[artemis-users] blastp

[Peter Reeves]

Dear all,

having got artemis to run, I am now trying to get it to run a blast search.

I have blastall with blastp etc in usr/local/ together with sequence databases, and genbank and sequence files in my user area.

Am not sure where in the run_blastp script to put the paths for these files. My first attempts generate error messages.

I understand that I have to make changes to the following section of run_blastp

----
# expand any ~ or environment variables
EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh`


### change this function to suit your site:

run_one_prog () {
INPUT_FILE=$1
OUTPUT_FILE=$2
DATABASE=$3


### change these lines:
EXEC=wublastp

echo "about to start $EXEC with input from $INPUT_FILE and output to"
echo "$OUTPUT_FILE using database $DATABASE"
echo "command line: $EXEC $DATABASE $INPUT_FILE"

# add/change the flags to suit your site:
$EXEC $DATABASE $INPUT_FILE 2>&1 > $OUTPUT_FILE |
tee ${PROG}_errors.new 1>&2

#### end of changes
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can someone advise please

Peter Reeves
--
Peter Reeves
Phone 61-2-93512536

Head of Microbiology Discipline,
School of Molecular and Microbial Biosciences (G08)
The University of Sydney
NSW 2006, Australia

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