Mercurial > repos > fubar > jbrowse2

changeset 66:bc10ad1dfb98 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
author fubar
date Thu, 28 Mar 2024 11:53:38 +0000
parents c81902830900
children cefe9dbf1d80
files autogenJB2.py
diffstat 1 files changed, 3 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/autogenJB2.py	Thu Mar 28 10:31:07 2024 +0000
+++ b/autogenJB2.py	Thu Mar 28 11:53:38 2024 +0000
@@ -9,13 +9,6 @@
 log = logging.getLogger("jbrowse")
 
 
-def makeDefaultLocation():
-
-    refName = jc.genome_firstcontig
-    defloc = "%s:100..10000" % refName
-    return defloc
-
-
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="", epilog="")
     parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
@@ -199,15 +192,14 @@
             # "quaternary_color": root.find("metadata/general/quaternary_color").text,
             # "font_size": root.find("metadata/general/font_size").text,
             # }
-            # jc.add_general_configuration(general_data)
+            jc.add_general_configuration({})
             trackconf = jc.config_json.get("tracks", [])
             for gnome in jc.genome_names:
                 trackconf += jc.tracksToAdd[gnome]
             jc.config_json["tracks"] = trackconf
             jc.write_config()
-            defLoc = makeDefaultLocation()
             default_session_data.update(
-                {"defaultLocation": defLoc, "session_name": sessName}
+                {"session_name": sessName}
             )
             track_conf.update(default_session_data)
             jc.add_default_session(default_session_data)
@@ -216,3 +208,4 @@
         sys.stderr.write(
             "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
         )
+