sokrypton / sokrypton/ColabFold
Database download suggestion
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Description
Hey folks,
I suggest you get rid of the tars post-extraction. It will free up some (usually much needed) disk space, and I am unaware of any other use of the tars post extraction and index creation
if [ ! -f COLABDB_READY ]; then
downloadFile "https://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz" "colabfold_envdb_202108.tar.gz"
tar xzvf "colabfold_envdb_202108.tar.gz"
mmseqs tsv2exprofiledb "colabfold_envdb_202108" "colabfold_envdb_202108_db"
# TODO: split memory value for createindex?
mmseqs createindex "colabfold_envdb_202108_db" tmp2 --remove-tmp-files 1
# SUGGESTED ADDITION:
rm "colabfold_envdb_202108.tar.gz"
touch COLABDB_READY
fi
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
Locate the setup block containing COLABDB_READY, the colabfold_envdb_202108 archive download, extraction, and MMseqs database creation. Verify the archive is no longer needed after indexing, then run the relevant setup flow and confirm the database is ready and the temporary archive is absent.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics, databases
- Issue type
- Feature
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 55/100