Mercurial > repos > blankenberglab > data_manager_refgenie_pull

changeset 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 43d2baff05cd
children b2fa406276e7
files data_manager/data_manager_refgenie_pull.py
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_refgenie_pull.py	Thu Sep 30 14:49:57 2021 +0000
+++ b/data_manager/data_manager_refgenie_pull.py	Fri Oct 01 14:40:21 2021 +0000
@@ -14,7 +14,10 @@
 
 
 def galaxy_code_get_refgenie_assets(refgenie_config_file):
-    rgc = refgenconf.RefGenConf(refgenie_config_file)
+    try:
+        rgc = refgenconf.RefGenConf(refgenie_config_file, writable=False, skip_read_lock=True)
+    except refgenconf.exceptions.RefgenconfError as e:
+        return[{'name': str(e), 'value': 'ERROR', 'options': [], 'selected': False}]
     rval = []
     for urlname, genomes in rgc.listr().items():
         urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8')