From 288c3e1887d4c13dcc922c612957460471977ff0 Mon Sep 17 00:00:00 2001
From: Richard Burhans <richard.burhans@gmail.com>
Date: Thu, 18 Apr 2024 12:44:59 -0400
Subject: [PATCH] minor updates, work around for a pulsar bug

---
 tools/segalign/diagonal_partition.py           | 2 +-
 tools/segalign/macros.xml                      | 2 +-
 tools/segalign/run_segalign_diagonal_partition | 1 -
 tools/segalign/segalign.xml                    | 4 +++-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/tools/segalign/diagonal_partition.py b/tools/segalign/diagonal_partition.py
index 1a06feb..0153023 100755
--- a/tools/segalign/diagonal_partition.py
+++ b/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.
diff --git a/tools/segalign/macros.xml b/tools/segalign/macros.xml
index 882a51a..2112c76 100644
--- a/tools/segalign/macros.xml
+++ b/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>
diff --git a/tools/segalign/run_segalign_diagonal_partition b/tools/segalign/run_segalign_diagonal_partition
index d76b33d..75e079f 100755
--- a/tools/segalign/run_segalign_diagonal_partition
+++ b/tools/segalign/run_segalign_diagonal_partition
@@ -3,7 +3,6 @@
 set -o errexit
 set -o nounset
 set -o pipefail
-#set -o xtrace
 
 ##
 ## parse arguments
diff --git a/tools/segalign/segalign.xml b/tools/segalign/segalign.xml
index b5f1f52..e95143c 100644
--- a/tools/segalign/segalign.xml
+++ b/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