SNP analysis Workflows on Docker

This container present three workflows:

• SNiPlay3 complete workflow: a package for exploration and large scale analyses of SNP polymorphisms (filtering, SNP density, diversity, linkagedisequilibrium) (Dereeper et al, 2015)
• Haplotype analysis workflow
• SNiPlay3 GWAS workflow: Tassel-based GWAS workflow (GLM model) including population structure and correction for structure (Dereeper et al, 2015)

This documentation is mostly inspired by the galaxy-rna-workbench documentation hosted by Björn Grüning.

• Usage
  • Requirement
  • Container launch
  • Users and passwords
• Available tools
  • Tools
  • Workflow
• Contributors

Usage

This Sniplay container implements a webserver based on the Galaxy Docker platform: a dedicated Galaxy instance wrapped in a Docker container. For advanced local deployments, we recommend to check out the upstream documentation.

▲ back to top

Requirement

To use the Sniplay container, you only need Docker, which can be installed in different ways, depending on the type of system you're running:

• non-linux users are encouraged to use Kitematic, which provides a Docker installation for OSX or Windows, coupled with a user friendly interface to run Docker containers;
• linux users and people familiar with the command line can follow the instruction on installing Docker from its website.

▲ back to top

Container launch

Using Kitematic

Kitematic users can launch the container directly from its interface.

Without Kitematic

With the Quay.io image

The docker-galaxy-sniplay images is hosted in Quay.io, a container hosting company

You just need to start the Docker image:

$ docker run -p 8080:80 quay.io/valentinmarcon/docker-galaxy-sniplay

• docker run starts the Image/Container

  In case the Container is not already stored locally, docker downloads it automatically

• The argument -p 8080:80 makes the port 80 (inside of the container) available on port 8080 on your host

  Inside the container a Apache web server is running on port 80 and that port can be bound to a local port on your host computer. With this parameter you can access your Galaxy instance via http://localhost:8080 immediately after executing the command above

• -d will start the docker container in Daemon mode.

• quay.io/valentinmarcon/docker-galaxy-sniplay is the Image/Container name.

With the Dockerfile recipe of this repository

You need to build and start the Docker image.

Build:

$ cd docker-galaxy-sniplay
$ docker build -t galaxy-sniplay .

• docker build create an image of the container from the Dockerfile recipe of the repository

• galaxy-sniplay is the Image/Container name.

Start:

$ docker run -d -p 8080:80 galaxy-sniplay

---

For an interactive session, one executes:

$ docker run -i -t -p 8080:80 quay.io/valentinmarcon/docker-galaxy-sniplay /bin/bash

and manually invokes the startup script to start PostgreSQL, Apache and Galaxy.

A detailed discussion of Docker's parameters is given in the Docker manual.

Docker images are "read-only". All changes during one session are lost after restart. This mode is useful to present Galaxy to your colleagues or to run workshops with it.

To install Tool Shed repositories or to save your data, you need to export the calculated data to the host computer. Fortunately, this is as easy as:

$ docker run -d -p 8080:80 -v /home/user/galaxy_storage/:/export/ quay.io/valentinmarcon/docker-galaxy-sniplay

Given the additional -v /home/user/galaxy_storage/:/export/ parameter, docker will mount the folder /home/user/galaxy_storage into the Container under /export/. A startup.sh script, that is usually starting Apache, PostgreSQL and Galaxy, will recognize the export directory with one of the following outcomes:

• In case of an empty /export/ directory, it will move the PostgreSQL database, the Galaxy database directory, Shed Tools and Tool Dependencies and various configure scripts to /export/ and symlink back to the original location.
• In case of a non-empty /export/, for example if you continue a previous session within the same folder, nothing will be moved, but the symlinks will be created.

This enables you to have different export folders for different sessions - meaning real separation of your different projects.

It will start the Sniplay container with the configuration and launch of a Galaxy instance and its population with the needed tools. The instance will be accessible at http://localhost:8080.

For a more specific configuration, you can have a look at the documentation of the Galaxy Docker Image by Björn A. Grüning .

▲ back to top

Users and passwords

The Galaxy Admin User has the username admin@galaxy.org and the password admin. In order to use the Workflow one has to be logged in. Also the installation of additional tools requires a login.

The PostgreSQL username is galaxy, the password galaxy and the database name galaxy.

If you want to create new users, please make sure to use the /export/ volume. Otherwise your user will be removed after your docker session is finished.

▲ back to top

Available tools

In this section we list all tools that have been integrated in the Sniplay container.

Tools

Tool	Description	Owner
FastME	A distance based phylogeny reconstruction algorithm	dereeper
MLMM	Multi-Locus Mixed-Model (MLMM) for GWAS analysis	dereeper
PLINK	Filter large VCF genotyping file	dereeper
Readseq	Convert various alignment formats	dereeper
sNMF	Fast and efficient program for estimating individual ancestry coefficients	dereeper
SnpEff	SNP annotation : coding/non-coding, synonymous/non-synonymous	dereeper
SnpSift Filter	Filter variants using arbitrary expressions (from Pablo Cingolani)	iuc
Tassel	Evaluate traits associations, evolutionary patterns, and linkage disequilibrium	dereeper
VCFtools Filter,Stats,Diversity	Subset of VCFtools fonctionalities : Filtering, Statistics, Diversity (slidingWindow)	dereeper
beagle	Performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection	dereeper
haplophyle	Create haplotype network from haplotype sequences	dereeper
cytoscape	Visualize interaction networks from JSON file	dereeper
Sniplay	SNiPlay3: a package for exploration and large scale analyses of SNP polymorphisms (filtering, density, vcftools, diversity, linkagedisequilibrium, GWAS) (does not include external tools) > See below <	dereeper

Sniplay

Sniplay is a package of 11 tools:

Tool	Description
SNP density	Calculate SNP densities along chromosome from a VCF input
Rooting	Midpoint rooting of newick tree
Diversity by gene	Calculates various diversity indexes with EggLib
HapmaptoMLMMFiles	Converts a hapmap file into MLMM input files
Get Haplotypes From Phased VCF	Get Haplotypes From Phased VCF
Ped2Fasta	Convert PED file to Fasta File
PLINK: ped2bed	Convert ped to bed
Get VCF annotation statistics	Get annotation fromi a VCF file annotated by snpeff
Check GWAS Inputs	Checks concordance between input files for GWAS analysis
VCF to Hapmap	Convert VCF to Hapmap
PLINK: MDS plot	IBS matrix / multi-dimensional scaling

▲ back to top

Workflows

Name	Description
sniplay3_complete_workflow	SNiPlay3 complete workflow: a package for exploration and large scale analyses of SNP polymorphisms (filtering, density, vcftools, diversity, linkagedisequilibrium, GWAS) (all SNiPlay3 components)

Name	Description
haplotype_analysis_workflow	Haplotype analysis workflow

Name	Description
sniplay3_gwas_analysis_workflow	SNiPlay3 GWAS workflow

▲ back to top

Contributors

• Valentin Marcon
• Alexis Dereeper

▲ back to top