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Last pushed: 2 years ago
Short Description
Dockerized homer for use in Cedars bioinformatics pipelines
Full Description

This is a fully containerized version of the widely used genomics and bioinformatics tool, Homer. For more information, please refer to the [Homer website] (http://homer.salk.edu/homer)

Fair warning, the image is large (>2 GB). A tagged version of the image is available with the human genome pre-installed. You can access this by pulling dennishazelett/homer:hg19 (or :hg38). See "Tags" for a full list of containers with pre-installed genomes. To run the container interactively after pulling the image, type

docker run -u user1 -it -v /path/to/my/data:/home/user1/data dennishazelett/homer:hg19

This will allow you to mount a local folder and save your work in the local context ("/path/to/my/data"). One can test the installation of homer by typing

findMotifs.pl

from the home directory.

Notes: The container image is based on Ubuntu 14.04 and has all of homer's dependencies preinstalled and visible in user1's PATH environment variable. These include UCSC genome browser's BLAT suite of bioinformatics tools and weblogo. See the Dockerfile for information about other preinstalled packages.

*How to create a customized installation of homer using Docker

The easiest way to do this (if your custom install is not included in the precomputed, tagged containers in this repo) is to build locally from a custom Dockerfile, for example:

## Dockerfile for dennishazelett/homer:fly
FROM dennishazelett/homer
RUN perl /home/user1/homer/configureHomer.pl -install dm3 fly-o
RUN chown -R user1:staff /home/user1

The build command would be something like this:

docker build -t dennishazelett/homer:fly -no-cache ~/path/to/Dockerfile/

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Another custom Dockerfile example (note the use of a tagged image as base container):

FROM dennishazelett/homer:hg19
RUN perl /home/user1/homer/configureHomer.pl -install human-o human-mRNA human-mRNA-3UTR
RUN chown -R user1:staff /home/user1
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dennishazelett
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