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Installation
Grandeur uses containers to manage the tools used in its processes. This simplifies things for the end user (we promise).
Grandeur needs
- nextflow (and nextflow's dependencies such as java and git)
- singularity or docker
Other container managers may also work, but we are not as familiar with those and may not be able to troubleshoot issues.
Nextflow has the most up-to-date installation instructions at https://www.nextflow.io/docs/latest/getstarted.html, but it is something like
wget -qO- https://get.nextflow.io | bash
chmod +x nextflow
Java version 11+ is required for nextflow. More instructions are found here: https://www.java.com/en/download/help/download_options.html
sudo apt-get install openjdk-11-jdk
Docker requires root access and instructions can be found here: https://docs.docker.com/desktop/install/linux-install/
UPHL installed Docker via yum
sudo yum install -y yum-utils
sudo yum-config-manager \
--add-repo \
https://download.docker.com/linux/centos/docker-ce.repo
sudo yum install docker-ce docker-ce-cli containerd.io docker-compose-plugin
sudo systemctl start docker
Don't forget to follow the post-install instructions here: https://docs.docker.com/engine/install/linux-postinstall/
Singularity installation instructions can be found here : https://docs.sylabs.io/guides/3.0/user-guide/installation.html
UPHL installed Singularity via yum
sudo yum update -y && \
sudo yum groupinstall -y 'Development Tools' && \
sudo yum install -y \
openssl-devel \
libuuid-devel \
libseccomp-devel \
wget \
squashfs-tools
nextflow pull UPHL-BioNGS/Grandeur
The end user can also just clone this github repository, and use your local path.
# cloning this repo
git clone https://github.com/UPHL-BioNGS/Grandeur.git
# enabling easy updating
cd Grandeur && git init
# updating Grandeur (while in Grandeur's root directory)
git pull
Nextflow can then run this workflow from the cloned repository.
nextflow run <path to cloned repo>/Grandeur -profile singularity --reads <directory of reads>
-
- amrfinderplus
- bbduk
- blastn
- blobtools_*
- core_genome_evaluation
- circulocov
- datasets_*
- drprg
- elgato
- emmtyper
- fastani
- fastp
- fastqc
- heatcluster
- iqtree2
- kaptive
- kleborate
- kraken2
- mash_*
- mashtree
- mlst
- multiqc
- mykrobe
- panaroo
- pbptyper
- phytreeviz
- plasmidfinder
- prokka
- quast
- seqsero2
- serotypefinder
- shigatyper
- snp_dists
- spades