Commit 28db8a6e authored by Martino Bertoni's avatar Martino Bertoni 🌋
Browse files

integrating TargeMate dependencies

parent debac366
Pipeline #2546 passed with stages
in 53 minutes and 11 seconds
......@@ -109,7 +109,7 @@ faiss.Kmeans(10, 20).train(numpy.random.rand(1000, 10).astype(numpy.float32))"'
# ML packages
pip install scikit-learn # entry level ML in python
pip install gensim==4.0.1 # topic modelling word2vec
pip install gensim # topic modelling word2vec
if ! test_faiss; then printf -- "\033[31m ERROR: faiss is failing! \033[0m\n"; else printf -- '\033[32m SUCCESS: faiss is working correctly. \033[0m\n'; fi
pip install tensorflow==2.5 # neural network library
if ! test_faiss; then printf -- "\033[31m ERROR: faiss is failing! \033[0m\n"; else printf -- '\033[32m SUCCESS: faiss is working correctly. \033[0m\n'; fi
......@@ -148,13 +148,13 @@ faiss.Kmeans(10, 20).train(numpy.random.rand(1000, 10).astype(numpy.float32))"'
pip install xgboost # Gradient Boosting framework
pip install hyperopt # Hyperparameters optimization
pip install shap # SHapley Additive exPlanations for ML models
pip install pyrfr # Python interface to RFR, an extensible C++ library for random forests
pip install auto-sklearn # Automated machine learning toolkit
pip install signaturizer # ChemicalChecker Signaturizer
# integration of D1
pip install git+git://github.com/Maayanlab/geode.git # Python implementation of the R package GeoDE
# in case some package changed numpy version, we really want this one
pip install numpy==1.19.2
conda install -y mkl-service
# Clone the chemical checker package (used as fallback)
cd /opt
......
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