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