Mercurial > repos > fubar > jbrowse2

diff autogenJB2.py @ 92:3c4db8203fad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78
author fubar
date Sun, 21 Apr 2024 04:42:29 +0000
parents 3b2ff9864995
children 4c517a0041a8
line wrap: on
line diff
--- a/autogenJB2.py	Thu Apr 18 10:57:29 2024 +0000
+++ b/autogenJB2.py	Sun Apr 21 04:42:29 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": " %s,%s " % (trackname,ipath)}}}}
+                        {"conf": {"options": {"bam": {"bam_index": " %s:%s," % (tpath,ipath)}}}}
                     )
                 elif trext == "cram":
                     ipath = track[3]
@@ -161,7 +161,7 @@
                         ]
                         jc.subprocess_check_call(cmd)
                     track_conf.update(
-                        {"conf": {"options": {"cram": {"cram_index": "%s,%s" % (trackname,ipath)}}}}
+                        {"conf": {"options": {"cram": {"cram_index": "%s:%s," % (tpath, ipath)}}}}
                     )
                 track_conf["path"] = tpath
                 track_conf["format"] = trext