Mercurial > repos > blankenberglab > data_manager_refgenie_pull

comparison data_manager/data_manager_refgenie_pull.py @ 2:2cb1863cd236 draft

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"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 2b81f6b9cadf15796ef7f1f6a0d12f05d3f405d7"
author blankenberglab
date Fri, 01 Oct 2021 14:40:21 +0000
parents aec9bc48cdb7
children b2fa406276e7
comparison
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1:43d2baff05cd 2:2cb1863cd236
12 12
13 log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull") 13 log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull")
14 14
15 15
16 def galaxy_code_get_refgenie_assets(refgenie_config_file): 16 def galaxy_code_get_refgenie_assets(refgenie_config_file):
17 rgc = refgenconf.RefGenConf(refgenie_config_file) 17 try:
18 rgc = refgenconf.RefGenConf(refgenie_config_file, writable=False, skip_read_lock=True)
19 except refgenconf.exceptions.RefgenconfError as e:
20 return[{'name': str(e), 'value': 'ERROR', 'options': [], 'selected': False}]
18 rval = [] 21 rval = []
19 for urlname, genomes in rgc.listr().items(): 22 for urlname, genomes in rgc.listr().items():
20 urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8') 23 urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8')
21 ul = [] 24 ul = []
22 for genome, assets in genomes.items(): 25 for genome, assets in genomes.items():