Mercurial > repos > richard-burhans > segalign

diff segalign.xml @ 2:9e34b25a8670 draft

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planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 288c3e1887d4c13dcc922c612957460471977ff0
author richard-burhans
date Thu, 18 Apr 2024 17:17:12 +0000
parents 5c72425b7f1b
children 36cafb694dd2
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--- a/segalign.xml	Thu Apr 18 16:51:46 2024 +0000
+++ b/segalign.xml	Thu Apr 18 17:17:12 2024 +0000
@@ -30,7 +30,9 @@
 #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