https://github.com/tiagoantao/congen-docker
A Docker repository for a course on analysis of genomic data
https://github.com/tiagoantao/congen-docker
bioinformatics conservation-genetics data-science docker population-genetics
Last synced: 7 months ago
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A Docker repository for a course on analysis of genomic data
- Host: GitHub
- URL: https://github.com/tiagoantao/congen-docker
- Owner: tiagoantao
- License: agpl-3.0
- Created: 2016-08-18T20:34:46.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2017-09-25T21:07:17.000Z (about 8 years ago)
- Last Synced: 2025-01-26T06:25:36.450Z (9 months ago)
- Topics: bioinformatics, conservation-genetics, data-science, docker, population-genetics
- Language: Shell
- Size: 378 KB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
A docker machine for data analysis of genomics data
===================================================
This machine is used for a course in conservation genetics at the
University of Montana
How to run it
-------------
**Requirements**
You should have a zip file with data (provided by the course).
**Initial note (for more advanced users)**
The docker container runs a VNC and SSH server. If you have a VNC client
installed you do not need to use the browser interface as it is slower.
Just point your VNC server to port 5901.
You can also connect directly via ssh. User root, password congen17.
You will have root access and that is fine. There will be no special user.
**If you are on Windows or Mac (see below for Linux)**
- Install Kitematic_ (Docker Toolbox).
- Start it
- Pull tiagoantao/congen-docker (using the search box)
- Make the congen container is running (UI - see below)
- Map your data volume (see below, the purple arrow)
.. image:: Docker_screenshot_volumes.png
- Restart the machine (look for the button on top)
- Go to settings (see image below)
.. image:: Docker_screenshot.png
- Click on the 6080 port (see below)
.. image:: Docker_screenshot_portsetttings.png
- This should start a browser
- Password is `congen17`
**If you get no connection to server on noVNC here is an alternative path**
- Stop the container
- On the Windows/Mac desktop click the "Docker Quickstart terminal"
- On the terminal type ``docker run -p 5901:5901 -p 6080:6080 -v /path/to/data:/data tiagoantao/congen-docker``
- If you get a error like ``port is already allocated`` make sure you stopped the container
- Now, use the IP from the **screenshot** above with the port 6080, in this case:
``http://192.168.99.100:6080/``
- Password is ``congen17``
**What to do if your base operating system is Linux**
- Install docker
- Make sure the docker server is running
- Your user has to be on the docker group
- ``docker pull tiagoantao/congen-docker``
- ``docker run -p 5901:5901 -p 6080:6080 -v /path_to_your_data:/data -t tiagoantao/congen-docker``
- Change `path_to_your_data` with the path to your data.
- Start a browser pointing to the address ``http://127.0.0.1:6080``
- Password is ``congen17``
- If you try to restart the machine, make sure the previous one is killed:
``docker ps; docker rm -f your_image``
.. _Kitematic: https://kitematic.com/