2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8910b01b8add/ changeset: 8910b01b8add branch: next-stable user: jgoecks date: 2013-03-21 13:50:38 summary: Update Cuffdiff wrapper to use working directory rather than a temporary directory. affected #: 1 file diff -r 765739078002bc1ea5b1384a605b810e9a0bc640 -r 8910b01b8addcc3967b46206be1d0518629dbdf9 tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -118,16 +118,13 @@ raise Exception except: sys.stdout.write( 'Could not determine Cuffdiff version\n' ) - - # Make temp directory for output. - tmp_output_dir = tempfile.mkdtemp() # If doing bias correction, set/link to sequence file. if options.do_bias_correction: if options.ref_file != 'None': # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. - seq_path = os.path.join( tmp_output_dir, "ref.fa" ) + seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. @@ -189,9 +186,9 @@ # Run command. try: - tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_name = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_name, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stderr=tmp_stderr.fileno() ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() tmp_stderr.close() @@ -213,31 +210,26 @@ raise Exception, stderr # check that there are results in the output file - if len( open( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), 'rb' ).read().strip() ) == 0: + if len( open( "isoforms.fpkm_tracking", 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: stop_err( 'Error running cuffdiff. ' + str( e ) ) - # Copy output files from tmp directory to specified files. + # Copy output files to specified files. try: - try: - shutil.copyfile( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), options.isoforms_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) - except Exception, e: - stop_err( 'Error in cuffdiff:\n' + str( e ) ) - finally: - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) + shutil.copyfile( "isoforms.fpkm_tracking", options.isoforms_fpkm_tracking_output ) + shutil.copyfile( "genes.fpkm_tracking", options.genes_fpkm_tracking_output ) + shutil.copyfile( "cds.fpkm_tracking", options.cds_fpkm_tracking_output ) + shutil.copyfile( "tss_groups.fpkm_tracking", options.tss_groups_fpkm_tracking_output ) + shutil.copyfile( "isoform_exp.diff", options.isoforms_exp_output ) + shutil.copyfile( "gene_exp.diff", options.genes_exp_output ) + shutil.copyfile( "tss_group_exp.diff", options.tss_groups_exp_output ) + shutil.copyfile( "splicing.diff", options.splicing_diff_output ) + shutil.copyfile( "cds.diff", options.cds_diff_output ) + shutil.copyfile( "cds_exp.diff", options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( "promoters.diff", options.promoters_diff_output ) + except Exception, e: + stop_err( 'Error in cuffdiff:\n' + str( e ) ) if __name__=="__main__": __main__() https://bitbucket.org/galaxy/galaxy-central/commits/2a19abf0f450/ changeset: 2a19abf0f450 user: jgoecks date: 2013-03-21 13:51:10 summary: Merge in next-stable affected #: 1 file diff -r 353a42c6aa216db1603d565ec7565d1cae68c050 -r 2a19abf0f450adbae1cc119abe3e50edbf05a18d tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -118,16 +118,13 @@ raise Exception except: sys.stdout.write( 'Could not determine Cuffdiff version\n' ) - - # Make temp directory for output. - tmp_output_dir = tempfile.mkdtemp() # If doing bias correction, set/link to sequence file. if options.do_bias_correction: if options.ref_file != 'None': # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. - seq_path = os.path.join( tmp_output_dir, "ref.fa" ) + seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. @@ -189,9 +186,9 @@ # Run command. try: - tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_name = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_name, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stderr=tmp_stderr.fileno() ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() tmp_stderr.close() @@ -213,31 +210,26 @@ raise Exception, stderr # check that there are results in the output file - if len( open( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), 'rb' ).read().strip() ) == 0: + if len( open( "isoforms.fpkm_tracking", 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: stop_err( 'Error running cuffdiff. ' + str( e ) ) - # Copy output files from tmp directory to specified files. + # Copy output files to specified files. try: - try: - shutil.copyfile( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), options.isoforms_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) - except Exception, e: - stop_err( 'Error in cuffdiff:\n' + str( e ) ) - finally: - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) + shutil.copyfile( "isoforms.fpkm_tracking", options.isoforms_fpkm_tracking_output ) + shutil.copyfile( "genes.fpkm_tracking", options.genes_fpkm_tracking_output ) + shutil.copyfile( "cds.fpkm_tracking", options.cds_fpkm_tracking_output ) + shutil.copyfile( "tss_groups.fpkm_tracking", options.tss_groups_fpkm_tracking_output ) + shutil.copyfile( "isoform_exp.diff", options.isoforms_exp_output ) + shutil.copyfile( "gene_exp.diff", options.genes_exp_output ) + shutil.copyfile( "tss_group_exp.diff", options.tss_groups_exp_output ) + shutil.copyfile( "splicing.diff", options.splicing_diff_output ) + shutil.copyfile( "cds.diff", options.cds_diff_output ) + shutil.copyfile( "cds_exp.diff", options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( "promoters.diff", options.promoters_diff_output ) + except Exception, e: + stop_err( 'Error in cuffdiff:\n' + str( e ) ) if __name__=="__main__": __main__() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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