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ifxupdate

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

Docker

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:

  1. A symbolic link "latest" is created that points to YYYYMM or YYYYMM-stable
  2. If the third most-recent directory is non-stable (YYYYMM), it is removed

Example

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

Example (Singularity)

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

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