KmerFinder database FTP no longer available - tool renamed to SpeciesFinder
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Description
Description of the bug
KmerFinder has been renamed to SpeciesFinder and the database download infrastructure has changed. This might affect the current database download functionality (ftp site is not accesisble anymore).
In addition:
Tool renamed: KmerFinder → SpeciesFinder
- Old repo (archived): https://bitbucket.org/genomicepidemiology/kmerfinder
- New repo: https://bitbucket.org/genomicepidemiology/speciesfinder
Database download broken: The previous FTP endpoint for versioned KmerFinder databases is no longer available
Current database location: Only provides latest unversioned tarball:
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the current database download configuration and entry point for KmerFinder in the bacass workflow, then compare it with the SpeciesFinder naming and the current speciesfinder_db.tar.gz location described here. Update the broken download references and verify that the database download workflow completes using the available unversioned archive.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, databases
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 65/100