| Previous changeset 2:c612f2d2881c (2021-05-17) Next changeset 4:8cc3862f8b8e (2021-05-25) |
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Commit message:
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 8afc84a2ccaa084b4eedb01a0b76e4c463931db3" |
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modified:
bionano_scaffold.xml |
| b |
| diff -r c612f2d2881c -r 295c0e28f4ee bionano_scaffold.xml --- a/bionano_scaffold.xml Mon May 17 21:26:16 2021 +0000 +++ b/bionano_scaffold.xml Sun May 23 17:23:03 2021 +0000 |
| [ |
| b'@@ -5,23 +5,24 @@\n </macros>\n <expand macro="edam_ontology"/>\n <expand macro="requirements"/>\n- <version_command>perl /HybridScaffold/hybridScaffold.pl --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n #set RefAligner = \'/usr/local/bin/RefAligner\'\n ## softlinks do not work\n cp \'${ngs_fasta}\' ./ngs.fasta\n && cp \'${bionano_cmap}\' ./bionano.cmap\n+ && export GALAXY_MEMORY_GB=\\$((\\${GALAXY_MEMORY_MB:-8192}/1024))\n+ ## return max out of GALAXY_SLOTS and 2 --> use a minimum 2 slots\n+ && export SLOTS=\\$(( \\${GALAXY_SLOTS:-2} > 2 ? \\${GALAXY_SLOTS:-2} : 2 ))\n #if $configuration_options.configuration == \'vgp\'\n && cp \'${vgp_mode}\' ./config.xml\n+ && sed -i "s|__MEMORY__|\\$GALAXY_MEMORY_GB|" ./config.xml\n+ && sed -i "s|__CORES__|\\$SLOTS|" ./config.xml\n #else\n- #import os\n- #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n- #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n && cp \'${configuration_file}\' ./config.xml\n- && sed -i \'s|attr="maxmem" val0=.* display|attr="maxmem" val0="$memory" display|\' ./config.xml\n- && sed -i \'s|attr="maxthreads" val0=.* display|attr="maxthreads" val0="$cores" display|\' ./config.xml\n- && sed -i \'s|attr="maxvirtmem" val0=.*/>|attr="maxvirtmem" val0="$cores"/>|\' ./config.xml\n- && sed -i \'s|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|\' ./config.xml\n+ && sed -i "s|attr=\\"maxmem\\" val0=.* display|attr=\\"maxmem\\" val0=\\"\\$GALAXY_MEMORY_GB\\" display|" ./config.xml\n+ && sed -i "s|attr=\\"maxthreads\\" val0=.* display|attr=\\"maxthreads\\" val0=\\"\\$SLOTS\\" display|" ./config.xml\n+ && sed -i "s|attr=\\"maxvirtmem\\" val0=.*/>|attr=\\"maxvirtmem\\" val0=\\"\\$GALAXY_MEMORY_GB\\"/>|" ./config.xml\n+ && sed -i "s|attr=\\"insertThreads\\" val0=.*/>|attr=\\"insertThreads\\" val0=\\"\\$SLOTS\\"/>|" ./config.xml\n #end if\n ## output the configuration file on stdout\n && cat ./config.xml\n@@ -53,24 +54,19 @@\n -f\n $zip_file\n -o ./\n- ##;\n- ##sleep 1000000\n \n ]]> </command>\n <configfiles>\n <configfile name="vgp_mode"><![CDATA[\n #if $configuration_options.configuration == \'vgp\'\n- #import os\n- #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n- #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n <hybridScaffold>\n <version>\n <flag attr="version" val0="\\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \\$"/>\n </version>\n <global>\n- <flag attr="maxmem" val0="$memory" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>\n- <flag attr="maxthreads" val0="$cores" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>\n- <flag attr="maxvirtmem" val0="$memory"/>\n+ <flag attr="maxmem" val0="__MEMORY__" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>\n+ <flag attr="maxthreads" val0="__CORES__" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>\n+ <flag attr="maxvirtmem" val0="__MEMORY__"/>\n <flag attr="RAmem" val0="3" val1="1"/>\n </global>\n <fasta2cmap>\n@@ -100,7 +96,7 @@\n <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="'..b'flag attr="insertThreads" val0="$cores"/>\n+ <flag attr="insertThreads" val0="__CORES__"/>\n <flag attr="BestRef" val0="1"/>\n <flag attr="BestRefPV" val0="1"/>\n <flag attr="ChimQuality"/>\n@@ -453,16 +449,16 @@\n </assert_contents>\n </output>\n <assert_stdout>\n- <has_text text=\'attr="maxmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxthreads" val0="2"\'/>\n+ <has_text text=\'attr="maxthreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="insertThreads" val0="2"\'/>\n+ <has_text text=\'attr="insertThreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxvirtmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n <has_text text="hybridScaffold"/>\n@@ -488,16 +484,16 @@\n <output name="ngs_contigs_scaffold_gap" file="test_02.gap" ftype="txt"/>\n <output name="report" file="test_02_report.txt" ftype="txt"/>\n <assert_stdout>\n- <has_text text=\'attr="maxmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxthreads" val0="2"\'/>\n+ <has_text text=\'attr="maxthreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="insertThreads" val0="2"\'/>\n+ <has_text text=\'attr="insertThreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxvirtmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n <has_text text="hybridScaffold"/>\n@@ -531,16 +527,16 @@\n </assert_contents>\n </output>\n <assert_stdout>\n- <has_text text=\'attr="maxmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxthreads" val0="2"\'/>\n+ <has_text text=\'attr="maxthreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="insertThreads" val0="2"\'/>\n+ <has_text text=\'attr="insertThreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxvirtmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n <has_text text="hybridScaffold"/>\n@@ -572,16 +568,16 @@\n </assert_contents>\n </output>\n <assert_stdout>\n- <has_text text=\'attr="maxmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxthreads" val0="2"\'/>\n+ <has_text text=\'attr="maxthreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="insertThreads" val0="2"\'/>\n+ <has_text text=\'attr="insertThreads" val0="1"\'/>\n </assert_stdout>\n <assert_stdout>\n- <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n+ <has_text text=\'attr="maxvirtmem" val0="8"\'/>\n </assert_stdout>\n <assert_stdout>\n <has_text text="hybridScaffold"/>\n' |