before_week3_setup.md

Build the conda environment

We'll explain more details on building a conda environment in the workshop. For now, follow instructions below to build the environment.

Create the conda environment

conda create --name intro-to-linux 

Type "y" and press enter to proceed.

Activate the conda environment

conda activate intro-to-linux

Make sure you have the environment name at the beginning of your command line, then proceed to the install software part.

Install the needed software

Run the following commands line by line:

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

To validate the software are installed successfully

We can test if a software was successfully installed by calling the help document of the software or calling out the software:

fastqc -h
trimmomatic -h 
bwa # bwa is not set up for the -h option for printing the help document 
samtools # samtools is not set up for the -h option for printing the help document 
bcftools -h 

Copy the data files to your own directory

Run the following commands line by line:

mkdir -p ~/intro_to_linux/data/untrimmed_fastq
cd ~/intro_to_linux/data/untrimmed_fastq
cp /home/u1133824/data/*.gz .