dennishazelett/peak repository overview

⁠README

This README documents the steps necessary to get the peak application up and running.

⁠What is this repository for?

• Custom automated peak caller for Cedars-Sinai bioinformatics. Depends Macs2, HOMER, SPP and MUSIC.
• Version 0.1
• Go to the Bitbucket repo⁠.
• Go to the Docker image⁠.

⁠How do I get set up?

• pull the Docker image from Dockerhub: docker pull dennishazelett/peak

• Configuration: Required: a directory with bam, bedgraph, wig etc Required: a manifest | SAMPLE | MARK | SRC | BUILD | FILE | |---------|-------|-----|-------|----------------------| | K562 | K4M1 | BAM | hg19 | myk562file1.bam | | K562 | K4M3 | WIG | hg19 | myk562file2.wig | | K562 | K4M3 | BDG | hg19 | ENCFF001XGT.bedgraph |

• Dependencies Docker image dennishazelett/peak

• How to run tests

• Deployment instructions

⁠Contribution guidelines

• Writing tests
• Code review
• Other guidelines

⁠Who do I talk to?

• Repo owner or admin
• Other community or team contact