Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 9:a26c41e304c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b
author fubar
date Fri, 19 Jan 2024 03:08:28 +0000
parents b04fd993b31e
children c60b17456297
comparison
equal deleted inserted replaced
8:9a168aa68f06 9:a26c41e304c3
373 return metadata 373 return metadata
374 374
375 375
376 class JbrowseConnector(object): 376 class JbrowseConnector(object):
377 def __init__(self, outdir, genomes): 377 def __init__(self, outdir, genomes):
378 self.usejson = True
379 self.giURL = GALAXY_INFRASTRUCTURE_URL 378 self.giURL = GALAXY_INFRASTRUCTURE_URL
380 self.outdir = outdir 379 self.outdir = outdir
381 os.makedirs(self.outdir, exist_ok=True) 380 os.makedirs(self.outdir, exist_ok=True)
382 self.genome_paths = genomes 381 self.genome_paths = genomes
383 self.genome_name = None 382 self.genome_name = None
929 } 928 }
930 }, 929 },
931 }, 930 },
932 "displays": [ 931 "displays": [
933 { 932 {
933 "type": "LinearBasicDisplay",
934 "displayId": "%s-LinearBasicDisplay" % tId,
935 },
936 {
934 "type": "LinearPileupDisplay", 937 "type": "LinearPileupDisplay",
935 "displayId": "%s-LinearPileupDisplay" % tId, 938 "displayId": "%s-LinearPileupDisplay" % tId,
936 },
937 {
938 "type": "LinearBasicDisplay",
939 "displayId": "%s-LinearBasicDisplay" % tId,
940 }, 939 },
941 {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId}, 940 {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
942 ], 941 ],
943 } 942 }
944 style_json = self._prepare_track_style(trackDict) 943 style_json = self._prepare_track_style(trackDict)
1425 pass 1424 pass
1426 track_conf["conf"] = etree_to_dict(track.find("options")) 1425 track_conf["conf"] = etree_to_dict(track.find("options"))
1427 jc.add_general_configuration(general_data) 1426 jc.add_general_configuration(general_data)
1428 x = open(args.xml, "r").read() 1427 x = open(args.xml, "r").read()
1429 jc.config_json["tracks"] = jc.tracksToAdd 1428 jc.config_json["tracks"] = jc.tracksToAdd
1430 if jc.usejson: 1429 jc.write_config()
1431 jc.write_config()
1432 jc.add_default_session(default_session_data) 1430 jc.add_default_session(default_session_data)
1433 1431
1434 # jc.text_index() not sure what broke here. 1432 # jc.text_index() not sure what broke here.