installing pyrosetta

[najibveto]

hello
i am trying to install pyrosetta in my env germinal but it give error:
`(germinal) nabdellaoui@slurm1:/shared/projects/salmon_egg_transcriptome/germinal$ uv pip install pyrosetta-installer
Using Python 3.10.18 environment at: /home/externe/asia/nabdellaoui/.conda/envs/germinal
Resolved 1 package in 389ms
Prepared 1 package in 110ms
Installed 1 package in 50ms

• pyrosetta-installer==0.1.2
  (germinal) nabdellaoui@slurm1:/shared/projects/salmon_egg_transcriptome/germinal$ python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'
  Installing PyRosetta:
  os: ubuntu
  type: Release
  Rosetta C++ extras:
  mirror: https://west.rosettacommons.org/pyrosetta/release/release
  extra packages: numpy

Traceback (most recent call last):
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/urllib/request.py", line 1348, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/http/client.py", line 1283, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/http/client.py", line 1329, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/http/client.py", line 1278, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/http/client.py", line 1038, in _send_output
self.send(msg)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/http/client.py", line 976, in send
self.connect()
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/http/client.py", line 1448, in connect
super().connect()
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/http/client.py", line 942, in connect
self.sock = self._create_connection(
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/socket.py", line 857, in create_connection
raise err
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/socket.py", line 845, in create_connection
sock.connect(sa)
OSError: [Errno 101] Network is unreachable

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/site-packages/pyrosetta_installer/init.py", line 80, in install_pyrosetta
wheel = get_latest_file(url)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/site-packages/pyrosetta_installer/init.py", line 28, in get_latest_file
with urllib.request.urlopen(dir_url+'latest.html') as f:
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/urllib/request.py", line 519, in open
response = self._open(req, data)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/urllib/request.py", line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/urllib/request.py", line 1391, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/home/externe/asia/nabdellaoui/.conda/envs/germinal/lib/python3.10/urllib/request.py", line 1351, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 101] Network is unreachable>
`
what is the possible solution?
thank you for your help.

[roccomoretti]

The error you're getting is because you can't contact the server which has the PyRosetta installation files.

The first thing to do is to check if you have network connectivity to the server on your machine. Try running something like ping west.rosettacommons.org (do this from the machine you're installing PyRosetta on). If working properly, that should give you something like 64 bytes from 128.95.160.153 repeatedly until you ctrl-C out of it. If the ping gives you an error, then there's something about your internet connection that's at issue, and you may want to contact your sysadmins.

Something else you can try is to pass mirror=1 to the install_pyrosetta command ('import pyrosetta_installer; pyrosetta_installer.install_pyrosetta(mirror=1)' That should use a different server, one which you may be able to see.

Also, are you using a Conda environment? (The (germinal) in the prompt indicates you may be.) Note that uv and conda don't necessarily play well together. If you're using conda, just do pip install pyrosetta-installer, rather than uv pip install pyrosetta-installer. I don't think that would result in your issue, though. -- I bring up Conda simply because RosettaCommons has a Conda channel, and you can possibly install PyRosetta through conda install, rather than the pyrosetta-installer, and the conda install may work where the pyrosetta_installer doesn't. (see the PyRosetta installation documentation for details.)

[najibveto]

thank you for your reply, i could make it work using the mirror=1.