| Previous changeset 65:c81902830900 (2024-03-28) Next changeset 67:cefe9dbf1d80 (2024-03-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty |
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modified:
autogenJB2.py |
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| diff -r c81902830900 -r bc10ad1dfb98 autogenJB2.py --- a/autogenJB2.py Thu Mar 28 10:31:07 2024 +0000 +++ b/autogenJB2.py Thu Mar 28 11:53:38 2024 +0000 |
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| @@ -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" ) + |