#!/bin/bash
THISDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

####################################################### Dependencies ##############################################################
sudo apt install -y unzip clang-7 cmake automake python3-dev libboost-program-options-dev libboost-filesystem-dev openjdk-11-jre libgsl23
sudo update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-7 100
sudo update-alternatives --install /usr/bin/clang clang /usr/bin/clang-7 100

# CPLEX: only to build biorseo, or needed at runtime ?
wget --no-check-certificate -O cplex_installer_12.8_Student.bin "https://onedrive.live.com/download?cid=C9F6894F7941BBFB&resid=C9F6894F7941BBFB%21416367&authkey=AC-d-946knh0Yo0"
chmod +x cplex_installer_12.8_Student.bin
printf "4\n\n1\n\n\n\n\n" | sudo ./cplex_installer_12.8_Student.bin

# Eigen: only to build biorseo (no need to give it to the docker image)
wget http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz -O eigen_src.tar.gz
tar -xf eigen_src.tar.gz
cd eigen-eigen-323c052e1731
mkdir build
cd build
cmake ..
sudo make install
cd ../..
rm -r eigen_src.tar.gz 

# ViennaRNA: needed for runtime. Build here on host, install later in image by the Dockerfile.
wget "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.13.tar.gz"
tar -zxvf ViennaRNA-2.4.13.tar.gz
cd ViennaRNA-2.4.13
./configure 
make -j 4 
cd ..
rm ViennaRNA-2.4.13.tar.gz

# Nupack: only to build biorseo (no need to give it to the docker image)
curl -u louis.becquey@univ-evry.fr:tQm03G29 http://www.nupack.org/downloads/serve_file/nupack3.2.2.tar.gz --output nupack3.2.2.tar.gz
tar -xf nupack3.2.2.tar.gz
cd nupack3.2.2
mkdir build
cd build
cmake ..
make -j4
sudo make install
cd ../..
rm nupack3.2.2.tar.gz
sudo cp nupack3.2.2/src/thermo/*.h /usr/local/include/nupack/thermo/

# BayesPairing: install on both the host (were we will train the models later) and the docker image (done by the Dockerfile)
sudo -H pip3 install --upgrade pip
sudo -H pip3 install networkx numpy regex wrapt biopython
git clone http://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing.git BayesPairing
cd BayesPairing
sudo -H pip3 install .
cd ..


######################################################### Build Biorseo ###########################################################
# build here, install later on the docker image (done by the Dockerfile)
git clone https://github.com/persalteas/biorseo.git
cd biorseo
mkdir -p results
make -j 4
make clean
cd ..

######################################################## RNA modules ##############################################################

# Rna3Dmotifs data
mkdir -p modules/DESC
wget https://github.com/McGill-CSB/RNAMoIP/raw/master/CATALOGUE.tgz
tar -xvzf CATALOGUE.tgz 
mv No_Redondance_DESC/*.desc modules/DESC/
rm -r No_Redondance_VIEW3D No_Redondance_DESC CATALOGUE.tgz

# The RNA 3D Motif Atlas
mkdir -p modules/BGSU
wget http://rna.bgsu.edu/data/jar3d/models/HL/HL_3.2_models.zip
unzip HL_3.2_models.zip
mv HL modules/BGSU
rm HL_3.2_models.zip
wget http://rna.bgsu.edu/data/jar3d/models/IL/IL_3.2_models.zip
unzip IL_3.2_models.zip
mv IL modules/BGSU
rm IL_3.2_models.zip

######################################################## Build Docker container ##################################################
# Execute the Dockerfile
docker build -t biorseo

# Train Bayes Pairing (it has been installed on the image and the source has been deleted, we train the models now, and will remount it as volume at run time)
cd BayesPairing/bayespairing/src
python3 parse_sequences.py -d rna3dmotif -seq ACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU -ss ".................................................................((...............)xxxx(...................................................)xxx).............."
python3 parse_sequences.py -d 3dmotifatlas -seq ACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU -ss ".................................................................((...............)xxxx(...................................................)xxx).............."
cd ../../..

# run it
# docker run -v `pwd`/modules:/modules -v `pwd`/BayesPairing/bayespairing:/byp -v `pwd`/results:/biorseo/results biorseo ls /byp/models


########################################################### More stuff ###########################################################

# # BiokoP
# mkdir biokop
# cd biokop
# wget --no-check-certificate "https://tanuki.ibisc.univ-evry.fr/media/filer_public/b5/ea/b5eadd8b-ebc6-49f7-821e-b1e30137cc21/biokop.tar"
# tar -xvf biokop.tar
# rm biokop.tar
# cd ..

# # RNA examples
# mkdir data
# echo ">__'CRYSTAL_STRUCTURE_OF_A_TIGHT-BINDING_GLUTAMINE_TRNA_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00376)" > data/tRNA.fa
# echo "GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA" >> data/tRNA.fa
# echo ">__'GUANINE_RIBOSWITCH_U22C,_A52G_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01023)" > data/Griboswitch.fa
# echo "GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCA" >> data/Griboswitch.fa
# echo ">__'SOLUTION_STRUCTURE_OF_THE_P2B-P3_PSEUDOKNOT_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00857)" > data/pseudoknot.fa
# echo "GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA" >> data/pseudoknot.fa
# mv biokop/PKB120.fasta data/