use_multiple_version_python.md

Snakemake on my Mac

Recently, I want to test snakemake for building up a pipeline. It requires python3, but I have python2.x installed.
It seems virtualenv and pyenv are the tools to manage multiple versions of python on the same machine. I tried pyenv on my mac OS.

install pyenv

brew update
brew install pyenv

add if which pyenv > /dev/null; then eval "$(pyenv init -)"; fi to my .zshrc file.

install python

## what version of python are avaiable
pyenv install --list

## install python 3.5
pyenv install 3.5.1

## install python 2.7
pyenv install 2.7.11 

## set global 
pyenv global 3.5.1
pyenv versions
system
  2.7.11
* 3.5.1 (set by /Users/mtang1/.pyenv/version)

## if you want to use python 3.5.1 in the current folder
pyenv local 3.5.1
python --version
3.5.1

## reset to 2.7.11
pyenv local 2.7.11
python --version
2.7.11

install snakemake:

pyenv install miniconda3-3.19.0
pyenv global miniconda3-3.19.0
conda install -c bioconda snakemake

I got an error when evoke snakemake in the terminal:

Traceback (most recent call last): File "/Users/mtang1/.pyenv/versions/miniconda3-3.19.0/bin/snakemake", line 6, in sys.exit(snakemake.main()) File "/Users/mtang1/.pyenv/versions/miniconda3-3.19.0/lib/python3.5/site-packages/snakemake/init.py", line 885, in main parser = get_argument_parser() File "/Users/mtang1/.pyenv/versions/miniconda3-3.19.0/lib/python3.5/site-packages/snakemake/init.py", line 494, in get_argument_parser const=available_cpu_count(), File "/Users/mtang1/.pyenv/versions/miniconda3-3.19.0/lib/python3.5/site-packages/snakemake/utils.py",

I have to add import multiprocessing in the utils.py to avoid that. The issue was fixed in the new release.

Snakemake on HPC

Samir has installed snakemake on nautilus using anaconda and set up the virtual environment by virtualenv. To activate it:

source activate Rconda

To inactivate it

source deactivate

visualize snakemake workflow

## this will install dot 
brew install graphviz

snakemake --dag | dot | display