I’m trying to get Galaxy 19.09 to load an LMOD module named FASTX-Toolkit/0.0.14-intel-2018b for the tool fasta_formatter.xml.
I’ve uncommented the lmod line in config/dependency_resolvers_conf.xml
I’ve also updated the fasta_formatter.xml tool to match the name of the LMOD module but the FASTX-Toolkit module is not getting loaded. Fails with ‘fasta_formatter: command not found’:
<requirements> <requirement type="package" version="0.0.14-intel-2018b">FASTX-Toolkit</requirement> </requirements>
the lmod path for lmodexec is in the variable LMOD_CMD and MODULEPATH is also set
I’ve also tried using the config/lmod_modules_mapping.yml approach. Is there some other configuration I am missing?