Question: Error: package "GenomeInfoDb" could not be loaded
0
gravatar for hortowe
10 days ago by
hortowe10
hortowe10 wrote:

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
Execution halted

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!

software error conda galaxy • 39 views
ADD COMMENTlink modified 6 days ago • written 10 days ago by hortowe10
0
gravatar for hortowe
6 days ago by
hortowe10
hortowe10 wrote:

Not exactly a solution, but I was able to fix this by turning off conda_copy_dependencies. I initially had switched that to true so that I could install MiXCR while running a particular tool.

I had the following behavior:

  • conda_copy_dependencies: false
    • Run script that depends on ShortRead - success
    • Run script that depends on mixcr - failure
  • conda_copy_dependencies: true
    • Run script that depends on mixcr - success
    • Re-run previously successful script that depends on ShortRead - failure

I also noticed that once conda_copy_dependencies: true was turned on, my jobs were taking a long time to run and a large amount of conda installation and uninstallation was going on in my output log, which seemed similar to what is described here, although that seems to be an issue with conda_auto_install.

So my solution:

  • Delete all of my pre-existing conda environments in `.../database/dependencies/_conda/envs
  • conda_copy_dependencies: false
  • Create MiXCR environment following the second option "Manual Install" here

After this, I was able to run both scripts.

ADD COMMENTlink modified 6 days ago • written 6 days ago by hortowe10
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