added installer.sh

installer.sh

@@ -0,0 +1,91 @@
+
+# this script installs biogpt requirements.
+# 1- creates virtual enviroment of python3.10 @ ~/venvs/biogpt
+# 2- clone and checkout fairseq v0.12.0 & moses & fastBPE
+# 3- pip install requirements
+
+export ve_name='biogpt'
+export py_version=3.10
+curl bit.ly/cfgvelinux -L | bash
+source ~/venvs/$ve_name/bin/activate
+ve_data_path=$HOME/venvs/$ve_name/data
+ve_code_path=$HOME/venvs/$ve_name/code
+export MOSES=$ve_code_path/mosesdecoder
+export FASTBPE=$ve_code_path/fastBPE
+
+
+mkdir $ve_code_path
+mkdir $ve_data_path
+
+
+cd $ve_code_path
+git clone https://github.com/pytorch/fairseq
+cd fairseq
+git checkout v0.12.0
+pip install .
+python setup.py build_ext --inplace
+
+cd $ve_code_path
+git clone https://github.com/moses-smt/mosesdecoder.git
+
+cd $ve_code_path
+git clone https://github.com/glample/fastBPE.git
+cd fastBPE
+g++ -std=c++11 -pthread -O3 fastBPE/main.cc -IfastBPE -o fast
+pip install .
+
+
+pip install sacremoses
+pip install scikit-learn
+# pip install torch==1.12.0
+
+mkdir $ve_data_path/checkpoints
+cd ~/venvs/biogpt/data/checkpoints
+
+# this downloads all checkpoints, remove as approriate
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/Pre-trained-BioGPT.tgz
+tar -zxvf Pre-trained-BioGPT.tgz
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/Pre-trained-BioGPT-Large.tgz
+tar -zxvf Pre-trained-BioGPT-Large.tgz
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/QA-PubMedQA-BioGPT.tgz
+tar -zxvf QA-PubMedQA-BioGPT.tgz
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/QA-PubMedQA-BioGPT-Large.tgz
+tar -zxvf QA-PubMedQA-BioGPT-Large.tgz
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/RE-BC5CDR-BioGPT.tgz
+tar -zxvf RE-BC5CDR-BioGPT.tgz
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/RE-DDI-BioGPT.tgz
+tar -zxvf RE-DDI-BioGPT.tgz
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/RE-DTI-BioGPT.tgz
+tar -zxvf RE-DTI-BioGPT.tgz
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/DC-HoC-BioGPT.tgz
+tar -zxvf DC-HoC-BioGPT.tgz
+
+
+cat <<EOF > ~/venvs/$ve_name/code/setup_env_var.sh
+export ve_name='biogpt'
+export py_version=3.10
+export ve_data_path=$HOME/venvs/$ve_name/data
+export ve_code_path=$HOME/venvs/$ve_name/code
+export MOSES=$ve_code_path/mosesdecoder
+export FASTBPE=$ve_code_path/fastBPE
+EOF
+
+
+mkdir ~/code || true
+cd ~/code
+git clone https://github.com/microsoft/BioGPT
+cd ./BioGPT
+git pull
+ln -s ~/venvs/$ve_name/data/checkpoints ./checkpoints
+
+
+cat <<EOF > run.sh
+source ~/venvs/biogpt/bin/activate  # activate virtual enviroment.
+source ~/venvs/biogpt/setup_env_var.sh  # declare enviroment variables
+cd ~/code/BioGPT  # head to the repostiroy
+python  # run stuff
+EOF
+
+echo "Done."
+echo "Source run.sh in ~/code/BioGPT then run any of the examples."
+