Commit c14f7629 authored by Martino Bertoni's avatar Martino Bertoni 🌋
Browse files

fix dependecy issues in definition file

parent 4f2ea2a7
Pipeline #2406 failed with stages
in 20 minutes and 22 seconds
...@@ -61,15 +61,16 @@ From: centos:8 ...@@ -61,15 +61,16 @@ From: centos:8
source activate py37 source activate py37
# conda-specific packages (~1 min) # conda-specific packages (~1 min)
conda install -y -c rdkit rdkit # Open-Source Cheminformatics Software conda install -y -c rdkit rdkit # Open-Source Cheminformatics Software
conda install -y -c openbabel openbabel # chemical toolbox conda install -y -c openbabel openbabel # chemical toolbox
conda install -y mkl-service # change the number of CPU’s MKL is using conda install -y mkl-service # change the number of CPU’s MKL is using
conda install -y anaconda-client # client that provides an interface to Anaconda Cloud conda install -y anaconda-client # client that provides an interface to Anaconda Cloud
conda install -y -c conda-forge hdbscan # clustering conda install -y -c conda-forge hdbscan # clustering
conda install -y -c efelix fpsim2 # fast compound similarity searches (used in TargetMate) conda install -y -c efelix fpsim2 # fast compound similarity searches (used in TargetMate)
conda install -y -c anaconda ipython # interactive python
conda install -y -c conda-forge jupyterlab # Jupyter notebooks conda install -y -c conda-forge jupyterlab # Jupyter notebooks
conda install -y -c anaconda ipython">7.19" # interactive python
conda install -y -c anaconda cython # C extensions
conda install -y -c pytorch faiss-cpu # efficient similarity search and clustering
# utility packages (~2 min) # utility packages (~2 min)
pip install six # py2/py3 compatibility pip install six # py2/py3 compatibility
...@@ -104,15 +105,13 @@ From: centos:8 ...@@ -104,15 +105,13 @@ From: centos:8
pip install tensorflow==2.3.1 # neural network library pip install tensorflow==2.3.1 # neural network library
pip install adanet # automl for NN pip install adanet # automl for NN
pip install keras # NN API pip install keras # NN API
pip install faiss-cpu # efficient similarity search and clustering
# numerical packages # numerical packages
pip install cython # C extensions
pip install numpy # best numerical library ever pip install numpy # best numerical library ever
pip install pandas # handles table-like datastracture pip install pandas # handles table-like datastracture
pip install openpyxl # open xlsx
pip install scipy # scientific python pip install scipy # scientific python
pip install theano # Optimize evaluate math expressions pip install theano # Optimize evaluate math expressions
pip install h5py==2.10.0 # HDF5 via python, the version <3 tries to avoid a bug due to original_keras_version = f.attrs['keras_version'].decode('utf8')
pip install fancyimpute # matrix completion and imputation algorithms pip install fancyimpute # matrix completion and imputation algorithms
pip install protobuf # Google serialization library pip install protobuf # Google serialization library
...@@ -132,7 +131,3 @@ From: centos:8 ...@@ -132,7 +131,3 @@ From: centos:8
# Clone the chemical checker package (used as fallback) # Clone the chemical checker package (used as fallback)
cd /opt cd /opt
git clone http://gitlabsbnb.irbbarcelona.org/packages/chemical_checker.git git clone http://gitlabsbnb.irbbarcelona.org/packages/chemical_checker.git
# FIXES
# fix numpy version issue
conda install -y -c pytorch faiss-cpu
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