Scale memory assignment to samtools

pavanvidem · Jan 28, 2024 · c36884f · c36884f
1 parent 7353a9e
commit c36884f
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/tools/hapog/hapog.xml b/tools/hapog/hapog.xml
@@ -11,11 +11,16 @@
         <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/
 
 --threads \${GALAXY_SLOTS:-1}
+--samtools-mem \$addmemory"M"
 
 #if str( $reads.type ) == "short":
     #for $i in $reads.pe1