Cyriac Kandoth ckandoth

On a Linux VM or Workstation with docker installed, fetch the GRCh38 FASTA, its index, and a pair of FASTQs:

wget -P /hot/ref https://storage.googleapis.com/genomics-public-data/references/GRCh38_Verily/GRCh38_Verily_v1.genome.fa{,.fai}
wget -P /hot/reads/test https://storage.googleapis.com/data.cyri.ac/test_L001_R{1,2}_001.fastq.gz

If on a Slurm cluster, here is an example of wrapping a docker run command in an sbatch request:

sbatch --chdir=/hot --output=ref/std.out --error=ref/std.err --nodes=1 --ntasks-per-node=1 --cpus-per-task=8 --mem=30G --time=4:00:00 --wrap="docker run --help"

Use apt to install the necessary packages:

sudo apt install -y slurm-wlm slurm-wlm-doc

Load file:///usr/share/doc/slurm-wlm/html/configurator.html in a browser (or file://wsl%24/Ubuntu/usr/share/doc/slurm-wlm/html/configurator.html on WSL2), and:

Set your machine's hostname in SlurmctldHost and NodeName.
Set CPUs as appropriate, and optionally Sockets, CoresPerSocket, and ThreadsPerCore. Use command lscpu to find what you have.
Set RealMemory to the number of megabytes you want to allocate to Slurm jobs,
Set StateSaveLocation to /var/spool/slurm-llnl.
Set ProctrackType to linuxproc because processes are less likely to escape Slurm control on a single machine config.

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

Instead of the official instructions, we will use conda to install VEP and its dependencies. If you don't already have conda, install it into $HOME/miniconda3 as follows:

curl -sL https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh -o /tmp/miniconda.sh
sh /tmp/miniconda.sh -bfp $HOME/miniconda3

Add the conda bin folder into your $PATH so that all installed tools are accessible via command-line. You can also add this to your ~/.bashrc

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'

sudo yum install -y git ncurses-devel

	# GOAL: Create test data for CI/CD of a germline variant calling pipeline (FASTQ to gVCF)

	# Steps below were performed on Ubuntu 24.04, but should be reproducible on any Linux distro

	# Download and install micromamba under your home directory and logout:
	"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

	# Log back in to add micromamba to your $PATH, and then use it to install the tools we need:
	micromamba create -y -n bio -c conda-forge -c bioconda htslib==1.21 samtools==1.21 bcftools==1.21 picard-slim==3.3.0
	micromamba activate bio

	# To follow these instructions, we'll assume your system admins have already installed these essentials:
	# Debian/Ubuntu system admins should run:
	sudo apt-get install -y build-essential libexpat1-dev libssl-dev libmysqlclient-dev libxml2-dev
	# RHEL/CentOS system admins should run:
	sudo yum groupinstall -y 'Development Tools'
	sudo yum install -y expat-devel openssl-devel mysql-devel libxml2-devel

	# Create a folder where you want to install different Perls, and cd into it:
	# Note that it doesn't need to be your home folder. Put it wherever you want to maintain such software:
	export PERL_BASE="$HOME/perl"

	# Create a folder where you want to install different Pythons, and cd into it:
	# Note that it doesn't need to be your home folder. Put it wherever you want to maintain such software:
	export PYTHON_BASE="$HOME/python"
	mkdir -p $PYTHON_BASE
	cd $PYTHON_BASE

	# Download source tarball into a subfolder named src, and untar:
	curl --create-dirs -L -o src/Python-2.7.10.tgz https://www.python.org/ftp/python/2.7.10/Python-2.7.10.tgz
	cd src
	tar -zxf Python-2.7.10.tgz