Utility for downloading/creating quarterly FAS Informatics reference databases.
Currently supported:
- BLAST: nr nt uniref90
- formatted as version 5, requiring NCBI BLAST >= 2.8.0 to use.
- HMMER profile database: pfam
Bind mount the host directory to populate to /mnt in the container.
ifxupdate will create a subdirectory based on the current date of the form:
- YYYYMM-stable, if there does not exist a -stable directory with the same YYYY
- YYYYMM, otherwise (i.e., non-"stable")
Upon successful completion:
- A symbolic link "latest" is created that points to YYYYMM or YYYYMM-stable
- If the third most-recent directory is non-stable (YYYYMM), it is removed
e.g., if BLASTDB_ROOT and HMMERDB_ROOT are set to directories that will contain containing quarterly subdirectories of BLAST and HMMER profile databases, respectively:
docker run --rm ifxupdate -v ${BLASTDB_ROOT}:/mnt nt nr uniref90
docker run --rm ifxupdate -v ${HMMERDB_ROOT}:/mnt pfam
singularity run --no-home --contain --cleanenv --pwd /mnt --bind ${BLASTDB_ROOT}:/mnt \
ifxdbupdate.simg nt nr uniref90
singularity run --no-home --contain --cleanenv --pwd /mnt --bind ${HMMERDB_ROOT}:/mnt \
ifxdbupdate.simg pfam