https://github.com/fjossinet/rnaseqdocker

A docker image providing RNA-seq algorithms
https://github.com/fjossinet/rnaseqdocker

Last synced: 14 days ago
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A docker image providing RNA-seq algorithms

• Host: GitHub
• URL: https://github.com/fjossinet/rnaseqdocker
• Owner: fjossinet
• License: mit
• Created: 2016-04-26T09:51:47.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-03-16T09:03:09.000Z (almost 8 years ago)
• Last Synced: 2024-11-06T12:19:24.733Z (2 months ago)
• Homepage:
• Size: 4.88 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
RNAseqDocker

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

A docker image containing the following algorithms fully configured:

* [SAMtools](http://samtools.sourceforge.net)

* [Tophat2](https://ccb.jhu.edu/software/tophat/)

* [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

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/rnaseq

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.

SAMtools algorithm:

    docker run -v /Users/fjossinet/my_files:/data fjossinet/rnaseq samtools view -c /data/my_file.bam