Merge pull request galaxyproject#5649 from wm75/hapog-update

Update Hapo-G from 1.3.6 to 1.3.7
pavanvidem · Jan 28, 2024 · 0da1ca3 · 0da1ca3
2 parents 58fa506 + c36884f
commit 0da1ca3
Showing 1 changed file with 10 additions and 5 deletions.
diff --git a/tools/hapog/hapog.xml b/tools/hapog/hapog.xml
@@ -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