Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.py @ 5:d123b6e6a633 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author mvdbeek
date Thu, 11 Jun 2015 09:07:35 -0400
parents 316124e85b8d
children 5d82f9b15957
comparison
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4:0975f2267809 5:d123b6e6a633
143 # /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f 143 # /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f
144 # /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat 144 # /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat
145 # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam - 145 # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam -
146 # generates an "unsorted.bam.sorted.bam file", NOT an 146 # generates an "unsorted.bam.sorted.bam file", NOT an
147 # "unsorted.bam.sorted" file 147 # "unsorted.bam.sorted" file
148 second_command_line = "samtools sort %s %s" % ( 148 second_command_line = "/usr/bin/env samtools sort %s %s" % (
149 path_to_unsortedBam, path_to_sortedBam) 149 path_to_unsortedBam, path_to_sortedBam)
150 # fileno() method return the file descriptor number of tmp_stderr 150 # fileno() method return the file descriptor number of tmp_stderr
151 p = subprocess.Popen( 151 p = subprocess.Popen(
152 args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) 152 args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
153 returncode = p.wait() 153 returncode = p.wait()