diff jbrowse2.py @ 3:2de9f585505b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b30d2e277cc360437a02fa812c577c0c8d997cff-dirty

--- a/jbrowse2.py	Mon Jan 08 09:23:19 2024 +0000
+++ b/jbrowse2.py	Tue Jan 09 02:35:52 2024 +0000
@@ -19,6 +19,9 @@
 log = logging.getLogger("jbrowse")
 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
 GALAXY_INFRASTRUCTURE_URL = None
+JB2REL="v2.10.0"
+# version pinned for cloning
+
 mapped_chars = {
     ">": "__gt__",
     "<": "__lt__",
@@ -451,7 +454,9 @@
             assemblies.append(assem)
             self.genome_names.append(genome_name)
             if self.genome_name is None:
-                self.genome_name = genome_name  # first one for all tracks - other than paf
+                self.genome_name = (
+                    genome_name  # first one for all tracks - other than paf
+                )
             if self.config_json.get("assemblies", None):
                 self.config_json["assemblies"] += assemblies
             else:
@@ -506,8 +511,6 @@
             "-v",
             " LinearGenomeView",
         ]
-        if self.debug:
-            log.info("### calling set-default-session with cmd=%s" % "  ".join(cmd))
         self.subprocess_check_call(cmd)
 
     def write_config(self):
@@ -592,7 +595,7 @@
             "plugins": [
                 {
                     "name": "MafViewer",
-                    "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
+                    "url": "https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
                 }
             ]
         }
@@ -935,13 +938,17 @@
         tId = trackData["label"]
         pgname = pafOpts["genome_label"]
         if len(pgname.split() > 1):
-            pgname = pgname.split()[0]  # trouble from spacey names in command lines avoidance
+            pgname = pgname.split()[
+                0
+            ]  # trouble from spacey names in command lines avoidance
         asstrack, gname = self.make_assembly(pafOpts["genome"], pgname)
         self.genome_names.append(pgname)
         if self.config_json.get("assemblies", None):
             self.config_json["assemblies"].append(asstrack)
         else:
-            self.config_json["assemblies"] = [asstrack,]
+            self.config_json["assemblies"] = [
+                asstrack,
+            ]
 
         style_json = self._prepare_track_style(trackData)
         url = "%s.paf" % (trackData["label"])
@@ -1256,7 +1263,7 @@
     def clone_jbrowse(self):
         """Clone a JBrowse directory into a destination directory."""
         dest = self.outdir
-        cmd = ["jbrowse", "create", "-f", dest]
+        cmd = ["jbrowse", "create", "-t",JB2REL, "-f", dest]
         self.subprocess_check_call(cmd)
         for fn in [
             "asset-manifest.json",
@@ -1268,7 +1275,7 @@
         ]:
             cmd = ["rm", "-rf", os.path.join(self.outdir, fn)]
             self.subprocess_check_call(cmd)
-        cmd = ["cp", os.path.join(INSTALLED_TO, "servejb2.py"), self.outdir]
+        cmd = ["cp", os.path.join(INSTALLED_TO, "webserver.py"), self.outdir]
         self.subprocess_check_call(cmd)