https://github.com/fjossinet/rnaseqdocker
A docker image providing RNA-seq algorithms
https://github.com/fjossinet/rnaseqdocker
Last synced: 5 months ago
JSON representation
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 (about 10 years ago)
- Default Branch: master
- Last Pushed: 2017-03-16T09:03:09.000Z (over 9 years ago)
- Last Synced: 2024-12-25T13:17:53.711Z (over 1 year ago)
- Homepage:
- Size: 4.88 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
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