Commit fcdbee13 authored by Eric CHARPENTIER's avatar Eric CHARPENTIER 🐍
Browse files

fixed option for univ nantes proxy

parent 662fcd32
......@@ -172,7 +172,6 @@ def downloadAndProcessFiles(ftp, provenance, files2download, outFolder, refName)
zippy = gzip.GzipFile(fileobj=sio)
chrM = zippy.readlines()
elif("chrM" in files2download and "bigZips/" in files2download["chrM"]):
#tempGenome = os.path.join(outFolder,refName+"_genomeTemp.fa")
print("INFO make_ref.py: No chrM file to download. DOWNLOADING full genome in order to extract chrM: "+getServer(provenance)+"/"+files2download["chrM"])
sio = io.BytesIO()
resp = ftp.retrbinary('RETR ' + files2download["chrM"], callback=sio.write)
......@@ -312,7 +311,7 @@ parser.add_argument('-p', '--provenance', help='Provenance of the reference tran
parser.add_argument('-s', '--species', help='Species of the reference transcriptome to be downloaded (default: %(default)s). If you need another species, you\'re going to have to build your reference manually. Have a look at this page: https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/usage/reference', choices=['human','mouse','rat','cow'], default='human', dest='species')
parser.add_argument('-r', '--reference-dir', metavar='DIR', help='Directory where the new reference will be built (default : %(default)s).', required=False, default='REF', dest='refdir')
parser.add_argument('-n', '--name', help='Name of the new reference (default to standard last build name according to chosen species. Ex: hg38,mm10,rn6,bosTau9). This name should be the same specified in the samplesheet describing the samples.', required=False, dest='refname')
parser.add_argument('-u', '--use-proxy', help='Use univ-nantes proxy', required=False, type=bool, default=False, dest='proxy')
parser.add_argument('-u', '--use-proxy', help='Use univ-nantes proxy', action='store_true', dest='proxy')
args = parser.parse_args()
......
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