Snakemake/DahakFlot

Main repository:

• https://charlesreid1.com:3000/dotfiles/dahak-flot
• https://github.com/charlesreid1/dahak-flot

Start

This tutorial is assuming you start out on a machine with a conda-based python distribution (Anaconda or Miniconda or other).

Installing Conda with Pyenv

If you don't have a version of conda, it is recommended you use Pyenv to manage versions of python.

A very simple pyenv installation script:

install_pyenv.py

#!/usr/bin/python3
import getpass
import subprocess


def install_pyenv():
    user = getpass.getuser()
    if(user=="root"):
        raise Exception("You are root - you should run this script as a normal user.")
    else:
        # Install pyenv 
        pyenvcmd = ["curl","-L","https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer","|","/bin/bash"]
        subprocess.call(pyenvcmd, shell=True)

        # We don't need to add ~/.pyenv/bin to $PATH,
        # it is already done.

if __name__=="__main__":
    install_pyenv()

As noted in the script, you will need to add ~/.pyenv/bin to the path, as that is where the Pyenv versions of Python live.

Next, we have a python script to install snakemake:

#!/usr/bin/python3
import getpass
import tempfile
import subprocess


def install_pyenv():
    user = getpass.getuser()
    if(user=="root"):
        raise Exception("You are root - you should run this script as a normal user.")
    else:
        # Install snakemake
        conda_version = "miniconda3-4.3.30"

        installcmd = ["pyenv","install",conda_version]
        subprocess.call(installcmd)
        
        globalcmd = ["pyenv","global",conda_version]
        subprocess.call(globalcmd)

        # ---------------------------
        # Install snakemake

        pyenvbin = os.environ['HOME']
        condabin = pyenvbin+"/.pyenv/shims/conda"

        subprocess.call([condabin,"update"])

        subprocess.call([condabin,"config","--all","channels","r"])
        subprocess.call([condabin,"config","--all","channels","default"])
        subprocess.call([condabin,"config","--all","channels","conda-forge"])
        subprocess.call([condabin,"config","--all","channels","bioconda"])

        subprocess.call([condabin,"install","--yes","-c","bioconda","snakemake"])

        # ---------------------------
        # Install osf cli client
        
        pyenvbin = os.environ['HOME']
        pipbin = pyenvbin+"/.pyenv/shims/pip"

        subprocess.call([pipbin,"install","--upgrade","pip"])
        subprocess.call([pipbin,"install","--user","osfclient"])


if __name__=="__main__":
    install_pyenv()

Get Tutorial Files

Start by getting the files needed for the tutorial:

wget https://bitbucket.org/snakemake/snakemake-tutorial/get/v3.11.0.tar.bz2
tar -xf v3.11.0.tar.bz2 --strip 1

First Snakefile

Create a Snakefile, and add the first rule:

rule bwa_map:
    input:
        "data/genome.fa",
        "data/samples/{sample}.fastq"
    output:
        "mapped_reads/{sample}.bam"
    shell:
        "bwa mem {input} | samtools view -Sb - > {output}"

This creates a folder with data in it, and an environment.yaml file for conda.

Create the conda environment:

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

Now activate the conda environment:

source activate snakemake-tutorial