Mercurial > repos > fubar > jbrowse2

diff autogenJB2.py @ 85:3b2ff9864995 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
author fubar
date Tue, 09 Apr 2024 00:26:49 +0000
parents 5c295cc220ed
children 3c4db8203fad
line wrap: on
line diff
--- a/autogenJB2.py	Wed Apr 03 02:56:39 2024 +0000
+++ b/autogenJB2.py	Tue Apr 09 00:26:49 2024 +0000
@@ -143,7 +143,7 @@
                         sys.stdout.write("#### calling %s" % " ".join(cmd))
                         jc.subprocess_check_call(cmd)
                     track_conf.update(
-                        {"conf": {"options": {"bam": {"bam_index": ipath}}}}
+                        {"conf": {"options": {"bam": {"bam_index": " %s,%s " % (trackname,ipath)}}}}
                     )
                 elif trext == "cram":
                     ipath = track[3]
@@ -161,7 +161,7 @@
                         ]
                         jc.subprocess_check_call(cmd)
                     track_conf.update(
-                        {"conf": {"options": {"cram": {"cram_index": ipath}}}}
+                        {"conf": {"options": {"cram": {"cram_index": "%s,%s" % (trackname,ipath)}}}}
                     )
                 track_conf["path"] = tpath
                 track_conf["format"] = trext