https://github.com/robsyme/docker-repet

The REPET package in a container.
https://github.com/robsyme/docker-repet

Last synced: 24 days ago
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The REPET package in a container.

• Host: GitHub
• URL: https://github.com/robsyme/docker-repet
• Owner: robsyme
• License: mit
• Created: 2016-04-07T08:13:10.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-10-25T03:40:33.000Z (about 7 years ago)
• Last Synced: 2023-10-25T19:05:25.236Z (about 1 year ago)
• Size: 5.86 KB
• Stars: 2
• Watchers: 2
• Forks: 4
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# docker-REPET

The REPET package in a container.

## Background

The REPET package has many dependencies, including a MySQL database

and the a scheduler such as the Sun Grid Engine (SGE). If you want to

identify repetitive elements in a single genome, installing all of

these prerequisites is quite onerous.

## Instructions

### Building the image

One of the important prerequisites are the RepBase libraries from

[girinst.org](http://www.girinst.org/). Licencing prevents

redistribution of these data, so you have to pull these in yourself

when you build the image. The `Dockerfile` includes a step to download

the libraries, but you need to supply your username and password to

the wget command by changing the lines:

```

ENV GIRINST_USERNAME AzureDiamond

ENV GIRINST_PASSWORD hunter2

```

to your own username and password.

After than, you can build the image by running `docker build -t repet .`

from the same folder as the `Dockerfile`.