Polypolish update dependencies (galaxyproject#5710)

* update samtool dependency 1.13 > 1.19 * update version suffix and add thread option to samtools
pavanvidem · Jan 11, 2024 · 2a8a85c · 2a8a85c
1 parent 1a763e3
commit 2a8a85c
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Showing 2 changed files with 14 additions and 9 deletions.
diff --git a/tools/polypolish/macro.xml b/tools/polypolish/macro.xml
@@ -1,9 +1,14 @@
 
 <macros>
   <token name="@TOOL_VERSION@">0.5.0</token>
-  <token name="@VERSION_SUFFIX@">1</token>
+  <token name="@VERSION_SUFFIX@">2</token>
   <token name="@PROFILE@">21.05</token>
-  <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token>
+
+  <token name="@THREADS@"><![CDATA[
+      ##compute the number of ADDITIONAL threads to be used by samtools (-@)
+      addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
+  ]]></token>
+
   <xml name="version_command">
      <version_command><![CDATA[polypolish -V]]></version_command>
   </xml>
@@ -15,7 +20,7 @@
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
-      <requirement type="package" version="1.13">samtools</requirement>
+      <requirement type="package" version="1.19">samtools</requirement>
     </requirements>
   </xml>
   <xml name="citations">

diff --git a/tools/polypolish/polypolish.xml b/tools/polypolish/polypolish.xml
@@ -15,7 +15,7 @@
         ======================================*#
         #if $input.sam_data_type.sam_selector == 'single'
             #if $input.sam_data_type.single_sam.is_of_type("unsorted.bam")
-                samtools view -h $input.sam_data_type.single_sam > input_sam &&
+                samtools view -@ \$addthreads -h $input.sam_data_type.single_sam > input_sam &&
             #elif $input.sam_data_type.single_sam.ext == 'sam'
                 ln -s $input.sam_data_type.single_sam input_sam &&
             #else
@@ -27,14 +27,14 @@
         ======================================*#
         #elif $input.sam_data_type.sam_selector == 'paired'
             #if $input.sam_data_type.R1_sam.is_of_type("unsorted.bam")
-                samtools view -h $input.sam_data_type.R1_sam > sample_R1.sam &&
+                samtools view -@ \$addthreads -h $input.sam_data_type.R1_sam > sample_R1.sam &&
             #elif $input.sam_data_type.R1_sam.ext == 'sam'
                 ln -s '$input.sam_data_type.R1_sam' sample_R1.sam &&
             #else
                 echo "${input.sam_data_type.single_sam} not a sam/bam file"
             #end if
             #if $input.sam_data_type.R2_sam.is_of_type("unsorted.bam")
-                samtools view -h $input.sam_data_type.R2_sam > sample_R2.sam &&
+                samtools view -@ \$addthreads -h $input.sam_data_type.R2_sam > sample_R2.sam &&
             #elif $input.sam_data_type.R2_sam.ext == 'sam'
                 ln -s '$input.sam_data_type.R2_sam' sample_R2.sam &&
             #else
@@ -58,7 +58,7 @@
             mkdir single_collection &&
             #for $value, $single_sam in enumerate($input.sam_data_type.single_collection):
                 #if $single_sam.is_of_type("unsorted.bam")
-                    samtools view -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' &&
+                    samtools view -@ \$addthreads -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' &&
                 #elif $single_sam.ext == 'sam'
                     ln -s $single_sam 'single_collection/$(single_sam.element_identifier).$(single_sam.ext)' &&
                 #else
@@ -73,12 +73,12 @@
             mkdir paired_collection &&
             #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection):
                 #if $paired_sam.forward.is_of_type("unsorted.bam")
-                    samtools view -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' &&
+                    samtools view -@ \$addthreads -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' &&
                 #else
                     ln -s '$paired_sam.forward' 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' &&
                 #end if
                 #if $paired_sam.reverse.is_of_type("unsorted.bam")
-                    samtools view -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' &&
+                    samtools view -@ \$addthreads -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' &&
                 #else
                     ln -s '$paired_sam.reverse' 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' &&
                 #end if