Enviroment installation

Command line preparation enviroment for our tutorial.

General installation configuration our machines

INTRODUCTION

All the softwares are already installed on your virtual machine. If you need assistance please let me know. You can install in your PC follow this tutorial

Setting up Anaconda

Anaconda is an environment and package manager for Python and it makes installation, environment management, etc. simple without requiring root or administrator privileges. Fortunately, its framework has been leveraged for a project called bioconda that extends these capabailities to external programs as well. All of the packages and programs we’re using today can easily be installed with Anaconda/bioconda with the following steps:

• First, install Miniconda version 3.5 available here. During installation, be sure to allow miniconda to append to your .bashrc or .bash_profile (this will add it and all programs it installs to your PATH). If installation goes well, the command which python should result in something like /Users/<yourusername>/anaconda/bin/python or /home/<yourusername>/anaconda/bin/python

• Add bioconda channels to conda with the following commands:

    conda config --add channels r
    conda config --add channels conda-forge
    conda config --add channels bioconda
  

• Create the environment we’ll be working in and install required packages with the command:

        conda create --name NGSBASE python=3.6 snakemake fastqc bwa samtools picard freebayes bcftools snpsift
  

  or

     git clone https://github.com/bioinfo-dirty-jobs/Data
     cd Data
     conda env create -f ngsbase.yml
  

• Load the new environment and add the samblaster package

    source activate NGSBASE
    conda install -c biobuilds samblaster
  

This will create a working environment called NGSBASE containing python 3.6 (python 3 is required for snakemake) and all of the tools listed in the command. You can see the full list of programs available through bioconda listed here and the full list of python packages available through Anaconda listed here.

If you want to load our new environment, you can do so with the command:

    source activate NGSBASE

and leave the environment with the command:

    source deactivate
    

If you’re in your environment, you can easily add additional programs (like we did for multiqc) and packages with the command:

    conda install <program/package name>

For example, if we also want to take a look at Bowtie2, another read mapper (we’ll use bwa today), we can easily add it by entering our environment source activate NGSBASE and typing conda install bowtie2

VMWARE

Please install VMWARE PLAYER Run the machine and modify the configurations for you PC.