Mercurial > repos > iuc > jbrowse

comparison jbrowse.py @ 40:17359b808b01 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
author iuc
date Fri, 21 Aug 2020 04:42:41 -0400
parents 9de82b4963e6
children 8774b28235bb
comparison
equal deleted inserted replaced
39:fd5dbf0f732e 40:17359b808b01
321 ) 321 )
322 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format( 322 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
323 galaxy=GALAXY_INFRASTRUCTURE_URL, 323 galaxy=GALAXY_INFRASTRUCTURE_URL,
324 encoded_id=metadata['dataset_id'], 324 encoded_id=metadata['dataset_id'],
325 tool_id=metadata['tool_tool_id'], 325 tool_id=metadata['tool_tool_id'],
326 tool_version=metadata['tool_tool_version'], 326 # tool_version=metadata['tool_tool_version'],
327 ) 327 )
328 return metadata 328 return metadata
329 329
330 330
331 class JbrowseConnector(object): 331 class JbrowseConnector(object):
332 332
333 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1): 333 def __init__(self, jbrowse, outdir, genomes, standalone=None, gencode=1):
334 self.cs = ColorScaling() 334 self.cs = ColorScaling()
335 self.jbrowse = jbrowse 335 self.jbrowse = jbrowse
336 self.outdir = outdir 336 self.outdir = outdir
337 self.genome_paths = genomes 337 self.genome_paths = genomes
338 self.standalone = standalone 338 self.standalone = standalone
339 self.gencode = gencode 339 self.gencode = gencode
340 self.tracksToIndex = [] 340 self.tracksToIndex = []
341 341
342 if standalone: 342 if standalone == "complete":
343 self.clone_jbrowse(self.jbrowse, self.outdir) 343 self.clone_jbrowse(self.jbrowse, self.outdir)
344 elif standalone == "minimal":
345 self.clone_jbrowse(self.jbrowse, self.outdir, minimal=True)
344 else: 346 else:
345 try: 347 try:
346 os.makedirs(self.outdir) 348 os.makedirs(self.outdir)
347 except OSError: 349 except OSError:
348 # Ignore if the folder exists 350 # Ignore if the folder exists
389 log.error('cd %s && %s', self.outdir, command) 391 log.error('cd %s && %s', self.outdir, command)
390 log.error(output) 392 log.error(output)
391 log.error(err) 393 log.error(err)
392 raise RuntimeError("Command failed with exit code %s" % (retcode)) 394 raise RuntimeError("Command failed with exit code %s" % (retcode))
393 395
396 def subprocess_check_output(self, command):
397 log.debug('cd %s && %s', self.outdir, ' '.join(command))
398 return subprocess.check_output(command, cwd=self.outdir)
399
394 def _jbrowse_bin(self, command): 400 def _jbrowse_bin(self, command):
395 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) 401 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
396 402
397 def process_genomes(self): 403 def process_genomes(self):
398 for genome_node in self.genome_paths: 404 for genome_node in self.genome_paths:
499 if blastOpts.get('index', 'false') == 'true': 505 if blastOpts.get('index', 'false') == 'true':
500 self.tracksToIndex.append("%s" % trackData['label']) 506 self.tracksToIndex.append("%s" % trackData['label'])
501 507
502 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): 508 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
503 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') 509 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
504 cmd = ['ln', '-s', data, dest] 510 cmd = ['cp', data, dest]
505 self.subprocess_check_call(cmd) 511 self.subprocess_check_call(cmd)
506 512
507 url = os.path.join('raw', trackData['label'] + '.bw') 513 url = os.path.join('raw', trackData['label'] + '.bw')
508 trackData.update({ 514 trackData.update({
509 "urlTemplate": url, 515 "urlTemplate": url,
1067 } 1073 }
1068 }) 1074 })
1069 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle: 1075 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
1070 json.dump(trackListJson, handle) 1076 json.dump(trackListJson, handle)
1071 1077
1072 def clone_jbrowse(self, jbrowse_dir, destination): 1078 def clone_jbrowse(self, jbrowse_dir, destination, minimal=False):
1073 """Clone a JBrowse directory into a destination directory. 1079 """Clone a JBrowse directory into a destination directory.
1074 """ 1080 """
1075 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks 1081 if minimal:
1076 # unlike copytree 1082 # Should be the absolute minimum required for JBrowse to function.
1077 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination] 1083 interesting = [
1078 log.debug(' '.join(cmd)) 1084 'dist', 'img', 'index.html', 'jbrowse.conf', 'jbrowse_conf.json', 'webpack.config.js'
1079 subprocess.check_call(cmd) 1085 ]
1086 for i in interesting:
1087 cmd = ['cp', '-r', os.path.join(jbrowse_dir, i), destination]
1088 self.subprocess_check_call(cmd)
1089 else:
1090 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
1091 # unlike copytree
1092 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
1093 self.subprocess_check_call(cmd)
1094
1080 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')] 1095 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
1081 log.debug(' '.join(cmd)) 1096 self.subprocess_check_call(cmd)
1082 subprocess.check_call(cmd)
1083 1097
1084 # http://unix.stackexchange.com/a/38691/22785 1098 # http://unix.stackexchange.com/a/38691/22785
1085 # JBrowse releases come with some broken symlinks 1099 # JBrowse releases come with some broken symlinks
1086 cmd = ['find', destination, '-type', 'l', '-xtype', 'l'] 1100 cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
1087 log.debug(' '.join(cmd)) 1101 symlinks = self.subprocess_check_output(cmd)
1088 symlinks = subprocess.check_output(cmd) 1102
1089 for i in symlinks: 1103 for i in symlinks:
1090 try: 1104 try:
1091 os.unlink(i) 1105 os.unlink(i)
1092 except OSError: 1106 except OSError:
1093 pass 1107 pass
1097 parser = argparse.ArgumentParser(description="", epilog="") 1111 parser = argparse.ArgumentParser(description="", epilog="")
1098 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration') 1112 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')
1099 1113
1100 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release') 1114 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
1101 parser.add_argument('--outdir', help='Output directory', default='out') 1115 parser.add_argument('--outdir', help='Output directory', default='out')
1102 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true') 1116 parser.add_argument('--standalone', choices=['complete', 'minimal', 'data'], help='Standalone mode includes a copy of JBrowse')
1103 parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.8.0") 1117 parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.8.0")
1104 args = parser.parse_args() 1118 args = parser.parse_args()
1105 1119
1106 tree = ET.parse(args.xml.name) 1120 tree = ET.parse(args.xml.name)
1107 root = tree.getroot() 1121 root = tree.getroot()