galaxyproject / galaxyproject/usegalaxy-tools
Quast configuration problem at ORG
- Dominant language
- Shell
- Stars
- 22
- Forks
- 70
- Avg merge
- 1d 3h
- Merged PRs (30d)
- 25
Description
http://toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 -- errors
`OSError: [Errno 30] Read-only file system: '/usr/local/lib/python3.9/site-packages/quast_libs/silva'`
But http://toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0 is Ok.
Same run, test data, all defaults
Test history https://usegalaxy.org/u/jen-galaxyproject/h/test-quast
Contributor guide
No contributing guide indexed for this repository
Research direction
Compare the Galaxy tool definitions for quast 5.2.0+galaxy0 and 5.2.0+galaxy1, then use the linked test history to reproduce the failure with the same test data and defaults. Investigate why galaxy1 writes to the read-only /usr/local/lib/python3.9/site-packages/quast_libs/silva path; done means the newer tool runs without the OSError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100