Commit c4834a47 authored by sajvanderzeeuw's avatar sajvanderzeeuw
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added docs

parent 539c2f05
......@@ -10,8 +10,17 @@ platform and reduce code duplication and increase maintainability.
## The Team
SASC:
Currently our team excists out of 5 members
- Leon Mei (LUMC-SASC)
- Wibowo Arindrarto (LUMC-SASC)
- Peter van 't Hof (LUMC-SASC)
- Wai Yi Leung (LUMC-SASC)
- Sander van der Zeeuw (LUMC-SASC)
## Contact
We even have a website: https://sasc.lumc.nl/
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check our website at: [SASC](https://sasc.lumc.nl/)
We are also reachable through email: [SASC mail](mailto:SASC@lumc.nl)
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# Welcome to Biopet
(Bio Pipeline Execution Tool)
###### (Bio Pipeline Execution Tool)
## Introduction
### System Requirements
- Java 7 JVM
- Maven 3 (does not need to be on shark)
### Compiling Biopet
1. Clone Biopet with `git clone git@git.lumc.nl:biopet/biopet.git`
2. Go to Biopet directory
3. run mvn_install_queue.sh, this install queue jars into the local maven repository
4. run `mvn verify` to compile and package or do `mvn install` to install the jars also in local maven repository
### Running a pipeline
- Help: `java -jar Biopet(version).jar (pipeline of interest) -h`
- Local: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -run`
- Shark: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub -jobParaEnv BWA -run`
- DryRun: `java -jar Biopet(version).jar (pipeline of interest) (pipeline options)`
- DryRun(shark): `java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub -jobParaEnv BWA`
- A dry run can be performed to see if the scheduling and creating of the pipelines jobs performs well. Nothing will be executed only the job commands are created. If this succeeds it's a good indication you actual run will be successful as well.
- Each pipeline can be found as an options inside the jar file Biopet[version].jar which is located in the target directory and can be started with `java -jar <pipelineJarFile>`
### Running a tool
### Pipelines
- [Flexiprep](https://git.lumc.nl/biopet/biopet/wikis/Flexiprep-Pipeline)
- [Mapping](https://git.lumc.nl/biopet/biopet/wikis/Mapping-Pipeline)
- [Gatk Variantcalling](https://git.lumc.nl/biopet/biopet/wikis/GATK-Variantcalling-Pipeline)
- BamMetrics
- Basty
- GatkBenchmarkGenotyping
- GatkGenotyping
- GatkPipeline
- GatkVariantRecalibration
- GatkVcfSampleCompare
- Gentrap (Under development)
- Sage
- Yamsvp (Under development)
__Note that each pipeline needs a config file written in JSON format__
- More info can be found here: [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config)
## About
Go to the [about page](/about)
Go to the [about page](about)
## License
See: [License](license)
Copyright [2013-2014] [Sequence Analysis Support Core]
Copyright [2013-2014] [Sequence Analysis Support Core](https://sasc.lumc.nl/)
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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