https://github.com/fjossinet/assemble2docker

A docker image containing the RNA algorithms needed by Assemble2
https://github.com/fjossinet/assemble2docker

Last synced: 14 days ago
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A docker image containing the RNA algorithms needed by Assemble2

• Host: GitHub
• URL: https://github.com/fjossinet/assemble2docker
• Owner: fjossinet
• License: mit
• Created: 2016-04-01T14:13:33.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2017-03-16T09:28:07.000Z (almost 8 years ago)
• Last Synced: 2024-11-06T12:19:52.569Z (2 months ago)
• Size: 6.84 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
Assemble2Docker

===============

A docker image containing the following algorithms fully configured:

* [RNAVIEW](http://ndbserver.rutgers.edu/ndbmodule/services/download/rnaview.html)

* [Vienna RNA package](https://www.tbi.univie.ac.at/RNA/)

* [foldalign](http://rth.dk/resources/foldalign/)

* [LocARNA](http://rna.informatik.uni-freiburg.de/LocARNA/)

Installation

------------

First you need to install Docker on your computer. You can find all the details [here](https://docs.docker.com/engine/installation/).

Then, to get our docker image, you need to type:

    docker pull fjossinet/assemble2

Usages and Examples

-------------------

In general, these algorithms need input files. Consequently, you have to mount the file system of your computer (the host) in the Docker container (the guest). This is done with the -v option.

LocARNA algorithm:

     docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 mlocarna /data/my_sequences.fasta

RNAVIEW algorithm:

    docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 rnaview -p /data/my_3D.pdb

RNAFold algorithm:

    docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 bash -c 'RNAfold < /data/my_sequence.fasta'"