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update DockM8 folder handling
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Tonylac77 committed Jul 22, 2024
1 parent 197f940 commit 7cee8aa
Showing 1 changed file with 8 additions and 13 deletions.
21 changes: 8 additions & 13 deletions setup_py310.sh
Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,9 @@ else
conda deactivate
conda activate $ENV_NAME

conda config --add channels conda-forge bioconda schrodinger
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels schrodinger

conda install rdkit=2023.09 ipykernel scipy spyrmsd kneed scikit-learn-extra molvs seaborn xgboost openbabel docopt chembl_structure_pipeline tqdm pydantic -q -y

Expand Down Expand Up @@ -159,27 +161,20 @@ if [[ -f dockm8.py ]]; then
DOCKM8_FOLDER=$(pwd)
else
if [ $USE_GIT -eq 1 ]; then
# Replace wget logic with Git logic for DockM8 repository download
echo -e "\nDownloading DockM8 repository using Git..."
rm -rf ./DockM8
git clone https://gitlab.com/DrugBud-Suite/DockM8.git -b main DockM8
DOCKM8_FOLDER=$(pwd)/DockM8
echo -e "\nDockM8 repository downloaded using Git."
else
# Use wget logic for DockM8 repository download (as in your original script)
echo -e "\nDownloading DockM8 repository using wget..."
rm -rf ./DockM8
# Fetch the latest release information
LATEST_RELEASE=$(curl -s "https://api.github.com/repos/DrugBud-Suite/DockM8/releases/latest")
# Extract the download URL for the tar.gz file
DOWNLOAD_URL=$(echo "$LATEST_RELEASE" | grep "tarball_url" | cut -d '"' -f 4)
# Download the latest release
wget "$DOWNLOAD_URL" -O DockM8.tar.gz --no-check-certificate -q --show-progress
tar -xf DockM8.tar.gz
mv -f DockM8-main DockM8
mkdir -p DockM8
LATEST_RELEASE=$(curl -s "https://api.github.com/repos/DrugBud-Suite/DockM8/releases/latest")
DOWNLOAD_URL=$(echo "$LATEST_RELEASE" | grep "tarball_url" | cut -d '"' -f 4)
wget "$DOWNLOAD_URL" -O - --no-check-certificate -q --show-progress | tar -xzf - -C DockM8 --strip-components=1
DOCKM8_FOLDER=$(pwd)/DockM8
rm DockM8.tar.gz
echo -e "\nDockM8 repository downloaded using wget."
echo -e "\nDockM8 repository downloaded using wget and extracted."
fi
fi

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