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test_setup.sh
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test_setup.sh
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# Boost dependencies
sudo apt-get update
sudo apt-get install -y libboost-all-dev
# TransSynW dependencies
python -m pip install --upgrade pip
pip install pytest
pip install -r requirements.txt
mkdir ./crgem/dependencies
cd ./crgem/dependencies
touch __init__.py
git clone --depth=1 https://gitlab.lcsb.uni.lu/CBG/transsynw.git transsynw
# Signet dependencies
wget https://github.com/Lan-lab/SIGNET/raw/main/SIGNET_Tutorial/SIGNET.py -O SIGNET.py
cd -
cd ./data
curl -O https://resources.aertslab.org/cistarget/databases/old/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-10kb-10species.mc9nr.feather
cd -
# if the user wants to download the latest data from TRRUST database
# # curl -s 'https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv' >> trrust_rawdata_human.tsv
# echo "Setup completed"