Working through some Snakemake examples.

charlesreid1 b16c257ad4 Update 'chain/' 3 weeks ago
chain Update 'chain/' 3 weeks ago
misnamed Adding "misnamed" snakemake example 3 weeks ago
.gitignore add gitignore 3 weeks ago
LICENSE Initial commit 3 weeks ago adding on-a-plane readme 3 weeks ago


Working through some Snakemake examples.

Setting up

Start by installing pyenv, and use pyenv to install conda (Miniconda or Anaconda).

Create conda env:

conda env create --name snakemake --file environment.yaml

Activate conda env:

source activate snakemake

The file environment.yaml should contain, at minimum:

  - conda-forge
  - bioconda
  - r
  - defaults
  - graphviz=2.38.0
  - python=3.5.1
  - snakemake=3.11.0
  - pyyaml=3.11


To run snakemake rules, use the snakemake command. Give it an output file, or a rule name:

snakemake file.out

The default name used is Snakefile. To specify a different snakefile, use the -s flag:

snakemake -s mysnakefile file.out