hlbfx-project

A CLI using to manage Haniffa Lab Bioinformatics projects.

Information

• If you are unsure of the steps below please contact vm11 for help setting up the project.
• Only proceed if you are familiar with using the command line, git, and python based installations.

Installation

Usage within farm - No installation needed

Bug: If you have been using hlbfx-projects before 12/12/2025 please go to your ~/.bashrc file and remove any previous hlbfx-projects PATH additions to avoid conflicts.

echo "
# hlbfx-project
export PATH=/software/cellgen/team298/shared/hlbfx-projects/bin/:\$PATH
" >> ~/.bashrc
source ~/.bashrc

Usage outside farm - Install using conda and pip

# Create conda environment per user
conda create -n hlbfx-projects python=3.12 -y
conda activate hlbfx-projects
# Install hlbfx-projects in a common dir for all users
conda create -p /software/cellgen/team298/shared/hlbfx-projects python=3.12 -y
conda activate /software/cellgen/team298/shared/hlbfx-projects
# Install hlbfx-projects in the conda env
git clone git@github.com:haniffalab/hlbfx_project.git
cd hlbfx_project
pip install -e .
# Add hlbfx-projects to your PATH
echo "
# hlbfx-project
export PATH=/software/cellgen/team298/shared/hlbfx-projects/bin/:\$PATH
" >> ~/.bashrc
source ~/.bashrc

Usage

hlbfx-projects --help

Find if your project is already created

hlbfx-projects ls

If project does not exist

hlbfx-projects create <project_name> 

If project exists

hlbfx-projects add <project_name>

Where to find the project

Your projects will be in the nfs team directory /nfs/team298/USERNAME/projects/. Change USERNAME to your username and <project_name> to the name of your project.

cd /nfs/team298/USERNAME/projects/<project_name>