# HG changeset patch
# User fubar
# Date 1709684582 0
# Node ID 3e53204c2419f9fc5add24e87857e03f547e689c
# Parent  4181e97c70a7b910c76d98175f4b4a65c6450a28
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty

diff -r 4181e97c70a7 -r 3e53204c2419 __pycache__/jbrowse2.cpython-310.pyc
Binary file __pycache__/jbrowse2.cpython-310.pyc has changed
diff -r 4181e97c70a7 -r 3e53204c2419 jb2_urlconf.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jb2_urlconf.py	Wed Mar 06 00:23:02 2024 +0000
@@ -0,0 +1,16 @@
+inconf = open('config.json', 'r').readlines()
+with open('config.json.local', 'w') as bak:
+    bak.write('\n'.join(inconf))
+urlbase = "https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/hum/"
+utag = '"uri":'
+for i, row in enumerate(inconf):
+    ispath = False
+    if row.strip().startswith(utag):
+            ispath = True
+            parth = row.split(utag)[1].strip()
+            inconf[i] = '%s%s' % (urlbase, parth)
+with open('config.json', 'w') as outconf:
+    outconf.write('\n'.join(inconf))
+
+
+
diff -r 4181e97c70a7 -r 3e53204c2419 jbrowse2.py
--- a/jbrowse2.py	Mon Mar 04 09:47:19 2024 +0000
+++ b/jbrowse2.py	Wed Mar 06 00:23:02 2024 +0000
@@ -1086,9 +1086,9 @@
         for i, gname in enumerate(pgnames):
             if len(gname.split()) > 1:
                 gname = gname.split()[0]
+                passnames.append(gname)
                 # trouble from spacey names in command lines avoidance
                 if gname not in self.genome_names:
-                    passnames.append(gname)
                     # ignore if already there - eg for duplicates among pafs.
                     asstrack = self.make_assembly(pgpaths[i], gname)
                     self.genome_names.append(gname)