Question: Blastn Q.
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gravatar for Todd Yilk
7.2 years ago by
Todd Yilk50
Todd Yilk50 wrote:
Hello all, I'm using the blastn tool and Galaxy is generating this command (pasting from the log file): command is: perl /opt/galaxy/dev/galaxy_dist_dev_umma/tools/blast/psub -l galaxy_normal.c --fasta /opt/galaxy/dev/galaxy_dist_dev_umma/databa se/files/001/dataset_1377.dat --cat /opt/galaxy/dev/galaxy_dist_dev_um ma/database/files/001/dataset_1378.dat blastn -query "/opt/galaxy/dev/ galaxy_dist_dev_umma/database/files/001/dataset_1377.dat" -db "/house/blast_db/ncbi/nt/2011-01-11/nt" -task blastn -evalue 0.001 -out /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1 378.dat -outfmt "6" It's failing in Galaxy and I get a "script psub: No such file" kind of error running it at the command line ... I'm assuming psub here isn't the Unix command. According to find, my Galaxy installation doesn't have a galaxy_normal.c file either. Is there something I didn't install? Thanks, - Todd Yilk Software Developer Los Alamos National Laboratory
galaxy • 904 views
ADD COMMENTlink modified 7.2 years ago by Kanwei Li270 • written 7.2 years ago by Todd Yilk50
0
gravatar for Kanwei Li
7.2 years ago by
Kanwei Li270
Kanwei Li270 wrote:
Hi Todd, Are you using the blastn wrapper from the galaxy-central repository? Thanks, K
ADD COMMENTlink written 7.2 years ago by Kanwei Li270
And sure enough I'm not. Thanks for the reply.
ADD REPLYlink written 7.2 years ago by Todd Yilk50
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