Mercurial > repos > gga > apollo_delete_features
annotate create_or_update_organism.py @ 9:2adc3aa47d15 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 49fe23e3fb330234900946352fbc3a86deeeb639
author | gga |
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date | Mon, 29 Jul 2019 10:09:19 -0400 |
parents | 3f0f2af50989 |
children | df0e4eb2dfa5 |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 from __future__ import print_function |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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3 |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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4 import argparse |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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5 import json |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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6 import logging |
7
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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7 import os |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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8 import shutil |
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7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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9 import subprocess |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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10 import sys |
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7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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11 import tempfile |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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12 import time |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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13 |
7
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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14 |
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f7e9c792047b
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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15 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 logging.basicConfig(level=logging.INFO) |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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17 log = logging.getLogger(__name__) |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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18 |
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7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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19 |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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20 def IsBlatEnabled(): |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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21 if 'BLAT_ENABLED' not in os.environ: |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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22 return False |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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23 value = os.environ['BLAT_ENABLED'] |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
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24 if value.lower() in ('true', 't', '1'): |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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25 return True |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
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26 else: |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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27 return False |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
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28 |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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29 |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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30 if __name__ == '__main__': |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance') |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 WAAuth(parser) |
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7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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33 parser.add_argument('jbrowse_src', help='Old JBrowse Data Directory') |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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34 parser.add_argument('jbrowse', help='JBrowse Data Directory') |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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35 parser.add_argument('email', help='User Email') |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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36 OrgOrGuess(parser) |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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37 parser.add_argument('--genus', help='Organism Genus') |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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38 parser.add_argument('--species', help='Organism Species') |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 parser.add_argument('--public', action='store_true', help='Make organism public') |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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40 parser.add_argument('--group', help='Give access to a user group') |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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41 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory') |
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7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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42 args = parser.parse_args() |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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43 CHUNK_SIZE = 2**20 |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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44 blat_db = None |
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4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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45 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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46 # Cleanup if existing |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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47 if(os.path.exists(args.jbrowse)): |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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48 shutil.rmtree(args.jbrowse) |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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49 # Copy files |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 2488ac4ea447c45886ce5c7b102fb28c5839d26b
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50 shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True) |
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7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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51 |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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52 path_fasta = args.jbrowse + '/seq/genome.fasta' |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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53 path_2bit = args.jbrowse + '/seq/genome.2bit' |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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54 |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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55 # Convert fasta if existing |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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56 if(IsBlatEnabled() and os.path.exists(path_fasta)): |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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57 arg = ['faToTwoBit', path_fasta, path_2bit] |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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58 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-twobit-converter-stderr") |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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59 proc = subprocess.Popen(args=arg, shell=False, cwd=args.jbrowse, stderr=tmp_stderr.fileno()) |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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60 return_code = proc.wait() |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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61 if return_code: |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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62 tmp_stderr.flush() |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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63 tmp_stderr.seek(0) |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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64 print("Error building index:", file=sys.stderr) |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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65 while True: |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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66 chunk = tmp_stderr.read(CHUNK_SIZE) |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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67 if not chunk: |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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68 break |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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69 sys.stderr.write(chunk) |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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70 sys.exit(return_code) |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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71 blat_db = path_2bit |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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72 tmp_stderr.close() |
7d885dfe3966
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
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73 |
0
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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74 wa = WebApolloInstance(args.apollo, args.username, args.password) |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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75 |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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76 org_cn = GuessOrg(args, wa) |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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77 if isinstance(org_cn, list): |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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78 org_cn = org_cn[0] |
4dd45d2fd904
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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79 |
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f7e9c792047b
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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80 # User must have an account, if not, create it |
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81 gx_user = wa.users.assertOrCreateUser(args.email) |
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82 |
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83 log.info("Determining if add or update required") |
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84 try: |
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85 org = wa.organisms.findOrganismByCn(org_cn) |
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86 except Exception: |
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87 org = None |
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88 |
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89 if org: |
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90 old_directory = org['directory'] |
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91 |
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92 if not PermissionCheck(gx_user, org_cn, "WRITE"): |
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93 print("Naming Conflict. You do not have permissions to access this organism. Either request permission from the owner, or choose a different name for your organism.") |
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94 sys.exit(2) |
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95 |
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96 log.info("\tUpdating Organism") |
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97 data = wa.organisms.updateOrganismInfo( |
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98 org['id'], |
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99 org_cn, |
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100 args.jbrowse, |
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101 # mandatory |
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102 genus=args.genus, |
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103 species=args.species, |
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104 public=args.public, |
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105 blatdb=blat_db |
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106 ) |
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107 time.sleep(2) |
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108 if args.remove_old_directory and args.jbrowse != old_directory: |
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109 shutil.rmtree(old_directory) |
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110 |
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111 data = [wa.organisms.findOrganismById(org['id'])] |
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112 |
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113 else: |
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114 # New organism |
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115 log.info("\tAdding Organism") |
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116 data = wa.organisms.addOrganism( |
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117 org_cn, |
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118 args.jbrowse, |
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119 genus=args.genus, |
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120 species=args.species, |
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121 public=args.public, |
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122 blatdb=blat_db |
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123 ) |
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124 |
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125 # Must sleep before we're ready to handle |
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126 time.sleep(2) |
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127 log.info("Updating permissions for %s on %s", gx_user, org_cn) |
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128 wa.users.updateOrganismPermission( |
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129 gx_user, org_cn, |
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130 write=True, |
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131 export=True, |
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132 read=True, |
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133 ) |
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134 |
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135 # Group access |
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136 if args.group: |
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137 group = wa.groups.loadGroupByName(name=args.group) |
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138 res = wa.groups.updateOrganismPermission(group, org_cn, |
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139 administrate=False, write=True, read=True, |
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140 export=True) |
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141 |
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142 data = [o for o in data if o['commonName'] == org_cn] |
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143 print(json.dumps(data, indent=2)) |