minor updates, work around for a pulsar bug

tools/segalign/diagonal_partition.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 """
 Diagonal partitioning for segment files output by SegAlign.

tools/segalign/macros.xml

@@ -7,7 +7,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.1.2.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="edam_ontology">
         <edam_operations>

tools/segalign/run_segalign_diagonal_partition

@@ -3,7 +3,6 @@
 set -o errexit
 set -o nounset
 set -o pipefail
-#set -o xtrace
 
 ##
 ## parse arguments

tools/segalign/segalign.xml

@@ -30,7 +30,9 @@ OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
 #if str($mode.mode_selector) == "segalign"
     #if str($mode.diagonal_partition_options.diagonal_partition) == "true"
         #set $segalign_mode = "segalign_diagonal_partition"
-        '$__tool_directory__/run_segalign_diagonal_partition'
+        ## explicitly calling bash to bypass a pulsar bug
+        ## https://github.com/galaxyproject/pulsar/issues/341
+        bash '$__tool_directory__/run_segalign_diagonal_partition'
             --tool_directory '$__tool_directory__'
             --max_segments '$mode.diagonal_partition_options.max_segments'
     #else