Mercurial > repos > gga > apollo_delete_features

comparison create_or_update_organism.py @ 7:7d885dfe3966 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
author gga
date Fri, 15 Mar 2019 06:05:55 -0400
parents f7e9c792047b
children 3f0f2af50989
comparison
equal deleted inserted replaced
6:c753a0ef794e 7:7d885dfe3966
2 from __future__ import print_function 2 from __future__ import print_function
3 3
4 import argparse 4 import argparse
5 import json 5 import json
6 import logging 6 import logging
7 import os
7 import shutil 8 import shutil
9 import subprocess
8 import sys 10 import sys
11 import tempfile
9 import time 12 import time
13
10 14
11 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance 15 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
12 logging.basicConfig(level=logging.INFO) 16 logging.basicConfig(level=logging.INFO)
13 log = logging.getLogger(__name__) 17 log = logging.getLogger(__name__)
14 18
19
20 def IsBlatEnabled():
21 if 'BLAT_ENABLED' not in os.environ:
22 return False
23 value = os.environ['BLAT_ENABLED']
24 if value.lower() in ('true', 't', '1'):
25 return True
26 else:
27 return False
28
29
15 if __name__ == '__main__': 30 if __name__ == '__main__':
16 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance') 31 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
17 WAAuth(parser) 32 WAAuth(parser)
18 33 parser.add_argument('jbrowse_src', help='Old JBrowse Data Directory')
19 parser.add_argument('jbrowse', help='JBrowse Data Directory') 34 parser.add_argument('jbrowse', help='JBrowse Data Directory')
20 parser.add_argument('email', help='User Email') 35 parser.add_argument('email', help='User Email')
21 OrgOrGuess(parser) 36 OrgOrGuess(parser)
22 parser.add_argument('--genus', help='Organism Genus') 37 parser.add_argument('--genus', help='Organism Genus')
23 parser.add_argument('--species', help='Organism Species') 38 parser.add_argument('--species', help='Organism Species')
24 parser.add_argument('--public', action='store_true', help='Make organism public') 39 parser.add_argument('--public', action='store_true', help='Make organism public')
25 parser.add_argument('--group', help='Give access to a user group') 40 parser.add_argument('--group', help='Give access to a user group')
26 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory') 41 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
42 args = parser.parse_args()
43 CHUNK_SIZE = 2**20
44 blat_db = None
27 45
28 args = parser.parse_args() 46 # Cleanup if existing
47 if(os.path.exists(args.jbrowse)):
48 shutil.rmtree(args.jbrowse)
49 # Copy files
50 shutil.copytree(args.jbrowse_src, args.jbrowse)
51
52 path_fasta = args.jbrowse + '/seq/genome.fasta'
53 path_2bit = args.jbrowse + '/seq/genome.2bit'
54
55 # Convert fasta if existing
56 if(IsBlatEnabled() and os.path.exists(path_fasta)):
57 arg = ['faToTwoBit', path_fasta, path_2bit]
58 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-twobit-converter-stderr")
59 proc = subprocess.Popen(args=arg, shell=False, cwd=args.jbrowse, stderr=tmp_stderr.fileno())
60 return_code = proc.wait()
61 if return_code:
62 tmp_stderr.flush()
63 tmp_stderr.seek(0)
64 print("Error building index:", file=sys.stderr)
65 while True:
66 chunk = tmp_stderr.read(CHUNK_SIZE)
67 if not chunk:
68 break
69 sys.stderr.write(chunk)
70 sys.exit(return_code)
71 blat_db = path_2bit
72 tmp_stderr.close()
73
29 wa = WebApolloInstance(args.apollo, args.username, args.password) 74 wa = WebApolloInstance(args.apollo, args.username, args.password)
30 75
31 org_cn = GuessOrg(args, wa) 76 org_cn = GuessOrg(args, wa)
32 if isinstance(org_cn, list): 77 if isinstance(org_cn, list):
33 org_cn = org_cn[0] 78 org_cn = org_cn[0]
54 org_cn, 99 org_cn,
55 args.jbrowse, 100 args.jbrowse,
56 # mandatory 101 # mandatory
57 genus=args.genus, 102 genus=args.genus,
58 species=args.species, 103 species=args.species,
59 public=args.public 104 public=args.public,
105 blatdb=blat_db
60 ) 106 )
61 time.sleep(2) 107 time.sleep(2)
62 if args.remove_old_directory and args.jbrowse != old_directory: 108 if args.remove_old_directory and args.jbrowse != old_directory:
63 shutil.rmtree(old_directory) 109 shutil.rmtree(old_directory)
64 110
70 data = wa.organisms.addOrganism( 116 data = wa.organisms.addOrganism(
71 org_cn, 117 org_cn,
72 args.jbrowse, 118 args.jbrowse,
73 genus=args.genus, 119 genus=args.genus,
74 species=args.species, 120 species=args.species,
75 public=args.public 121 public=args.public,
122 blatdb=blat_db
76 ) 123 )
77 124
78 # Must sleep before we're ready to handle 125 # Must sleep before we're ready to handle
79 time.sleep(2) 126 time.sleep(2)
80 log.info("Updating permissions for %s on %s", gx_user, org_cn) 127 log.info("Updating permissions for %s on %s", gx_user, org_cn)