local galaxy not finding some tools installed from toolshed

Question

[michael.law26]

I have installed Galaxy locally and have some tools running with no issue (Bowtie 2). However, not all of the tools are working as seamlessly. For example, BWA crashes with the following message:

$PATH

job_working_directory/000/15/galaxy_15.sh: line 20: bwa: command not found. 

One major problem is that when the tools are installed, they are not going to the "job_working_directory". I have looked, and the installation instructions for the tools do not specify how to change the galaxy.ini file to change the download location.

I don't think this could be the solution to the problem(s), since all tools have been downloaded to the same file path. I am open to any suggestions.

Thanks!

Mike

Answer 1

[Devon Ryan]

You probably meant to post this on the Galaxy biostar, rather than here.

The simplest fix is probably to remove and reinstall this tool from the toolshed. For where the tool is actually installed, it's probably under galaxy-central/tool_deps/bwa/some_version/.... The actual $PATH that the job runner gets is modified from what you'll get when logged into the server via ssh.