From cfb194f0a069e254007dd50d8e97a87309d5e52a Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 5 Nov 2013 13:46:06 -0600 Subject: [PATCH] Enhance megablast to utilize GALAXY_SLOTS configuration when available. --- tools/metag_tools/megablast_wrapper.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/tools/metag_tools/megablast_wrapper.py b/tools/metag_tools/megablast_wrapper.py index e7c0d286b1a..80b80ae797a 100644 --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -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