gatb / gatb-tools-machine

Build a single Docker image containing all GATB-Tools ready to be used. This is an official repository, not a mirror.

GATB-TOOLS and Docker

This document explains how you can setup and use GATB-Tools within a Docker container.

What are GATB-Tools?

GATB-Tools are softwares built upon the GATB-Core Library.

As of June 2017, this projet includes within a single Docker image :

• Simka
• DSK
• BLOOCOO
• MindTheGap
• Minia
• Short Read Connector
• DiscoSNP++
• TakeABreak

About this project

It aims at providing you with the material (i.e. a Dockerfile) to build a single Docker image containing all above mentioned GATB-Tools binaries.

It is worth noting that this Dockerfile packages the latest available binary release of each GATB-Tool as it is available in the respective project. In other words, this Dockerfile DOES NOT compile anything.

Requirements

Of course, you need to have Docker installed on your system.

We also suppose that you are familiar with docker build and docker run commands.

Note: provided Dockerfile was made and tested using Docker version 17 on Mac OSX Yosemite. However, it should work on other releases of Docker and OS (Linux, Windows or OSX).

How to build the image?

Jump to wiki

How to use the image on the command-line?

Jump to wiki

How to use the image on GoDocker?

Read the Wiki

Files

File name	Description
Dockerfile	Production ready material: the main Docker file to use to create the GATB-Tools machine. This is the one cited in above sections.
Dockerfile.alpine	An alternative way to build the GATB-Tools machine, using Alpine Linux instead of Debian. Experimental material: use with caution. Read more here.
Dockerfile.alpine-compiler	Production ready material: an Alpine based c/c++ compiler to prepare Alpine native binaries of GATB-Tools. Read more here.
Dockerfile.alpine2	Production ready material: the Dockerfile to use to create a compact GATB-Tools machine. Read more here.
build.sh	Companion file of Dockerfile.alpine-compiler
make_all.sh	Companion file of Dockerfile.alpine-compiler. Actually, it is the one to use to generate GATB-Tool Alpine binaries: 'make_all.sh' script invokes 'Dockerfile.alpine-compiler' container.
run-tool.sh	Starter script of Docker containers (i.e. ENTRYPOINT)
test-gcore.sh	Companion file of Dockerfile
data	Directory with test material for all GATB-Tools
godocker	Directory with material illustrating how to use GATB-Tools machine on the GoDocker platform.

License

All GATB-Tools and GATB-Core are covered by .