| Previous changeset 66:bc10ad1dfb98 (2024-03-28) Next changeset 68:c4eb6a85db70 (2024-03-29) |
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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 bc10ad1dfb98 -r cefe9dbf1d80 autogenJB2.py --- a/autogenJB2.py Thu Mar 28 11:53:38 2024 +0000 +++ b/autogenJB2.py Thu Mar 28 12:17:24 2024 +0000 |
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| @@ -5,10 +5,10 @@ from jbrowse2 import JbrowseConnector as jbC -logging.basicConfig(level=logging.debug) + +logging.basicConfig(level=logging.DEBUG) log = logging.getLogger("jbrowse") - if __name__ == "__main__": parser = argparse.ArgumentParser(description="", epilog="") parser.add_argument("--sessName", help="Session name", default="AutoJBrowse") @@ -62,7 +62,8 @@ outdir=args.outdir, jbrowse2path=args.jbrowse2path, ) - genomes=[ + genomes = ( + [ { "path": x, "label": genome_names[i], @@ -74,6 +75,7 @@ } for i, x in enumerate(genome_paths) ], + ) logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes)) assref_name = jc.process_genomes(genomes[0]) default_session_data = { @@ -89,7 +91,11 @@ tnames = [x[2] for x in listtracks] texts = [x[1] for x in listtracks] for i, track in enumerate(listtracks): - track_conf = {"trackfiles": [], "category": "autogenerated", "assemblyNames": assref_name} + track_conf = { + "trackfiles": [], + "category": "autogenerated", + "assemblyNames": assref_name, + } tpath, trext, trackname = track[:3] track_conf["dataset_id"] = trackname useuri = "no" @@ -165,7 +171,8 @@ for key in keys: if trext in [ "bigwig", - "gff", "gff3", + "gff", + "gff3", "vcf", "maf", ]: @@ -179,9 +186,9 @@ if trext == "vcf": ttype = "LinearVariantDisplay" style_json = { - "type": ttype, - "trackShowLabels": False, - "trackShowDescriptions": False + "type": ttype, + "trackShowLabels": False, + "trackShowDescriptions": False, } default_session_data["style"][key] = style_json # general_data = { @@ -196,11 +203,12 @@ trackconf = jc.config_json.get("tracks", []) for gnome in jc.genome_names: trackconf += jc.tracksToAdd[gnome] + logging.warn( + "^^%% adding trackconf=%s for gnome %s" % (trackconf, gnome) + ) jc.config_json["tracks"] = trackconf jc.write_config() - default_session_data.update( - {"session_name": sessName} - ) + default_session_data.update({"session_name": sessName}) track_conf.update(default_session_data) jc.add_default_session(default_session_data) # jc.text_index() not sure what broke here. @@ -208,4 +216,3 @@ sys.stderr.write( "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process" ) - |