4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9591da01c73a/ Changeset: 9591da01c73a User: nsoranzo Date: 2013-11-16 00:52:36 Summary: Enhance trinity to utilize GALAXY_SLOTS configuration when available. Affected #: 1 file diff -r 69f348f4b3c7fac9c406b1666309f82810566802 -r 9591da01c73a5af50b87aba15ada6c22e70a94a7 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -36,7 +36,7 @@ --JM 10G ## CPU and butterfly options. - --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 + --CPU \${GALAXY_SLOTS:-6} --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command><inputs><conditional name="inputs"> https://bitbucket.org/galaxy/galaxy-central/commits/1cfe8a7b1885/ Changeset: 1cfe8a7b1885 User: nsoranzo Date: 2013-11-16 00:53:35 Summary: Enhance mosaik to utilize GALAXY_SLOTS configuration when available. Affected #: 1 file diff -r 9591da01c73a5af50b87aba15ada6c22e70a94a7 -r 1cfe8a7b18856e160565afb7fe6160ca2c717569 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -3,7 +3,7 @@ <description/><requirements><requirement type="package">mosaik</requirement></requirements><command> - #set $processors = '-p 4' + #set $processors = '-p ${GALAXY_SLOTS:-4}' #set $lm = '' #if $paired.kind == 'single': #set $mfl = '' https://bitbucket.org/galaxy/galaxy-central/commits/1b19cd2a77b5/ Changeset: 1b19cd2a77b5 User: nsoranzo Date: 2013-11-16 00:53:52 Summary: Enhance bowtie2 to utilize GALAXY_SLOTS configuration when available. Affected #: 1 file diff -r 1cfe8a7b18856e160565afb7fe6160ca2c717569 -r 1b19cd2a77b52a8a0003bdc27f4073ff07ddbbd4 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -21,7 +21,7 @@ bowtie2 ## number of threads - -p 4 + -p \${GALAXY_SLOTS:-4} ## index file path -x $index_path https://bitbucket.org/galaxy/galaxy-central/commits/6ce38346b347/ Changeset: 6ce38346b347 User: natefoo Date: 2013-11-16 01:05:06 Summary: Merged in nsoranzo/galaxy-central (pull request #262) Convert other 3 tools to $GALAXY_SLOTS Affected #: 3 files diff -r a461269e7fd2cf7cf012fa16582f4bc5bd5dd1da -r 6ce38346b347dab8f4c7522df7a43874789e40ce tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -36,7 +36,7 @@ --JM 10G ## CPU and butterfly options. - --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 + --CPU \${GALAXY_SLOTS:-6} --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command><inputs><conditional name="inputs"> diff -r a461269e7fd2cf7cf012fa16582f4bc5bd5dd1da -r 6ce38346b347dab8f4c7522df7a43874789e40ce tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -21,7 +21,7 @@ bowtie2 ## number of threads - -p 4 + -p \${GALAXY_SLOTS:-4} ## index file path -x $index_path diff -r a461269e7fd2cf7cf012fa16582f4bc5bd5dd1da -r 6ce38346b347dab8f4c7522df7a43874789e40ce tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -3,7 +3,7 @@ <description/><requirements><requirement type="package">mosaik</requirement></requirements><command> - #set $processors = '-p 4' + #set $processors = '-p ${GALAXY_SLOTS:-4}' #set $lm = '' #if $paired.kind == 'single': #set $mfl = '' 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.