bgruening / docker-galaxy-ngs-preprocessing

:whale::bar_chart::books: Docker Images for NGS data preprocessing

Galaxy Workbench for NGS-preprocessing

🐳 Galaxy Docker repository for preprocessing of NGS data

Installed tools

• Bowtie2
• FASTQC
• deepTools
• BWA
• Bowtie2

Requirements

• Docker for Linux / Windows / OSX
• Kitematic for Windows / OS-X (Optional)

Usage

To launch:

docker run -i -t -p 8080:80 bgruening/galaxy-ngs-preprocessing

For more details about this command line or specific usage, please consult the README of the main Galaxy Docker image, on which the current image is based.

Contributers

• Bjoern Gruening
• Bérénice Batut

History

• 0.1: Initial release!

Support & Bug Reports

You can file an github issue or ask us on the Galaxy development list.

docker-galaxy-ngs-preprocessing's Issues

New tools

Should we add HiSAT and TopHat2 as well? Star?

Javascript not loaded in newest dockerfile

There is some error with access to js libraries in the newest version:

$  docker run -i -t -p 8081:80 bgruening/galaxy-ngs-preprocessing

while running the older version works without issue

$ docker run -i -t -p 8080:80 bgruening/galaxy-ngs-preprocessing:18.01 # this works

readme.md overhaul

We should link to the readme of the main Docker image and not repeat text, this will soon be outdated or very hard to update. License, contributors and so on should stay, but for all docs just point our users to

https://github.com/bgruening/docker-galaxy-stable

Adding MultiQC ?

Maybe it can be of interest to add MultiQC tool ?

tool_panel_section_id: quality_control
tool_panel_section_label: Quality Control
tool_shed_url: toolshed.g2.bx.psu.edu

• install_repository_dependencies: true
  install_resolver_dependencies: true
  install_tool_dependencies: true
  name: stacks_clonefilter
  owner: iuc
  revisions:
  • a0a51078cb61