Skip to content

Updated fetch_submodules script #67

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bonitavw merged 1 commit into from
Jun 19, 2026
Merged

Updated fetch_submodules script #67

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 9 additions & 0 deletions fetch_submodules.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ PAVIAN_ENV_DIR="$ENVS_DIR/pavian"

mkdir -p "$BASE_DIR/submodules/10x_saturate"
mkdir -p "$BASE_DIR/submodules/GeneExt"
mkdir -p "$BASE_DIR/submodules/pavianCore"
mkdir -p "$ENVS_DIR"

echo "Fetching submodules..."
Expand All @@ -30,6 +31,14 @@ if [ ! -f "$BASE_DIR/submodules/GeneExt/environment.yaml" ]; then
rm -rf /tmp/GeneExt-main /tmp/GeneExt.zip
fi

# PavianCore
if [ ! -f "$BASE_DIR/submodules/pavianCore/exec/install_pavianCoreTools_packges.R" ]; then
echo "Downloading pavianCore..."
curl -L -o /tmp/pavianCore.zip https://github.com/Enthusiasm23/pavianCore/archive/refs/heads/master.zip
unzip -q /tmp/pavianCore.zip -d /tmp
cp -r /tmp/pavianCore-master/* "$BASE_DIR/submodules/pavianCore/"
rm -rf /tmp/pavianCore-master /tmp/pavianCore.zip

echo "Submodules downloaded successfully!"

echo "Setting up Pavian Conda environment..."
Expand Down
Loading