Mercurial > repos > fubar > jbrowse2

diff jbrowse2.py @ 54:d6b0feb22584 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c
author fubar
date Thu, 14 Mar 2024 00:59:36 +0000
parents bdfa6a7c4543
children 469c0f6d87d7
line wrap: on
line diff
--- a/jbrowse2.py	Thu Mar 07 09:23:06 2024 +0000
+++ b/jbrowse2.py	Thu Mar 14 00:59:36 2024 +0000
@@ -1085,7 +1085,8 @@
                 # trouble from spacey names in command lines avoidance
                 if gname not in self.genome_names:
                     # ignore if already there - eg for duplicates among pafs.
-                    asstrack = self.make_assembly(pgpaths[i], gname)
+                    useuri = pgpaths[i].startswith('http://') or pgpaths[i].startswith('https://')
+                    asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                     self.genome_names.append(gname)
                     if self.config_json.get("assemblies", None):
                         self.config_json["assemblies"].append(asstrack)