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.
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.
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.
Kitematic users can launch the container directly from its interface.
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 runstarts the Image/ContainerIn case the Container is not already stored locally, docker downloads it automatically
-
The argument
-p 8080:80makes the port 80 (inside of the container) available on port 8080 on your hostInside 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:8080immediately after executing the command above -
-dwill start the docker container in Daemon mode. -
quay.io/valentinmarcon/docker-galaxy-sniplayis the Image/Container name.
You need to build and start the Docker image.
Build:
$ cd docker-galaxy-sniplay
$ docker build -t galaxy-sniplay .
-
docker buildcreate an image of the container from the Dockerfile recipe of the repository -
galaxy-sniplayis 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 .
The Galaxy Admin User has the username [email protected] 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.
In this section we list all tools that have been integrated in the Sniplay container.
| 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 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 |
| 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 |
