Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 118:794aecef8327 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7b6920fd88a86cdb48dc4af2c6be77161eb85699-dirty
author fubar
date Sat, 21 Sep 2024 04:01:38 +0000
parents 56f9a6e0fe80
children af482048ca1a
comparison
equal deleted inserted replaced
117:c4b77883c0a7 118:794aecef8327
409 self.assmeta = {} 409 self.assmeta = {}
410 self.ass_first_contigs = ( 410 self.ass_first_contigs = (
411 [] 411 []
412 ) # for default session - these are read as first line of the assembly .fai 412 ) # for default session - these are read as first line of the assembly .fai
413 self.giURL = GALAXY_INFRASTRUCTURE_URL 413 self.giURL = GALAXY_INFRASTRUCTURE_URL
414 self.outdir = outdir 414 self.outdir = os.path.abspath(outdir)
415 self.jbrowse2path = jbrowse2path 415 self.jbrowse2path = jbrowse2path
416 os.makedirs(self.outdir, exist_ok=True) 416 os.makedirs(self.outdir, exist_ok=True)
417 self.genome_names = [] 417 self.genome_names = []
418 self.trackIdlist = [] 418 self.trackIdlist = []
419 self.tracksToAdd = {} 419 self.tracksToAdd = {}
442 def subprocess_popen(self, command, cwd=True): 442 def subprocess_popen(self, command, cwd=True):
443 if logCommands: 443 if logCommands:
444 log.debug(command) 444 log.debug(command)
445 p = subprocess.Popen( 445 p = subprocess.Popen(
446 command, 446 command,
447 cwd=self.get_cwd(cwd), 447 cwd=self.outdir,
448 shell=True, 448 shell=True,
449 stdin=subprocess.PIPE, 449 stdin=subprocess.PIPE,
450 stdout=subprocess.PIPE, 450 stdout=subprocess.PIPE,
451 stderr=subprocess.PIPE, 451 stderr=subprocess.PIPE,
452 ) 452 )
1438 logging.info( 1438 logging.info(
1439 "@@@ no track location for default session - please add one!" 1439 "@@@ no track location for default session - please add one!"
1440 ) 1440 )
1441 session_views.append(view_json) 1441 session_views.append(view_json)
1442 session_name = default_data.get("session_name", "New session") 1442 session_name = default_data.get("session_name", "New session")
1443 for key, value in mapped_chars.items():
1444 session_name = session_name.replace(value, key)
1445 session_json["name"] = session_name 1443 session_json["name"] = session_name
1446 1444
1447 if "views" not in session_json: 1445 if "views" not in session_json:
1448 session_json["views"] = session_views 1446 session_json["views"] = session_views
1449 else: 1447 else: