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baker-laboratory / RoseTTAFold-All-Atom

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installing RFAA using only PIP and avoiding conda and mamba #119

Open Sinsilcobio opened 1 month ago

Sinsilcobio commented 1 month ago

Hello,

Thanks for developing this nice tool!

I am trying to install it on a cluster that does not allow for the installation of packages through Conda and Mamba.

I am trying to adjust the installation using a requirement.txt file to be utilized with Python and Pip. I have provided the content of the requirement file in the following and was able to use PIP to install all the packages in the file. Now I am stuck with installing the signal package.

Could you help me know how I could adjust my installation using pip to install the Signalp?

I already tried installing it by accessing the following GitHub repository. However, I can not find the directory "model_weights" directory in "RFAA/lib/python3.10/site-packages/signalp/" $ pip install --no-deps git+https://github.com/fteufel/signalp-6.0.git

Your help is much appreciated!

contents of requiremets.txt file:

absl-py aiohttp aiosignal asttokens astunparse async-timeout attrs blinker brotli

brotli-python

bzip2

c-ares

cached-property cached_property cachetools certifi cffi charset-normalizer click colorama contourpy cryptography cycler deepdiff dgl executing filelock flatbuffers fonttools frozenlist fsspec gast gmpy2 google-auth google-auth-oauthlib google-pasta grpcio h5py icecream idna importlib-metadata jinja2 joblib keras keras-preprocessing kiwisolver markdown markupsafe matplotlib multidict networkx numpy oauthlib openbabel opt_einsum orjson packaging pandas protobuf psutil pyasn1 pyasn1-modules pycparser pygments pyjwt pyopenssl pyparsing pysocks python-dateutil

python-flatbuffers

python-tzdata

pytz pyu2f requests requests-oauthlib rsa scikit-learn scipy setuptools six tensorboard tensorboard-data-server tensorboard-plugin-wit tensorflow tensorflow-estimator termcolor threadpoolctl tk toml tomli torch torchaudio torchvision tornado tqdm typing-extensions typing_extensions unicodedata2 urllib3 werkzeug wheel wrapt yarl zipp

antlr4-python3-runtime assertpy configparser docker-pycreds e3nn gitdb gitpython hydra-core omegaconf opt-einsum-fx pathtools promise pynvml pyrsistent pyyaml sentry-sdk shortuuid smmap subprocess32 wandb

pavelToman commented 1 week ago

Hello! I am either trying to install RoseTTA on cluster for UGent researches - we are using EasyBuild for this. I need to use pip too, not mamba or conda. @Sinsilcobio SignalP seems could be only optional dep - https://github.com/baker-laboratory/RoseTTAFold-All-Atom/issues/44