[galaxy-commits] commit/galaxy-central: 5 new changesets

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b65e618f2e8/ Changeset: 8b65e618f2e8 User: jmchilton Date: 2013-11-05 20:16:00 Summary: Bug fix for tool functional tests with repeat elements. Affected #: 1 file diff -r 1cf293a66f0f3b9677e6f777898a89c2ce0e8db6 -r 8b65e618f2e875ece55ac323222abf57bd2744e6 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1320,9 +1320,12 @@ self.visit_url( "%s/tool_runner/index?tool_id=%s" % (self.url, tool_id) ) if repeat_name is not None: repeat_button = '%s_add' % repeat_name + # Must click somewhere in tool_form, to disambiguate what form + # is being targetted. + tc.browser.clicked( tc.browser.get_form( 'tool_form' ), None ) # Submit the "repeat" form button to add an input) tc.submit( repeat_button ) - print "button '%s' clicked" % repeat_button + #print "button '%s' clicked" % repeat_button tc.find( 'runtool_btn' ) self.submit_form( **kwd ) https://bitbucket.org/galaxy/galaxy-central/commits/de332b3e02d3/ Changeset: de332b3e02d3 User: jmchilton Date: 2013-11-05 20:46:06 Summary: Enhance GATK tools to utilize GALAXY_SLOTS configuration when available. Affected #: 6 files diff -r 8b65e618f2e875ece55ac323222abf57bd2744e6 -r de332b3e02d31e60b706671d4c44e12b1d6f3b09 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -17,7 +17,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "CountCovariates" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": diff -r 8b65e618f2e875ece55ac323222abf57bd2744e6 -r de332b3e02d31e60b706671d4c44e12b1d6f3b09 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -19,7 +19,7 @@ -T "RealignerTargetCreator" -o "${output_interval}" -et "NO_ET" ##ET no phone home - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" diff -r 8b65e618f2e875ece55ac323222abf57bd2744e6 -r de332b3e02d31e60b706671d4c44e12b1d6f3b09 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -19,7 +19,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} --out "${output_vcf}" --metrics_file "${output_metrics}" -et "NO_ET" ##ET no phone home diff -r 8b65e618f2e875ece55ac323222abf57bd2744e6 -r de332b3e02d31e60b706671d4c44e12b1d6f3b09 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -17,7 +17,7 @@ -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantEval" --out "${output_report}" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": diff -r 8b65e618f2e875ece55ac323222abf57bd2744e6 -r de332b3e02d31e60b706671d4c44e12b1d6f3b09 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -15,7 +15,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantRecalibrator" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": diff -r 8b65e618f2e875ece55ac323222abf57bd2744e6 -r de332b3e02d31e60b706671d4c44e12b1d6f3b09 tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -14,7 +14,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "SelectVariants" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home -o "${output_vcf}" https://bitbucket.org/galaxy/galaxy-central/commits/1e63531be31a/ Changeset: 1e63531be31a User: jmchilton Date: 2013-11-05 20:46:06 Summary: Enhance megablast to utilize GALAXY_SLOTS configuration when available. Affected #: 1 file diff -r de332b3e02d31e60b706671d4c44e12b1d6f3b09 -r 1e63531be31a4b3ac8eac83242f2a6ca92ccaa91 tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -59,9 +59,13 @@ 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 https://bitbucket.org/galaxy/galaxy-central/commits/99d8158df290/ Changeset: 99d8158df290 User: jmchilton Date: 2013-11-05 20:46:06 Summary: Enhance tophats to utilize GALAXY_SLOTS configuration when available. Affected #: 3 files diff -r 1e63531be31a4b3ac8eac83242f2a6ca92ccaa91 -r 99d8158df2906fc3e431533db8fc4b35e296c89b tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -28,7 +28,7 @@ tophat2 ## Change this to accommodate the number of threads you have available. - --num-threads 4 + --num-threads \${GALAXY_SLOTS:-4} ## Set params. #if $params.settingsType == "full": diff -r 1e63531be31a4b3ac8eac83242f2a6ca92ccaa91 -r 99d8158df2906fc3e431533db8fc4b35e296c89b tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -6,7 +6,7 @@ <command interpreter="python"> tophat_wrapper.py ## Change this to accommodate the number of threads you have available. - --num-threads="4" + --num-threads="\${GALAXY_SLOTS:-4}" ## base- or color-space --color-space diff -r 1e63531be31a4b3ac8eac83242f2a6ca92ccaa91 -r 99d8158df2906fc3e431533db8fc4b35e296c89b tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -10,8 +10,7 @@ <command interpreter="python"> tophat_wrapper.py ## Change this to accommodate the number of threads you have available. - --num-threads="4" - + --num-threads="\${GALAXY_SLOTS:-4}" ## Provide outputs. --junctions-output=$junctions --hits-output=$accepted_hits https://bitbucket.org/galaxy/galaxy-central/commits/9493825685ee/ Changeset: 9493825685ee User: jmchilton Date: 2013-11-05 20:46:06 Summary: Enhance bfast to utilize GALAXY_SLOTS configuration when available. Affected #: 1 file diff -r 99d8158df2906fc3e431533db8fc4b35e296c89b -r 9493825685ee557c4a33b37614b22c4c21463219 tools/sr_mapping/bfast_wrapper.xml --- a/tools/sr_mapping/bfast_wrapper.xml +++ b/tools/sr_mapping/bfast_wrapper.xml @@ -1,7 +1,7 @@ <tool id="bfast_wrapper" name="Map with BFAST" version="0.1.3"><description></description><command interpreter="python">bfast_wrapper.py - --numThreads="4" ##HACK: hardcode numThreads for now, should come from a location file + --numThreads="\${GALAXY_SLOTS:-4}" --fastq="$input1" #if $input1.extension.startswith( "fastqcs" ): ##if extention starts with fastqcs, then we have a color space file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.