I am trying to integrate my own tool into galaxy on a remote server (LSF). I have made myself admin on the instance and work from there. This pipeline runs Trimmomatic, Tophat, Cufflinks, Cufflinks Annotation (and many more).
I started out small and ran Trimmomatic alone and it failed with a:
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory.
Galaxy is able to write the run config file and execute the wrapper script but it won't run Trimmomatic (same is the case with Tophat).
My understanding is that galaxy is able to write all the output in the directory I ask it to (so no permission issues here) but since the tools that I need to leverage are not in galaxy's path it won't execute them (Note: all the tools that I use are included in my pipeline (since it's Perl so: use <tool name>;) and hence I face no issues in running it through the server).
I don't know what the issue here is exactly if it's not the above mentioned hence any inputs or advice from anyone will be highly appreciated.
Also, could someone point me to documentation which helps configure galaxy on LSF? I have tried using the link below:
But the /galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so that needs to be exported isn't found in the galaxy directory so I am not sure if I am looking at the most current documentation for it.