I was able to get local blast within Artemis to work using NCBI's BLAST 2.2.21+
under MacOSX; I've only done this so far for blastp against uniprot, but
similar fixes should work for other databases, scripts and UNIX flavors. Thanks
to Torsten Seemann for his suggestions.
After installing Artemis fom the disk image, and downloading and installing the
latest NCBI BLAST+, I ended up needing to edit three files to get everything
working. Note that I chose a different location for blast
(/Users/plunkettg/blast) in order to have it more readily available ouside of
Artemis as well; I just put a copy of the edited legacy_blast.pl where the
Artemis scripts looked for blastall, etc.
(1) /Applications/Artemis.app/Contents/blast-data/setup_dbs.sh
changed
BLAST=../blast/formatdb
to
BLAST=../blast/makeblastdb
and
changed
$BLAST -i uniprot -o T -p T -t uniprot &
to
$BLAST -in uniprot -dbtype prot -parse_seqids -title uniprot &
(could do the same for uniprot_bacteria, etc.)
(2) /Applications/Artemis.app/Contents/blast/legacy_blast.pl
changed
use constant DEFAULT_PATH => "/usr/bin";
to
use constant DEFAULT_PATH => "/Users/plunkettg/blast/bin";
(3) /Applications/Artemis.app/Contents/artemis/etc/run_blastp
changed
EXEC=${EXEC-`which blastall 2>/dev/null`}
if [ ! -x "$EXEC" ]; then
EXEC=`find Artemis* -name blastall 2>/dev/null`
fi
to
EXEC=${EXEC-`which legacy_blast.pl 2>/dev/null`}
if [ ! -x "$EXEC" ]; then
EXEC=`find Artemis* -name legacy_blast.pl 2>/dev/null`
fi
and
changed
nice -19 $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
to
nice -19 $EXEC blastall -d $DATABASE -i $INPUT_FILE -p blastp \
(could do the same for other run_ scripts)
This might not be the most elegant way to acheive this, but it does work
Cheers,
Guy
Dr. Guy Plunkett III
Senior Scientist, DNASTAR
Senior Scientist, Laboratory of Genetics & Genome Center, UW-Madison
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