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https://github.com/bigdatagenomics/recipes
Recipes using BDG projects. Apache 2 licensed.
https://github.com/bigdatagenomics/recipes
Last synced: about 2 months ago
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Recipes using BDG projects. Apache 2 licensed.
- Host: GitHub
- URL: https://github.com/bigdatagenomics/recipes
- Owner: bigdatagenomics
- License: apache-2.0
- Created: 2014-10-07T22:50:13.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2015-03-25T19:45:54.000Z (almost 10 years ago)
- Last Synced: 2024-03-27T11:27:47.975Z (9 months ago)
- Language: Shell
- Size: 166 KB
- Stars: 4
- Watchers: 6
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
Big Data Genomics Recipes
===========
Recipes using BDG projects. Apache 2 licensed.
# Introduction
This repository is a home for "recipes" that use a [Big Data Genomics](http://bdgenomics.org)
project to accomplish some task. By default, these recipes use EC2 to create a Spark cluster,
on which we run [ADAM](https://www.github.com/bigdatagenomics/adam)/etc. These recipes serve three purposes:
* As a quickstart for people new to the BDG project, who would like to figure out how to use
BDG software to replace their current workflows.
* As a benchmarking/regression testing environment for the various BDG tools.
* As a sandbox where we can set up head-to-head tests against other tools (e.g., for experiments
for papers).
# Recipes
Our recipe book contains the following recipes:
* Single node recipes:
** [bqsr-head-to-head](bqsr-head-to-head/README.md): Runs a head-to-head single node speed test of the
[ADAM](https://www.github.com/bigdatagenomics/adam) and [GATK](https://www.github.com/broadgsa/gatk-protected)
base quality score recalibration (BQSR) engines.
** [flagstat-head-to-head](flagstat-head-to-head/README.md): Runs a head-to-head performance test of `Flagstat`
using [ADAM](https://www.github.com/bigdatagenomics/adam), [samtools](https://www.github.com/samtools/samtools),
and [sambamba](https://www.github.com/lomereiter/sambamba).
** [indel-realignment-head-to-head](indel-realignment-head-to-head/README.md): Runs a head-to-head single node speed test of the
[ADAM](https://www.github.com/bigdatagenomics/adam) and [GATK](https://www.github.com/broadgsa/gatk-protected)
INDEL realignment engines.
** [markdup-head-to-head](markdup-head-to-head/README.md): Runs a head-to-head performance test of duplicate marking
using [ADAM](https://www.github.com/bigdatagenomics/adam), [samtools](https://www.github.com/samtools/samtools),
and [sambamba](https://www.github.com/lomereiter/sambamba), and [picard](https://www.github.com/broadinstitute/picard).
** [sort-head-to-head](sort-head-to-head/README.md): Runs a head-to-head performance test of sorting
using [ADAM](https://www.github.com/bigdatagenomics/adam), [samtools](https://www.github.com/samtools/samtools),
and [sambamba](https://www.github.com/lomereiter/sambamba), and [picard](https://www.github.com/broadinstitute/picard).
* Multiple node recipes:
** [adam-transforms](adam-transforms/README.md): Runs scale-out performance testing on [ADAM](https://www.github.com/bigdatagenomics/adam)'s
BQSR, Flagstat, INDEL realignment, duplicate marking, and sort implementations.
## Running a Single Node Recipe
To run a single node recipe, run:
```
fab _configure_master_aptitude
fab bake:
```
## Running a Multi Node Recipe
To run a multi node recipe with _n_ nodes, run:
```
fab provision:
fab _configure_master_yum
fab bake:
```
# Adding a New Recipe
If you are adding a new recipe, you should add a directory. Under this directory, you should create a Bash
script named `run.sh` that runs the recipe. If the recipe needs setup, you should add the necessary details to
the fabfile configuration target.
# Getting In Touch
## Mailing List
[The ADAM mailing list](https://groups.google.com/forum/#!forum/adam-developers) is a good
way to sync up with other people who use bdg projects including the core developers. You can
subscribe by sending an email to `[email protected]` or just post using
the [web forum page](https://groups.google.com/forum/#!forum/adam-developers).
## IRC Channel
A lot of the developers are hanging on the [#adamdev](http://webchat.freenode.net/?channels=adamdev)
freenode.net channel. Come join us and ask questions.
# License
bdg-recipes is released under an [Apache 2.0 license](LICENSE).