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I am behind a university proxy and trying to download the human genome using genomepy. This yields the following error:
$ genomepy install hg38
13:04:17 | WARNING | GENCODE appears to be offline.
13:05:07 | INFO | Downloading assembly summaries from UCSC
Traceback (most recent call last):
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/connection_cext.py", line 268, in _open_connection
self._cmysql.connect(**cnx_kwargs)
_mysql_connector.MySQLInterfaceError: Can't connect to MySQL server on 'genome-mysql.soe.ucsc.edu:3306' (110)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/mabe/.conda/envs/mabe/bin/genomepy", line 10, in <module>
sys.exit(cli())
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/cli.py", line 262, in install
genomepy.install_genome(
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/functions.py", line 208, in install_genome
provider = _provider_selection(name, localname, genomes_dir, provider)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/functions.py", line 371, in _provider_selection
return _lazy_provider_selection(name, provider)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/functions.py", line 342, in _lazy_provider_selection
for p in online_providers(provider):
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/__init__.py", line 104, in online_providers
yield create(provider)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/__init__.py", line 60, in create
return p()
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 72, in __init__
self.genomes = get_genomes(ADRESSES["api"])
File "/home/mabe/.conda/envs/mabe/lib/python3.10/contextlib.py", line 79, in inner
return func(*args, **kwds)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/diskcache/core.py", line 1875, in wrapper
result = func(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 430, in get_genomes
genomes = add_accessions1(genomes)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 457, in add_accessions1
df = pd.DataFrame.from_records(ret)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/pandas/core/frame.py", line 2297, in from_records
first_row = next(data)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 526, in query_ucsc
cnx = mysql.connector.connect(
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/pooling.py", line 286, in connect
return CMySQLConnection(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/connection_cext.py", line 101, in __init__
self.connect(**kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/abstracts.py", line 1108, in connect
self._open_connection()
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/connection_cext.py", line 273, in _open_connection
raise get_mysql_exception(
mysql.connector.errors.DatabaseError: 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.soe.ucsc.edu:3306' (110)
I found that there is no mention of proxy support in README or when googling.
Is there any plan to add proxy support in the near future?
The text was updated successfully, but these errors were encountered:
Hello,
I am behind a university proxy and trying to download the human genome using genomepy. This yields the following error:
I found that there is no mention of proxy support in README or when googling.
Is there any plan to add proxy support in the near future?
The text was updated successfully, but these errors were encountered: