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biopet.biopet
Commits
3ec60672
Commit
3ec60672
authored
Mar 11, 2015
by
bow
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1113 additions
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114 deletions
+1113
-114
protected/biopet-gatk-extensions/src/test/resources/log4j.properties
...iopet-gatk-extensions/src/test/resources/log4j.properties
+3
-13
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
+5
-0
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+5
-0
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
...lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
+5
-0
protected/biopet-gatk-pipelines/src/test/resources/log4j.properties
...biopet-gatk-pipelines/src/test/resources/log4j.properties
+3
-13
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+5
-0
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+5
-0
protected/biopet-protected-package/src/test/resources/log4j.properties
...pet-protected-package/src/test/resources/log4j.properties
+3
-13
protected/log4j.properties
protected/log4j.properties
+3
-13
protected/src/src/test/resources/log4j.properties
protected/src/src/test/resources/log4j.properties
+3
-13
public/bam2wig/pom.xml
public/bam2wig/pom.xml
+17
-0
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+15
-0
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+15
-0
public/basty/pom.xml
public/basty/pom.xml
+17
-0
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+15
-0
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
...ain/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
...src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+12
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+12
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
...c/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+12
-3
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+11
-4
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
...rk/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
+12
-2
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
.../main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala
+15
-0
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
...st/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
...ala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
...la/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+13
-2
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
...scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
+13
-2
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
...xtensions/picard/CollectAlignmentSummaryMetricsTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
...opet/extensions/picard/CollectInsertSizeMetricsTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
...mc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
+13
-2
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
...est/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqstatTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/tools/SeqstatTest.scala
+13
-2
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VEPNormalizerTest.scala
...t/scala/nl/lumc/sasc/biopet/tools/VEPNormalizerTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+15
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
...est/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+15
-0
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+15
-0
public/flexiprep/src/test/resources/fqc_contaminants_v0101.txt
...c/flexiprep/src/test/resources/fqc_contaminants_v0101.txt
+16
-0
public/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
...xiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
+16
-0
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+15
-0
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/fix_mpileup.py
...lumc/sasc/biopet/pipelines/gentrap/scripts/fix_mpileup.py
+16
-0
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/hist2count.py
.../lumc/sasc/biopet/pipelines/gentrap/scripts/hist2count.py
+16
-0
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
.../lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
+0
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
...umc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
+15
-0
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+15
-0
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala
...c/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala
+12
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
.../biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
+15
-0
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RscriptCommandLineFunction.scala
...lines/gentrap/extensions/RscriptCommandLineFunction.scala
+12
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
...sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
+12
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala
...mc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala
+12
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
...t/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
+12
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
...c/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
+12
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
.../lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
+12
-3
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+13
-2
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+15
-0
public/shiva/pom.xml
public/shiva/pom.xml
+17
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+15
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+15
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+15
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+15
-0
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+15
-0
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+15
-0
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+15
-0
No files found.
protected/biopet-gatk-extensions/src/test/resources/log4j.properties
View file @
3ec60672
#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
View file @
3ec60672
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
3ec60672
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
View file @
3ec60672
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
...
...
protected/biopet-gatk-pipelines/src/test/resources/log4j.properties
View file @
3ec60672
#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
3ec60672
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
com.google.common.io.Files
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
3ec60672
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.File
...
...
protected/biopet-protected-package/src/test/resources/log4j.properties
View file @
3ec60672
#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
...
...
protected/log4j.properties
View file @
3ec60672
#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
...
...
protected/src/src/test/resources/log4j.properties
View file @
3ec60672
#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
...
...
public/bam2wig/pom.xml
View file @
3ec60672
<?xml version="1.0" encoding="UTF-8"?>
<!--
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
-->
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
...
...
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.File
...
...
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.bamtobigwig
import
java.io.
{
PrintWriter
,
File
}
...
...
public/basty/pom.xml
View file @
3ec60672
<!--
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
-->
<!--
Due to the license issue with GATK, this part of Biopet can only be used inside the
...
...
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.pipelines.basty
import
nl.lumc.sasc.biopet.core.PipelineCommand
...
...
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.core.summary
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.core.summary
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.core.summary
import
java.io.
{
FileInputStream
,
PrintWriter
,
File
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
View file @
3ec60672
/**
* Copyright (c) 2014 Leiden University Medical Center
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* @author Wibowo Arindrarto
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
View file @
3ec60672
/**
* Copyright (c) 2014 Leiden University Medical Center
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* @author Wibowo Arindrarto
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
import
java.io.
{
FileOutputStream
,
File
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.bwa
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
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3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.bwa
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.bwa
import
java.io.File
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
View file @
3ec60672
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.bwa