Pirus_PipeGatkSnpIndels

The gatk pipe for snp/indels (using haplotypecaller) implementation for Pirus This pipeline is not yet stable and is still being worked on.

How to use it in a Pirus container

Requirement

• You need LXD on your computer to create it
• You should read the official doc of Pirus and LXD (be sure that the LXD bridge is well configured. Your container will need to access to internet).

Instructions

# create a container
lxc launch images:ubuntu/xenial GatkHaplotypeCaller
# configure it
lxc exec GatkHaplotypeCaller -- /bin/bash

# following directories are mandatory
mkdir -p /pipeline/{inputs,outputs,logs,db,conda}

# need curl if you want to notify server with the progress of your run
apt update
apt install wget curl jq nano git --fix-missing  # optional : graphviz (if you need to draw snakemake graph)

# Install miniconda3
cd /pipeline/conda
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
# Proceed to the installation ("yes" and default option everywhere)
./Miniconda3-latest-Linux-x86_64.sh

# Set the conda environment for the pipe
git clone https://github.com/REGOVAR/Pirus_PipeGatkSnpIndels.git
cd Pirus_PipeGatkSnpIndels
/root/miniconda3/bin/conda env create -n gatk_snp_indels -f environment.yml

# Activate GATK with your license (free)
# 1 : Create/Login your account on their website : https://software.broadinstitute.org/gatk/download/licensing.php
# 2 : Choose in the download section the license you need and download 
# 3 : save the tar.bz2 from the website on your computer (by example in /tmp/ forlder)
# 4 : put the file into the container
# exit the container. The next command shall be run from the host
exit 
lxc file push /var/tmp/GenomeAnalysisTK-3.7.tar.bz2 GatkHaplotypeCaller/pipeline/conda/
lxc exec GatkHaplotypeCaller -- /bin/bash
cd /pipeline/conda
# 5 : activate the conda environment
source activate gatk_snp_indels
# 6 : activate the license
gatk-register GenomeAnalysisTK-3.7.tar.bz2

# exit the container
exit

# stop it and create an image
lxc stop GatkHaplotypeCaller
lxc publish GatkHaplotypeCaller --alias=PirusGatkHaplotypeCaller

lxc image export PirusGatkHaplotypeCaller

# following command must be done as root to avoid image corruption 
# (as it will try to create symlink to computer resource in /dev folder by example)
sudo tar xf <the_name_of_lxc_export_something_like_a8d44d24fcs...8fzef54e5>.tar.gz

# append folowing informations into the metadata.yaml file (/!\ don't forget the "," in json dictionnary)
sudo nano metadata.yaml

# if json
"pirus":
{
    "name" : "Gatk HaplotypeCaller",
    "description" : "The GATK haplotypecaller pipeline for SNP and Indels.",
    "version": "1.0.0",
    "pirus_api": "1.0.0",
    "license" : "AGPLv3",
    "developers" : ["Anne-Sophie DENOMME-PICHON", "Jérémie ROQUET", "Olivier GUEUDELOT", "Sacha SCHUTZ"],
    "run" : "/pipeline/conda/Pirus_PipeGatkSnpIndels/run.sh",
    "inputs" : "/pipeline/inputs",
    "outputs" : "/pipeline/outputs",
    "databases" : "/pipeline/db",
    "logs" : "/pipeline/logs",
    "form" : "/pipeline/conda/Pirus_PipeGatkSnpIndels/form.json",
    "icon" : "/pipeline/conda/Pirus_PipeGatkSnpIndels/gatk-logo.png"
}

# Repackage the image in tar.xz
sudo tar cfJ PirusGatkHaplotypeCaller.tar.xz metadata.yaml rootfs templates
sudo rm -fr metadata.yaml rootfs templates
sudo chown $USER:$USER PirusGatkHaplotypeCaller.tar.xz