Run blast+ or blastall in parallel on an LSF compute farm.
Python3 module to run blast+ or blastall in parallel on an LSF compute farm.
Farm_blast has the following dependencies:
- blastall
Details for installing Farm_blast are provided below. If you encounter an issue when installing Farm_blast please contact your local system administrator. If you encounter a bug please log it here or email us at path-help@sanger.ac.uk.
pip3 install farm_blast
The test can be run from the top level directory:
python3 setup.py test
Compare a query and a reference using blast+ blastn:
farm_blast reference.fasta query.fasta
Compare a query and a reference using blastall blastn:
farm_blast --blastall reference.fasta query.fasta
Run blast+ megablast:
farm_blast --blast_type megablast reference.fasta query.fasta
Run blastall tblastx:
farm_blast --blast_type tblastx --blastall reference.fasta query.fasta
Set the e-value and word length and do not filter the query sequence:
farm_blast --no_filter -e 0.1 -W 30 reference.fasta query.fasta
To get all the options, use --help:
farm_blast --help
Farm_blast is free software, licensed under GPLv3.
Please report any issues to the issues page