🐳 Galaxy Docker repository for NGS analysis (Galaxy flavour) - this is a base image containing NGS tools for:
- QC
- Pre-processing
- Mapping
- SAM/BAM/BED manipulations
- Transcriptomics tools
Note: For more tools see galaxy-NGSM repo which upgrades more tools on top of this base image.
In folder /config file job_conf.xml is preconfigured for some tools to use multi-core resources - 16CPU (--ntasks=16).
Note: File can be manually installed by user.
At first you need to install docker. Please follow the instruction on https://docs.docker.com/installation/
After the successful installation, all what you need to do is:
docker run -d -p 8080:80 quay.io/vebaev/galaxy-ngs
or alternative (from Docker Hub)
docker run -d -p 8080:80 vebaev/galaxy-ngs
Docker images are "read-only", all your changes inside one session will be 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/vebaev/galaxy-ngs
With 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 config scripts to /export/ and symlink back to the original location. - In case of a non-empty
/export/, for example if you continue a previouse 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 - means real separation of your different projects.
By default, Galaxy instances launched with this image will have on-demand access to approximately 3TB of
reference genomes and indexes. These are the same reference data available on the main Galaxy server.
This is achieved by connecting to Galaxy's CernVM filesystem (CVMFS) at data.galaxyproject.org repository,
which is geographically distributed among numerous servers.
The CVMFS capability doesn't add to the size of the Docker image, but when running, CVMFS maintains
a cache to keep the most recently used data on the local disk.
Note: If you want to use on-demand the CVMFS reference genomes and indexes, you must launch Docker as --privileged
The Galaxy Admin User has the username admin@galaxy.org and the password admin.
The PostgreSQL username is galaxy, the password is galaxy and the database name is galaxy (I know I was really creative ;)).
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.
Many thanks Saskia Hiltemann! and of course Björn Grüning for the Galaxy-Docker!
Vesselin Baev vebaev@plantgene.eu, University of Plovdiv. BG
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