How_to_start_a_new_project.md

This is a high level overview on how to start a new project in the CME lab.

1. Make a new folder

To keep things organized, make a new folder where you'll keep your projects (I use a Projects folder in my home), so if you wanted to name your project something like dna_cg for a coarse-grain DNA project, you would use this command:

mkdir ~/Projects/dna_cg

2. Initialize a git repository

It is never to early to start using git, even if you haven't written any code yet. cd into your project and create a git repository. Using the same example from above:

cd ~/Projects/dna_cg
git init

3. Create and commit your first file

A good first file to create is a "README" file which describes your project. In the early stages of a project you can use the README to keep track of ideas and outline what you want to do. Fire up your favorite text editor and create the README file, vim README.md Now that we've made our README file, lets add it to our git repo.

git add README.md
git commit -m "added README file"

4. Add project to CME lab github team

1. Go to https://github.com/ and click on the + in the upper right then select "New Repository"

2. Set the owner to cmelab, give the repo a name.

3. GitHub will then tell you the commands to run to push the repository to github, they will look something like this

   cd ~/Projects/dna_cg
   git remote add origin git@github.com:cmelab/dna_cg.git
   git push -u origin master
   

5. Set up a conda environment (if project is python based)

It's nice to have a conda environment per project to prevent version conflicts between different software dependencies. You can keep track of your dependencies in a yml file and install them like:

conda env create -f environment.yml