safe_projects

Project management with git

Configuration

Create a file named ~/.projects with the path where you'd like your repositories to be stored. This should ideally be a location that is backed up regularly.

vim ~/.projects

An example file looks like this:

export REPOSITORY_ROOT=/net/eichler/vol4/home/jlhudd/projects/repositories

Clone safe projects code and add scripts to $PATH.

mkdir -p ~/src
cd ~/src
git clone https://github.com/huddlej/safe_projects.git
PATH=$PATH:$HOME/src/safe_projects
export PATH

Usage

Create a new project.

create_project.sh 2015-05-23-analyze_copy_number_distributions

Change into new project directory.

cd 2015-05-23-analyze_copy_number_distributions

Add environmental configuration to config.sh. Add rules for your analyses to Snakefile. Add configuration parameters for snakemake to config.json.

Run your analysis.

snakemake

Add your changes to the repository and commit them.

git add Snakefile config.json config.sh
git commit -m "added initial rules and configuration"

Save your changes to the repository root (i.e., your backed up path from the configuration section above).

git push origin master

If your current working directory is already a git repository without a remote, you can quickly initialize a remote repository and push all your changes there by running the following command from the top-level of the working directory.

initialize_project.sh