| Previous changeset 1:7d56a813fd24 (2023-10-10) Next changeset 3:5287036a797a (2024-04-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 0da1ca313d02ca780a671247e434a424fa67887b |
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modified:
hapog.xml |
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| diff -r 7d56a813fd24 -r ee0d6e789958 hapog.xml --- a/hapog.xml Tue Oct 10 17:29:42 2023 +0000 +++ b/hapog.xml Sun Jan 28 23:46:07 2024 +0000 |
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| @@ -1,21 +1,26 @@ <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>genome polishing</description> <macros> - <token name="@TOOL_VERSION@">1.3.6</token> + <token name="@TOOL_VERSION@">1.3.7</token> <token name="@VERSION_SUFFIX@">0</token> </macros> + <xrefs> + <xref type="bio.tools">hapog</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">hapog</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ +##Compute samtools memory settings like in samtools_sort +##use only 75% of available: https://github.com/samtools/samtools/issues/831 +addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && +((addmemory=addmemory*75/100)) && hapog --genome '${genome}' --output output/ -## setting default threads to 2 until -## https://github.com/institut-de-genomique/HAPO-G/issues/34 -## gets addressed, at least ---threads \${GALAXY_SLOTS:-2} +--threads \${GALAXY_SLOTS:-1} +--samtools-mem \$addmemory"M" #if str( $reads.type ) == "short": #for $i in $reads.pe1 |