fix: handle refgenconf write lock error

bio/refgenie/wrapper.py

@@ -5,17 +5,25 @@
 
 import os
 import refgenconf
+from refgenconf.exceptions import RefgenconfError
 
 genome = snakemake.params.genome
 asset = snakemake.params.asset
 tag = snakemake.params.tag
 
 conf_path = os.environ["REFGENIE"]
 
-rgc = refgenconf.RefGenConf(conf_path, writable=False)
-
+# BUG If there are multiple concurrent refgenie commands, this will fail due to
+# unable to acquire lock of the config file.
+try:
+    rgc = refgenconf.RefGenConf(conf_path, writable=True)
+except RefgenconfError:
+    # If read lock timeout, attempt to skip the read lock
+    rgc = refgenconf.RefGenConf(conf_path,
+                                writable=True,
+                                skip_read_lock=True,
+                                genome_exact=False)
 # pull asset if necessary
-# BUG Times out when pulling large assets
 gat, archive_data, server_url = rgc.pull(genome, asset, tag, force=False, force_large=True)
 
 for seek_key, out in snakemake.output.items():