Commit 9ee68f3c authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

first changes for 0.3.0

parent 09103695
......@@ -12,7 +12,7 @@ Biopet is an abbreviation of ( Bio Pipeline Execution Tool ) and packages severa
### System Requirements
Biopet is build on top of GATK Queue, which requires having `java` installed on the analysis machine(s).
Biopet is build on top of GATK Queue, which requires having `java 7 JVM` installed on the analysis machine(s).
For end-users:
......@@ -58,7 +58,7 @@ If one performs a dry run the config report will be generated. From this config
In the SHARK compute cluster, a module is available to load the necessary dependencies.
$ module load biopet/v0.2.0
$ module load biopet/v0.3.0
Using this option, the `java -jar Biopet-<version>.jar` can be ommited and `biopet` can be started using:
......@@ -70,25 +70,32 @@ Using this option, the `java -jar Biopet-<version>.jar` can be ommited and `biop
$ biopet pipeline <pipeline_name>
- [Flexiprep](pipelines/flexiprep)
- [Mapping](pipelines/mapping)
- [Gatk Variantcalling](https://git.lumc.nl/biopet/biopet/wikis/GATK-Variantcalling-Pipeline)
- [Gentrap](pipelines/gentrap)
- [Sage](pipelines/sage)
- Bam2Wig
- BamMetrics
- Carp
- ConiferPipeline
- Toucan
- Yamsvp
- Basty
Note that all pipelines are still in the experimental phase and therefore one needs to be careful interpreting the results and stability of the pipelines
- GatkBenchmarkGenotyping
- GatkGenotyping
- GatkPipeline
- GatkVariantRecalibration
- GatkVcfSampleCompare
- [Gentrap](pipelines/gentrap)
- [Sage](pipelines/sage)
- Yamsvp (Under development)
__Note that each pipeline needs a config file written in JSON format see [config](general/config.md) & [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.
There are multiple configs that can be passed to a pipeline, for example the sample, settings and executables where from sample and settings are mandatory.
- [Here](general/config.md) 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)
......@@ -97,20 +104,33 @@ There are multiple configs that can be passed to a pipeline, for example the sam
$ biopet tool <tool_name>
- BedToInterval
- BedtoolsCoverageToCounts
- BiopetFlagstat
- CheckAllelesVcfInBam
- ExtractAlignedFastq
- FastqSplitter
- FindRepeatsPacBio
- MpileupToVcf
- SageCountFastq
- SageCreateLibrary
- SageCreateTagCounts
- VcfFilter
- VcfToTsv
- WipeReads
- AnnotateVcfWithBed
- BastyGenerateFasta
- BedToInterval
- BedtoolsCoverageToCounts
- BiopetFlagstat
- CheckAllelesVcfInBam
- ExtractAlignedFastq
- FastqSplitter
- FastqSync
- FindRepeatsPacBio
- MergeAlleles
- MpileupToVcf
- SageCountFastq
- SageCreateLibrary
- SageCreateTagCounts
- SamplesTsvToJson
- Seqstat
- VEPNormalizer
- VcfFilter
- VcfStats
- VcfToTsv
- WipeReads
Each tool has its own help screen and can be accessed like this:
$ biopet tool <tool_name> -h
## Developers
......@@ -122,8 +142,7 @@ There are multiple configs that can be passed to a pipeline, for example the sam
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
## About
## About
Go to the [about page](about)
## License
......
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