Commit 5e556be9 authored by sajvanderzeeuw's avatar sajvanderzeeuw
Browse files

added docs

parent b3f5cd2e
......@@ -18,13 +18,13 @@ For end-users:
* Java 7 JVM
* Minimum 2 GB RAM, more when analysis is also run on this machine.
* [Cran R 2.15.3](http://cran.r-project.org/)
* [Cran R 3.1.1](http://cran.r-project.org/)
For developers:
* OpenJDK 7 or Oracle-Java JDK 7
* Minimum of 4 GB RAM {todo: provide more accurate estimation on building}
* [Cran R 2.15.3](http://cran.r-project.org/)
* [Cran R 3.1.1](http://cran.r-project.org/)
* Maven 3
* [GATK + Queue](https://www.broadinstitute.org/gatk/download)
* IntelliJ or Netbeans 8.0 for development
......@@ -48,7 +48,7 @@ In the SHARK compute cluster, a module is available to load the necessary depend
$ module load biopet/v0.2.0
Using this option, the `java -jar Biopet-<version>.jar` can be omnited and `biopet` can be started using:
Using this option, the `java -jar Biopet-<version>.jar` can be ommited and `biopet` can be started using:
$ biopet
......@@ -73,7 +73,16 @@ Using this option, the `java -jar Biopet-<version>.jar` can be omnited and `biop
- [Sage](pipelines/sage)
- Yamsvp (Under development)
__Note that each pipeline needs a config file written in JSON format__
__Note that each pipeline needs a config file written in JSON format see [config](config) & [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config) __
There are multiple configs that can be passed to a pipeline, for example the sample, settings and executables wherefrom sample and settings are mandatory.
- [Here](config) one can find how to create a sample and settings config
- More info can be found here: [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config)
### Running a tool
......@@ -96,7 +105,6 @@ __Note that each pipeline needs a config file written in JSON format__
- WipeReads
- More info can be found here: [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config)
## Developers
......@@ -105,8 +113,8 @@ __Note that each pipeline needs a config file written in JSON format__
1. Clone biopet with `git clone git@git.lumc.nl:biopet/biopet.git biopet`
2. Go to biopet directory
3. run mvn_install_queue.sh, this install queue jars into the local maven repository
3. alternatively download the `queue.jar` from the GATK website
4. run `mvn verify` to compile and package or do `mvn install` to install the jars also in local maven repository
4. alternatively download the `queue.jar` from the GATK website
5. run `mvn verify` to compile and package or do `mvn install` to install the jars also in local maven repository
......
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