Conda and snakemake for reproducible command line

This compiles my notes for conda and snakemake.

conda command

update conda environment from yaml

source activate myenv
conda env update --file environment.yaml

snakemake notes

Snakemake is a fantastic tool to keep the running environment constant, document data processing and reproduce the analysis when necessary. I think it currently lacks the functionality of recording down the thought process behind each data processing decision, but perhaps that can be left as comments in the file and finally documented somewhere else.

use directory as output


use mutliple files as input

Refer to here. Basically one needs to extend both the input and output file names for the function to work.

no-rule error

Sometimes no-rule error can be caused because a similar rule has been executed. Use -R rule_name to resolve this issue.

Timing Liu
Computational Biologist & Medical Student

Personalizing medicine