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biolib / openprotein

A PyTorch framework for prediction of tertiary protein structure
MIT License
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Provide a description on how to use it with anaconda #39

Open matthiasbrix opened 5 years ago

matthiasbrix commented 5 years ago

Hi,

I have had struggles to get it running in a conda environment because it did not allow me to install from the pipfile. What I did is this:

conda create -n openprotein

source activate openprotein

conda install pip

~/anaconda3/envs/openprotein/bin/pip install pipenv

~/anaconda3/envs/openprotein/bin/pipenv install

Perhaps provide a requirements file for conda environments?

biocubinacci commented 5 years ago

In what way does the above fail to install the Pipfile? If you could provide error logs that would be helpful.

amjadalfawal commented 4 years ago

use this yml import it as env its work with conda
this is documentation for export and import env https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html 


channels:
  - menpo
  - jmcmurray
  - anaconda
  - pytorch
  - soumith
  - conda-forge
  - defaults
dependencies:
  - _tflow_190_select=0.0.1=gpu
  - absl-py=0.3.0=py35_0
  - alabaster=0.7.11=py35_0
  - asn1crypto=0.24.0=py35_0
  - astor=0.7.1=py35_0
  - astroid=2.0.2=py35_0
  - babel=2.6.0=py35_0
  - backcall=0.1.0=py35_0
  - backports=1.0=py35he88aa47_1
  - backports.weakref=1.0.post1=py35hf13df52_0
  - blas=1.0=mkl
  - bleach=2.1.3=py35_0
  - ca-certificates=2019.11.28=hecc5488_0
  - certifi=2018.8.24=py35_1001
  - cffi=1.11.5=py35h945400d_0
  - chardet=3.0.4=py35_1
  - cloudpickle=0.5.3=py35_0
  - colorama=0.3.9=py35h32a752f_0
  - cryptography=2.3=py35h74b6da3_0
  - cryptography-vectors=2.3=py35_0
  - cudatoolkit=9.0=1
  - cudnn=7.1.4=cuda9.0_0
  - cycler=0.10.0=py_1
  - cython=0.28.5=py35h6538335_0
  - decorator=4.3.0=py35_0
  - docutils=0.14=py35h8ccb97f_0
  - entrypoints=0.2.3=py35hb91ced9_2
  - ffmpeg=3.2.4=1
  - freetype=2.8.1=ha63716d_1
  - gast=0.2.0=py35_0
  - git=2.18.0=h6bb4b03_0
  - glew=2.0.0=h2fa13f4_0
  - grpcio=1.12.1=py35h1a1b453_0
  - h5py=2.8.0=py35hb24199d_1
  - hdf5=1.10.2=he51fdeb_2
  - html5lib=1.0.1=py35h047fa9f_0
  - icc_rt=2017.0.4=h97af966_0
  - icu=58.2=ha66f8fd_1
  - idna=2.7=py35_0
  - imageio=2.3.0=py35_0
  - imagesize=1.0.0=py35_0
  - intel-openmp=2018.0.3=0
  - ipykernel=4.8.2=py35_0
  - ipython=6.5.0=py35_0
  - ipython_genutils=0.2.0=py35ha709e79_0
  - isort=4.3.4=py35_0
  - jedi=0.12.1=py35_0
  - jpeg=9b=hb83a4c4_2
  - json=0.1.1=0
  - jsonschema=2.6.0=py35h27d56d3_0
  - jupyter_client=5.2.3=py35_0
  - jupyter_core=4.4.0=py35h629ba7f_0
  - keras=2.2.2=py35_0
  - keras-applications=1.0.4=py_1
  - keras-preprocessing=1.0.2=py_1
  - keyring=13.2.1=py35_0
  - kivy=1.10.1=py35h47ee06f_1
  - kiwisolver=1.0.1=py35he980bc4_2
  - lazy-object-proxy=1.3.1=py35he996729_0
  - libgpuarray=0.7.6=hfa6e2cd_1003
  - libpng=1.6.34=h79bbb47_0
  - libprotobuf=3.5.2=he0781b1_0
  - libsodium=1.0.16=h9d3ae62_0
  - libtiff=4.0.9=hb8ad9f9_1
  - make=3.82=0
  - mako=1.0.7=py_1
  - markdown=2.6.11=py35_0
  - markupsafe=1.0=py35hc253e08_1
  - matplotlib=2.2.2=py35h153e9ff_1
  - mccabe=0.6.1=py35_1
  - mistune=0.8.3=py35hfa6e2cd_1
  - mkl=2018.0.3=1
  - mkl_fft=1.0.4=py35h1e22a9b_1
  - mkl_random=1.0.1=py35h9258bd6_0
  - nbconvert=5.3.1=py35h98d6c46_0
  - nbformat=4.4.0=py35h908c9d9_0
  - ninja=1.9.0=h1ad3211_1
  - numpy=1.15.0=py35h9fa60d3_0
  - numpy-base=1.15.0=py35h4a99626_0
  - numpydoc=0.8.0=py35_0
  - olefile=0.45.1=py35_0
  - opencv3=3.1.0=py35_0
  - openssl=1.0.2t=hfa6e2cd_0
  - packaging=17.1=py35_0
  - pandas=0.23.4=py35h830ac7b_0
  - pandoc=2.2.1=h1a437c5_0
  - pandocfilters=1.4.2=py35h978f723_1
  - parso=0.3.1=py35_0
  - path.py=11.0.1=py35_0
  - pickleshare=0.7.4=py35h2f9f535_0
  - pillow=5.2.0=py35_0
  - prompt_toolkit=1.0.15=py35h89c7cb4_0
  - protobuf=3.5.2=py35h6538335_1
  - psutil=5.4.6=py35hfa6e2cd_0
  - pycodestyle=2.4.0=py35_0
  - pycparser=2.18=py35h15a15da_1
  - pyflakes=2.0.0=py35_0
  - pygments=2.2.0=py35h24c0941_0
  - pygpu=0.7.6=py35_0
  - pylint=2.1.1=py35_0
  - pyopenssl=18.0.0=py35_0
  - pyparsing=2.2.0=py35hcabcaab_1
  - pyqt=5.9.2=py35h6538335_2
  - pyreadline=2.1=py35_0
  - pysocks=1.6.8=py35_0
  - python=3.5.5=h0c2934d_2
  - python-dateutil=2.7.3=py35_0
  - pytorch=1.1.0=py3.5_cuda90_cudnn7_1
  - pytz=2018.5=py35_0
  - pywin32=223=py35hfa6e2cd_1
  - pywin32-ctypes=0.2.0=py35_0
  - pyyaml=3.13=py35hfa6e2cd_1
  - pyzmq=17.1.0=py35hfa6e2cd_0
  - qt=5.9.6=vc14h62aca36_0
  - qtawesome=0.4.4=py35h639d0ff_0
  - qtconsole=4.3.1=py35hc47b0dd_0
  - qtpy=1.4.2=py35_1
  - qutil=3.2.1=6
  - requests=2.19.1=py35_0
  - requests_download=0.1.2=py_1
  - rope=0.10.7=py35_0
  - scipy=1.1.0=py35hc28095f_0
  - sdl2=2.0.8=1
  - sdl2_image=2.0.2=0
  - sdl2_mixer=2.0.1=h6538335_1
  - sdl2_ttf=2.0.14=h8909db8_1
  - selenium=3.14.0=py35hfa6e2cd_0
  - setuptools=40.0.0=py35_0
  - simplegeneric=0.8.1=py35_2
  - singledispatch=3.4.0.3=py35h33f66b4_0
  - sip=4.19.8=py35h6538335_0
  - six=1.11.0=py35_1
  - smpeg2=2.0.0=h6538335_1
  - snowballstemmer=1.2.1=py35h4c55bfa_0
  - sphinx=1.7.6=py35_0
  - sphinxcontrib=1.0=py35h45f5ca3_1
  - sphinxcontrib-websupport=1.1.0=py35_1
  - spyder=3.3.0=py35_0
  - spyder-kernels=0.2.4=py35_0
  - sqlite=3.24.0=h7602738_0
  - tensorboard=1.9.0=py35he025d50_0
  - tensorflow=1.9.0=gpu_py35h0075c17_1
  - tensorflow-base=1.9.0=gpu_py35h6e53903_0
  - tensorflow-gpu=1.9.0=hf154084_0
  - termcolor=1.1.0=py35_1
  - testpath=0.3.1=py35h06cf69e_0
  - theano=1.0.2=py35_0
  - tk=8.6.7=hcb92d03_3
  - torchvision=0.3.0=py35_cu90_1
  - tornado=5.1=py35hfa6e2cd_0
  - traitlets=4.3.2=py35h09b975b_0
  - typed-ast=1.1.0=py35hfa6e2cd_0
  - typing=3.6.4=py35_0
  - urllib3=1.23=py35_0
  - vc=14.1=h0510ff6_3
  - vs2015_runtime=15.5.2=3
  - wcwidth=0.1.7=py35h6e80d8a_0
  - webencodings=0.5.1=py35h5d527fb_1
  - wheel=0.31.1=py35_0
  - win_inet_pton=1.0.1=py35hbef1270_1
  - win_unicode_console=0.5=py35h56988b5_0
  - wincertstore=0.2=py35hfebbdb8_0
  - wrapt=1.10.11=py35h54666f7_0
  - yaml=0.1.7=hfa6e2cd_1001
  - zeromq=4.2.5=he025d50_1
  - zlib=1.2.11=h8395fce_2
  - pip:
    - biopython==1.76
    - click==7.0
    - flask==1.1.1
    - flask-cors==3.0.8
    - itsdangerous==1.1.0
    - jinja2==2.10.3
    - peptidebuilder==1.0.4
    - pip==19.3.1
    - werkzeug==0.16.0
prefix: D:\ProgramData\Anaconda3\envs\openprotien```