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go-blast

A docker image for running NCBI BLAST+, with a local blast database - designed for querying the Gene Ontology databases.

Running

The Docker image built by the Dockerfile is designed to be used by docker-pipeline.

blast+ is installed via apt-get. The image's default command, go-blast.sh is built to replace run_BLAST.py from YoderLab/MMAP.

Environment Variables

Variable Description Type Required? Default
CONT_INPUT_ORFS_FILE File containing sequence ORFs to query Input Yes
CONT_INPUT_BLAST_DB The path to the blastdb to use Input Yes
CONT_OUTPUT_BLAST_RESULTS Results file, in BLAST CSV format with subject titles (outfmt 10 std stitle) Output Yes
CONT_BLAST_EVALUE BLAST evalue Parameter No 1e-15
CONT_BLAST_SEG BLAST seg Parameter No yes

Notes

  1. The CONT_INPUT_BLAST_DB can be generated by makeblastdb-go.
  2. The CSV format is used in the output for consumption by extract-go-terms.
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dukegcb
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