I manage a NGS core lab and also teach a grad level intro to Bioinformatics course. We used to have a private instance of Galaxy on our servers but we had all sorts of permission issues. I recently was awarded an Xsede allocation and I have launched a pre-configured instance of Galaxy on Jetstream. Now I thought my issues with getting tools to work would be over since this pre-configured Galaxy has Conda, well I was wrong. Some of the tools that are pre-loaded don't even work. Specifically, I am trying to get Trimmomatic or Cutadapt to work but I get this error:
ERROR: A required extension module could not be imported because it is incompatible with your system. A quick fix is to recompile the extension modules with the following command:
/opt/galaxy/galaxy-app/database/jobs/000/14/conda-env/bin/python setup.py build_ext -i
See the documentation for alternative ways of installing the program.
The original error message follows.
Can anyone help? I tried to recomplile as suggested but there is no file called setup.py in the specified directory.