I have a local instance of galaxy (release 18.05) and am trying to use a custom R script that uses the bioconductor package ShortRead.
I am developing tools in a context where I have been instructed to use conda to handle all dependencies, so am trying to find a solution in this manner.
When I run said tool, my output in the galaxy gui is:
Fatal error: Exit code 1 ()
Error: package ‘GenomeInfoDb’ could not be loaded
I have a macros.xml file with the following:
<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> <requirement type="package" version="1.36.0">bioconductor-shortread</requirement> </requirements> </xml> </macros>
My tool.xml file has this pertaining to the macros:
<macros> <import>macros.xml</import> </macros> <expand macro="requirements"/>
This method of macros.xml and tool.xml works for other dependencies, just not ShortRead. I also tried explicitly stating genomeinfodb and genomeinfodbdata as dependencies in the macros.xml, and received the same error. I have the following relevant to conda in my galaxy.yml:
conda_prefix: /path/galaxy/database/dependencies/_conda/bin/conda conda_debug: false conda_ensure_channels: 'iuc,bioconda,r,conda-forge,defaults' conda_auto_install: false conda_auto_init: true conda_copy_dependencies: true
Thanks for any help!