00_set_up_3.md

Set up conda environment on the RSB Wright server

1. Add conda channels and set priorities

conda config --prepend channels conda-forge
conda config --prepend channels bioconda 

conda config --show channels

The correct output should look like:

channels:
  - conda-forge
  - bioconda
  - defaults

2. Create a conda environment

conda create -n ecoli-vc

3. Install packages

conda activate ecoli-vc

conda install -c bioconda fastqc
conda install -c bioconda trimmomatic
conda install -c bioconda bwa
conda install -c bioconda samtools=1.9
conda install -c bioconda bcftools=1.9

4. Test if the packages are working

fastqc -h
trimmomatic
bwa
samtools
bcftools