Astir Manuscript

Setup

1. Clone this repo

Navigate to where you would like to work, e.g. your home directory:

cd ~

then

git clone https://github.com/camlab-bioml/imc-2020.git

2. Branch this repo

cd into the repo

cd imc-2020

git checkout -b [name of your branch]

This is the branch you'll work on and merge back into master. To push your branch to github, call

git push -u origin [name of your branch]

If you want to checkout master again then

git checkout master

The usual git rules apply: do some work, add any new or modified files with git add, then commit your work with git commit -m [commit message here]. Having clear commit messages is important.

3. Setup conda environment

Anaconda or Miniconda should be installed on your machine to activate a conda environment.

You can create the necessary conda environment via

conda create -f envs/imc.yml

which will install all necessary python packages. Make sure you are in the correct directory before running the above command. This can be then loaded via

conda activate imc

Note this needs performed at every startup (or modify your .bashrc file).

If you update your conda environment you can update it for all users via

conda env export > envs/imc.yml

and git commit.

4. Sync raw data

The raw data the pipeline starts at is kept in a data-raw/ directory. This is populated with symbolic links to the raw files that are stored in /home/home/ltri/campbell/share/datasets/. These should never be modified without speaking to Kieran first. To create symbolic links to these and setup your data-raw/ file, run

./setup-galen.sh

5. Check you can run snakemake

You can do a dry run of snakemake via

snakemake -n