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BUSCO_DOWNLOAD_PATH environment variable not used #101
Description
Hi there,
From the README, the recommended command to run funannotate2 through Docker is:
# pull the latest image (~8 GB; databases are baked in)
docker pull nextgenusfs/funannotate2:latest
# or from GHCR
docker pull ghcr.io/nextgenusfs/funannotate2:latest
# quick sanity check
docker run --rm nextgenusfs/funannotate2:latest funannotate2 --version
docker run --rm nextgenusfs/funannotate2:latest funannotate2 install -s
# run against a local data directory, persisting the BUSCO cache across runs
mkdir -p $PWD/data $PWD/busco_cache
docker run --rm -it \
-v $PWD/data:/data \
-v $PWD/busco_cache:/opt/busco_cache \
-e BUSCO_DOWNLOAD_PATH=/opt/busco_cache \
nextgenusfs/funannotate2:latest \
funannotate2 predict -i /data/genome.fa -o /data/out --species "My species"
However, from my tests, funannotate2 seems not to use the /opt/busco_cache mounted volume. From looking at the code (https://github.com/search?q=repo%3Anextgenusfs%2Ffunannotate2+BUSCO_DOWNLOAD_PATH&type=code), it seems the env variable BUSCO_DOWNLOAD_PATH is actually never used. Instead, from fde0e10, it seems that what is used is FUNANNOTATE2_DB.
Activity
thegrebe commentedon Oct 20, 2026
Closed as pull request #102 has been merged