🐳 Galaxy Workbench with HiCExplorer
This Docker image is a flavor of Galaxy Docker image customized by integrating HiCExplorer tools and workflows.
Table of Contents
- Installation and Setup
- Usage - How to run Galaxy-HiCExplorer
- Support & Bug Reports
Installation and Setup:
The only requirement to run this webserver locally is Docker. Docker supports the three major desktop operating systems Linux, Windows and Mac OSX. Please refer to Docker installation guideline for details.
For Windows and Mac systems it is additionally possible to use Kitematic and launch Galaxy HiCExplorer using the OS graphical user interface.
Alternatively Galaxy-HiCExplorer can be integrated into a running Galaxy server. All the Galaxy-HiCExplorer tools and workflows needed to run the HiCExplorer pipeline are listed in workflows and tools-list. The Freibug Galaxy Instance for example offers next to 700 other tools also the entire HiCExplorer suite.
Running the Galaxy server
From the command line (Linux/Windows/MacOS):
docker run -i -t -p 8080:80 quay.io/bgruening/galaxy-hicexplorer
For more details about this command line or specific usage, please consult the Galaxy Docker
Using graphic interface (Windows/MacOS):
Please check this step-by-step guide.
Galaxy-HiCExplorer has been tested One of these operating systems:
- Windows : 10 using Kitematic
- MacOSx: 10.1x or higher using Kitematic
- Linux: Kernel 4.2 or higher, preferably with aufs support (see FAQ)
Hardware (depending on your input data):
- Minimum 8GB RAM
- Minimum 20GB Free disk space
In case you encountered problems please check the FAQ page or contact us using Issues tab.
Usage - How to run Galaxy-GraphClust:
Browser access to the server:
After running the Galaxy server, a web server is established under the host IP/URL and designated port (default 8080).
Inside your browser goto IP/URL:PORT
Following same settings as previous step
Import or upload a workflow
To import or upload an existing workflow, on the top panel go to Workflow menu. On top right side of the screen click on Upload or import workflow button. You can either upload workflow from your local system or by providing the URL of the workflow. To have an access to workflow menu you must be logged in. You can download workflows from the following links
Support & Bug Reports
Publications that uses HiCExplorer
Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke, High-resolution TADs reveal DNA sequences underlying genome organization in flies
Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Bjoern A Gruening, David Kranzhoefer, et al., Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo