First check you have root priviliges
- Then install wget, but in most cases use sudo yum install
- Check python version, mostly comes with python2.7
- To install python3 - https://linuxize.com/post/how-to-install-python-3-on-centos-7/
- sudo yum install centos-release-scl
- sudo yum install rh-python36
- After typing python --version , if it outputs the latest 3.7 its fine or else type scl enable rh-python36 bash
Install Anaconda - https://linuxize.com/post/how-to-install-anaconda-on-centos-7/
- conda config --add channels bioconda
- conda config --add channels conda-forge
- Add at least 2 environmnets python2 and python3
*** Always insatll conda environment in the following as recommended by Bioconda
https://bioconda.github.io/#set-up-channels
Install R - https://linuxize.com/post/how-to-install-r-on-centos-7/
- sudo yum install epel-release
- sudo yum install R
- R --version
** Setting up WGS/WES pipeline requiremnets
- Conda Install the following tools-
- Bwa-mem
- GATK ** Download a licensed copy of GATK from the Broad Institute(https://www.broadinstitute.org/gatk/download/ (in my case GATK 3.8 from Archives) gatk3-register GenomeAnalysisTK.jar file
- Picard tools
- Samtools ** Got an error "samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory" conda install -c bioconda r-rcurl openssl=1.0
- Platypus
- Snpeff and Snpsift
- Gemini - flexible framework for exploring genetic variation, popultaion data https://gemini.readthedocs.io/en/latest/index.html# For this however craete a sperate environmnet, like conda create -n gemeini, because its downgrading a lot of other dpeendant packages, which might cause error while running other packages!