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Published 20 hours ago • verified publisher icon galaxyproject

[WIP] fixes for <parallelism> with containers

Open bernt-matthias opened this issue 5 years ago • 0 comments
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Some problems that I stumbled upon here: https://github.com/galaxyproject/tools-devteam/pull/555 when containerized testing is used:

  • [ ] GALAXYROOT/extract_dataset_parts.sh: .venv/bin/activate: line 157: syntax error: bad substitution
  • [ ] /tmp/tmpd3oovgq5/job_working_directory/000/2/task_10/tool_script.sh: line 22: /tmp/tmpd3oovgq5/job_working_directory/000/2/task_10/dataset_91ad311f-7f82-4fd0-9324-6652beb11bfe.dat: Read-only file system

Another bug already 'fixed'

  • [x] egrep in sam.merge
  • [ ] maybe use grep -E?

bernt-matthias avatar Jun 04 '20 10:06 bernt-matthias