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Commit a6d21264 authored by Nuno Miguel Caetano Alves's avatar Nuno Miguel Caetano Alves
Browse files

fixing windows env

parent 92c81bc9
Pipeline #1581 passed with stage
in 29 minutes and 22 seconds
......@@ -5,7 +5,7 @@ COPY . /biotmpy
WORKDIR /biotmpy
# Create the environment:
RUN conda env create -f conda_environment.yml
RUN conda env create -f conda_environment_lin.yml
# Make RUN commands use the new environment:
SHELL ["conda", "run", "-n", "biotmpygpu", "/bin/bash", "-c"]
......
......@@ -11,7 +11,11 @@ git clone https://gitlab.bio.di.uminho.pt/biotextminingpy/biotmpy.git
To use BioTMPy you first need to install either [Anaconda](https://www.anaconda.com/products/individual) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html), and then create a conda environment with the "conda_environment.yml" file. This file will allow you to install the packages required to use all the available features of this tool (Note: The Tensorflow version used in this environment supports computations on one or more GPUs).
```bash
cd biotmpy
conda env create -f conda_environment.yml
#Windows
conda env create -f conda_environment_win.yml
#Linux
conda env create -f conda_environment_lin.yml
conda enable biotmpygpu
```
......
name: biotmpygpu
channels:
- conda-forge
- anaconda
- salilab
- defaults
dependencies:
- _tflow_select=2.3.0
- absl-py=0.10.0
- aiohttp=3.6.3
- astunparse=1.6.3
- async-timeout=3.0.1
- attrs=20.2.0
- blas=1.0
- blinker=1.4
- brotlipy=0.7.0
- ca-certificates=2020.12.5
- cachetools=4.1.1
- certifi=2020.12.5
- cffi=1.14.3
- chardet=3.0.4
- click=7.1.2
- cryptography=3.1.1
- cudatoolkit=10.2.89
- cudnn=7.6.5
- cycler=0.10.0
- dataclasses=0.8
- filelock=3.0.12
- flask=1.1.2
- freetype=2.10.4
- gast=0.4.0
- google-auth=1.22.1
- google-auth-oauthlib=0.4.1
- google-pasta=0.2.0
- grpcio=1.31.0
- h5py=2.10.0
- hdf5=1.10.4
- icc_rt=2019.0.0
- icu=68.1
- idna=2.10
- importlib-metadata=2.0.0
- intel-openmp=2020.2
- itsdangerous=1.1.0
- jinja2=2.11.3
- joblib=1.0.1
- jpeg=9d
- keras-applications=1.0.8
- keras-preprocessing=1.1.0
- kiwisolver=1.3.1
- lcms2=2.12
- libblas=3.9.0
- libcblas=3.9.0
- libclang=11.1.0
- libpng=1.6.37
- libprotobuf=3.13.0.1
- libtiff=4.2.0
- lz4-c=1.9.3
- m2w64-gcc-libgfortran=5.3.0
- m2w64-gcc-libs=5.3.0
- m2w64-gcc-libs-core=5.3.0
- m2w64-gmp=6.1.0
- m2w64-libwinpthread-git=5.0.0.4634.697f757
- markdown=3.3.2
- markupsafe=1.1.1
- matplotlib=3.4.1
- matplotlib-base=3.4.1
- mkl=2020.2
- mkl-service=2.3.0
- mkl_fft=1.3.0
- mkl_random=1.1.1
- msys2-conda-epoch=20160418
- multidict=4.7.6
- nltk=3.6.2
- numpy=1.19.2
- numpy-base=1.19.2
- oauthlib=3.1.0
- olefile=0.46
- openjpeg=2.4.0
- openssl=1.1.1k
- opt_einsum=3.1.0
- packaging=20.9
- pandas=1.2.4
- patsy=0.5.1
- pillow=8.1.2
- pip=21.0.1
- protobuf=3.13.0.1
- pyasn1=0.4.8
- pyasn1-modules=0.2.8
- pycparser=2.20
- pyjwt=1.7.1
- pyopenssl=19.1.0
- pyparsing=2.4.7
- pyqt=5.12.3
- pyqt-impl=5.12.3
- pyqt5-sip=4.19.18
- pyqtchart=5.12
- pyqtwebengine=5.12.1
- pyreadline=2.1
- pysocks=1.7.1
- python=3.8.8
- python-dateutil=2.8.1
- python_abi=3.8
- pytz=2021.1
- qt=5.12.9
- regex=2021.4.4
- requests=2.24.0
- requests-oauthlib=1.3.0
- rsa=4.6
- sacremoses=0.0.43
- scikit-learn=0.24.2
- scipy=1.6.2
- seaborn=0.11.1
- seaborn-base=0.11.1
- setuptools=52.0.0
- six=1.15.0
- sqlite=3.35.4
- statsmodels=0.12.2
- tensorboard=2.4.0
- tensorboard-plugin-wit=1.6.0
- tensorflow=2.3.0
- tensorflow-base=2.3.0
- tensorflow-estimator=2.3.0
- tensorflow-gpu=2.3.0
- termcolor=1.1.0
- threadpoolctl=2.1.0
- tk=8.6.10
- tokenizers=0.10.1
- tornado=6.1
- tqdm=4.60.0
- transformers=4.5.1
- urllib3=1.25.11
- vc=14.2
- vs2015_runtime=14.27.29016
- werkzeug=1.0.1
- wheel=0.36.2
- win_inet_pton=1.1.0
- wincertstore=0.2
- wrapt=1.12.1
- xz=5.2.5
- yarl=1.6.2
- zipp=3.3.1
- zlib=1.2.11
- zstd=1.4.9
- pip:
- bioc==1.3.5
- boto==2.49.0
- boto3==1.17.67
- botocore==1.20.67
- cython==0.29.14
- docutils==0.15.2
- gensim==3.8.3
- jmespath==0.10.0
- jsonlines==1.2.0
- lxml==4.4.1
- pdfminer-six==20201018
- pdftitle==0.7
- s3transfer==0.4.2
- smart-open==2.1.1
- sortedcontainers==2.3.0
prefix: C:\Users\nunoa\Anaconda3\envs\biotmpygpu
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