diff jbrowse2.py @ 71:e26a8a6d2d2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b

--- a/jbrowse2.py	Fri Mar 29 09:35:57 2024 +0000
+++ b/jbrowse2.py	Sat Mar 30 07:15:04 2024 +0000
@@ -378,7 +378,6 @@
         self.assmeta = {}
         self.giURL = GALAXY_INFRASTRUCTURE_URL
         self.outdir = outdir
-        self.genome_firstcontig = None
         self.jbrowse2path = jbrowse2path
         os.makedirs(self.outdir, exist_ok=True)
         self.genome_names = []
@@ -1125,21 +1124,22 @@
                 gname = gname.split()[0]
             passnames.append(gname)
             # trouble from spacey names in command lines avoidance
+            useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
+                "https://"
+            )
+            if not useuri:
+                url = "%s.paf" % (lab)
+            else:
+                url = data
             if gname not in self.genome_names:
                 # ignore if already there - eg for duplicates among pafs.
-                useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
-                    "https://"
-                )
                 asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                 self.genome_names.append(gname)
                 self.tracksToAdd[gname] = []
                 self.assemblies.append(asstrack)
                 if not useuri:
-                    url = "%s.paf" % (lab)
                     dest = "%s/%s" % (self.outdir, url)
                     self.symlink_or_copy(os.path.realpath(data), dest)
-                else:
-                    url = data
         trackDict = {
             "type": "SyntenyTrack",
             "trackId": tId,
@@ -1582,7 +1582,7 @@
                     }
                 else:
                     default_session_data["style"][key] = {}
-                    logging.warn("@@@@ no options/style found for %s" % (key))
+                    logging.debug("@@@@ no options/style found for %s" % (key))
 
                 if track.find("options/style_labels"):
                     default_session_data["style_labels"][key] = {
@@ -1607,14 +1607,13 @@
     }
     jc.add_general_configuration(general_data)
     trackconf = jc.config_json.get("tracks", [])
-    logging.warn("++++++++++++ genome_names=%s" % jc.genome_names)
     for gnome in jc.genome_names:
         trackconf += jc.tracksToAdd[gnome]
     jc.config_json["tracks"] = trackconf
     assconf = jc.config_json.get("assemblies", [])
     assconf += jc.assemblies
     jc.config_json["assemblies"] = assconf
-    logging.warn("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
+    logging.debug("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
     jc.write_config()
     jc.add_default_session(default_session_data)
     # jc.text_index() not sure what broke here.