Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.py @ 71:e26a8a6d2d2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b
author fubar
date Sat, 30 Mar 2024 07:15:04 +0000
parents 7230a2422507
children 2bdb748df098
comparison
equal deleted inserted replaced
70:5f0ee87daef4 71:e26a8a6d2d2e
74 }, 74 },
75 } 75 }
76 for i, x in enumerate(genome_paths) 76 for i, x in enumerate(genome_paths)
77 ], 77 ],
78 ) 78 )
79 logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes)) 79 logging.debug("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
80 assref_name = jc.process_genomes(genomes[0]) 80 assref_name = jc.process_genomes(genomes[0])
81 default_session_data = { 81 default_session_data = {
82 "visibility": { 82 "visibility": {
83 "default_on": [], 83 "default_on": [],
84 "default_off": [], 84 "default_off": [],
201 # } 201 # }
202 jc.add_general_configuration({}) 202 jc.add_general_configuration({})
203 trackconf = jc.config_json.get("tracks", []) 203 trackconf = jc.config_json.get("tracks", [])
204 for gnome in jc.genome_names: 204 for gnome in jc.genome_names:
205 trackconf += jc.tracksToAdd[gnome] 205 trackconf += jc.tracksToAdd[gnome]
206 logging.warn( 206 logging.debug(
207 "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome) 207 "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
208 ) 208 )
209 jc.config_json["tracks"] = trackconf 209 jc.config_json["tracks"] = trackconf
210 assconf = jc.config_json.get("assemblies", []) 210 assconf = jc.config_json.get("assemblies", [])
211 assconf += jc.assemblies 211 assconf += jc.assemblies
212 jc.config_json["assemblies"] = assconf 212 jc.config_json["assemblies"] = assconf
213 logging.warn("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) 213 logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
214 jc.write_config() 214 jc.write_config()
215 default_session_data.update({"session_name": sessName}) 215 default_session_data.update({"session_name": sessName})
216 track_conf.update(default_session_data) 216 track_conf.update(default_session_data)
217 jc.add_default_session(default_session_data) 217 jc.add_default_session(default_session_data)
218 # jc.text_index() not sure what broke here. 218 # jc.text_index() not sure what broke here.