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Enhance megablast to utilize GALAXY_SLOTS configuration when available.

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This commit is contained in:
John Chilton
2013-11-05 13:46:06 -06:00
parent b097a37d25
commit cfb194f0a0
1 changed files with 6 additions and 2 deletions
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tools/metag_tools/megablast_wrapper.py
+6 -2
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@@ -59,9 +59,13 @@ def __main__():
if not os.path.exists( os.path.split( options.db_build )[0] ):
stop_err( 'Cannot locate the target database directory. Please check your location file.' )
try:
threads = int( os.environ['GALAXY_SLOTS'])
except Exception:
threads = 8
# arguments for megablast
megablast_command = "blastn -task megablast -db %s -query %s -out %s -outfmt '6 qseqid sgi slen ppos length mismatch gaps qstart qend sstart send evalue bitscore' -num_threads 8 -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \
% ( options.db_build, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query )
megablast_command = "blastn -task megablast -db %s -query %s -out %s -outfmt '6 qseqid sgi slen ppos length mismatch gaps qstart qend sstart send evalue bitscore' -num_threads %d -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \
% ( options.db_build, query_filename, mega_temp_output, threads, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query )
print megablast_command