| Previous changeset 0:932410434dd1 (2020-01-24) Next changeset 2:22bf5b566ce2 (2020-03-13) |
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Commit message:
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 3b0789f0a28a87952049d74a9250338221f9b286" |
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modified:
ParSNP.xml |
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| diff -r 932410434dd1 -r 2e855db9b19b ParSNP.xml --- a/ParSNP.xml Fri Jan 24 17:45:42 2020 -0500 +++ b/ParSNP.xml Thu Mar 12 19:38:17 2020 -0400 |
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| @@ -14,6 +14,8 @@ </requirements> <version_command><![CDATA[parsnp -V |& tail -n1]]></version_command> <command detect_errors="aggressive"><![CDATA[ + export MEMORY_LIMIT=`expr ${GALAXY_MEMORY_MB:-0} \* 1000`; + [[ $MEMORY_LIMIT -eq 0 ]] && export MEMORY_LIMIT=; export GENOME_DIR=\$(mktemp -d -p `pwd`) #for $genome in $genomes && ln -sf '$genome' @@ -23,7 +25,7 @@ \$GENOME_DIR/\$(basename '$genome') #end if #end for - && parsnp -v -o `pwd` -p \${GALAXY_SLOTS:-1} -P \${GALAXY_MEMORY_MB:-15000000} -d "\$GENOME_DIR" + && parsnp -v -o `pwd` -p \${GALAXY_SLOTS:-1} -P \${MEMORY_LIMIT:-15000000} -d "\$GENOME_DIR" #if $ref_or_gbk.ref_type == "fasta" #if $ref_or_gbk.ref_genome.random_ref -r '!' |