variable (i.e. \$REPOSITORY_INSTALL_DIR/add_vaf_and_ccf.py ...) it doesn't work properly. Unless of course I drop the interpreter (which causes other issues).
Please let me know if there is a work around this, or do I need to drop the interpreter. My code uses pybedtools and is having issues locating the bed functions (I'm assuming this was the issue, but could be wrong).
I can email the tool dependency and config files upon request.
Thanks so much!
Marco Albuquerque