Description

This package does combine all biopet tools into a single jar for easy access. All tools can still be used as separated jars if required, this is just to make it easier for you as user.

Installation

ToolsPackage requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.

Download the latest version of ToolsPackage here. To generate the usage run:

java -jar <ToolsPackage_jar> --help

Manual

Tool name Version Documentation
Vcf tools
VcfStats 1.1 Release / Develop
VcfFilter 0.1 Release / Develop
VcfToTsv 0.1 Release / Develop
VcfWithVcf 0.1 Release / Develop
VepNormalizer 0.1 Release / Develop
ValidateVcf 0.1 Release / Develop
SnptestToVcf 0.1 Release / Develop
MergeSv 0.1 Release / Develop
MpileupToVcf 0.1 Release / Develop
ReplaceContigsVcfFile 0.2 Release / Develop
GvcfToBed 0.1 Release / Develop
FindOverlapMatch 0.1 Release / Develop
DigenicSearch 0.1 Release / Develop
CountAlleles 0.1 Release / Develop
CorrectRefAlleles 0.1 Release / Develop
AnnotateVcfWithBed 0.1 Release / Develop
Bam tools
WipeReads 0.1 Release / Develop
MultiCoverage 0.1 Release / Develop
ExtractAlignedFastq 0.1 Release / Develop
DownsampleRegions 0.1 Release / Develop
BamStats 0.1 Release / Develop
Fatq tools
ValidateFastq 0.1.1 Release / Develop
SeqStat 0.1 Release / Develop
FastqSync 0.1 Release / Develop
FastqSplitter 0.1 Release / Develop
ExtractAdaptersFastqc 0.2 Release / Develop
Annotation tools
ValidateAnnotation 0.1 Release / Develop
BaseCounter 0.1 Release / Develop
GtftoRefflat 0.1 Release / Develop
ReplaceContigsGtfFile 0.1 Release / Develop
RefflatStats 0.1 Release / Develop
ExtractTagsFromGtf 0.1 Release / Develop
AddGenesAndTranscriptsToGtf 0.1 Release / Develop
Other tools
XcnvToBed 0.1 Release / Develop
SquishBed 0.1 Release / Develop
SampleConfig 0.1 Release / Develop
SamplesTsvToConfig 0.1 Release / Develop
RebuildContigMap 0.1 Release / Develop
PipelineStatus 0.1 Release / Develop
NcbiReportToContigMap 0.1 Release / Develop
MergeOtuMaps 0.1 Release / Develop
KrakenReportToJson 0.1 Release / Develop
DownloadNcbiAssembly 0.1 Release / Develop
BastyGenerateFasta 0.1 Release / Develop

Example

Get a list of tools:

java -jar <ToolsPackage_jar> 

Normal tools:

java -jar <ToolsPackage_jar> <tool_name> <arguments to tool>

Spark tools:

spark-submit <spark arguments> <ToolsPackage_jar> <tool_name> <arguments to tool>

Usage

Usage for ToolsPackage:

Option Required Can occur multiple times Description
--log_level, -l no no Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
--help, -h no no Print usage
--version, -v no no Print version
toolName no no Name of the tool to execute
tool args no yes (unlimited) Arguments for the tool

About

ToolsPackage is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contributing

The source code of ToolsPackage can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

ToolsPackage is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on ToolsPackage. We have had good results with this IDE.

Contact

For any question related to ToolsPackage, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.