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Commit 405222b6 authored by Peter van 't Hof's avatar Peter van 't Hof
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public/biopet-framework/.gitignore deleted 100644 → 0
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public/biopet-framework/README.md deleted 100644 → 0
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Biopet Framework
=======================
Framework to build pipelines with
License
===
A dual licensing mode is applied. The source code within this project 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 sasc@lumc.nl to purchase a separate license.
public/biopet-framework/examples/bam-metrics.json deleted 100644 → 0
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{
"reference": "bla",
"bedtools": { "exe": "test"},
"samtools": { "exe": "test"},
"targetBed": ["target_1", "target_2"]
}
public/biopet-framework/examples/biopet-defaults.json deleted 100644 → 0
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{
"genotypegvcfs": { "scattercount": 100 },
"variantannotator": { "scattercount": 10 },
"realignertargetcreator": { "scattercount": 30 },
"combinevariants": { "scattercount": 10 },
"printreads_temp": { "scattercount": 30 },
"indelrealigner": { "scattercount": 30 },
"haplotypecaller": { "scattercount": 100 },
"unifiedgenotyper": { "scattercount": 100 },
"baserecalibrator": { "scattercount": 30 },
"basty": {
"haplotypecaller": { "scattercount": 20 },
"unifiedgenotyper": { "scattercount": 1 },
"multisample": { "unifiedgenotyper": { "scattercount": 100 } },
"baserecalibrator": { "scattercount": 1 },
"indelrealigner": { "scattercount": 1 },
"printreads_temp": { "scattercount": 1 },
"realignertargetcreator": { "scattercount": 1 },
"genotypegvcfs": { "scattercount": 1 },
"combinevariants": { "scattercount": 1 }
}
}
public/biopet-framework/examples/flexiprep.json deleted 100644 → 0
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{
"fastqc": { "exe": "/data/DIV5/SASC/common/programs/FastQC/fastqc_v0.11.2/fastqc" },
"flexiprep": {
"seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
"cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
"sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
}
}
public/biopet-framework/examples/gatk-benchmark-genotyping.json deleted 100644 → 0
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{
"gvcffiles": ["test4.vcf", "test5.vcf"],
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"dbsnp": "bla",
"haplotypecaller": {
"stand_call_conf": 20,
"stand_emit_conf": 20
}
}
public/biopet-framework/examples/gatk-genotypeing.json deleted 100644 → 0
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{
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"dbsnp": "bla",
"haplotypecaller": {
"stand_call_conf": 20,
"stand_emit_conf": 20
}
}
public/biopet-framework/examples/gatk-pipeline.json deleted 100644 → 0
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{
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"samtools": { "exe": "test"},
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"flexiprep": {
"seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
"cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
"sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
},
"star" : {"exe":"test"},
"bwa" : {"exe":"test"},
"gatk": {
"mapping": {
"flexiprep": {
}
},
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"dbsnp": "test",
"hapmap": "test",
"omni": "test",
"1000G": "test",
"mills": "test",
"haplotypecaller": {
"stand_call_conf": 20,
"stand_emit_conf": 20
}
},
"cutadapt": {"exe":"test"},
"samples": {
"test": {
"libraries": {
"3" : {
"bam" : "/data/DIV5/SASC/project-072-vcf_Comparison/analysis/runs/01/losekoot_redo_FC59b_L5_I12_S41/run_01/losekoot_redo_FC59b_L5_I12_S41-01.dedup.bam"
}
}
}
},
"correct_readgroups": true
}
public/biopet-framework/examples/gatk-variantcalling.json deleted 100644 → 0
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{
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"dbsnp": "bla",
"haplotypecaller": {
"stand_call_conf": 20,
"stand_emit_conf": 20
},
"scattercount": 10
}
public/biopet-framework/examples/gatk-vcf-sample-compare.json deleted 100644 → 0
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{
"gvcffiles": ["test4.vcf", "test5.vcf"],
"reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
"dbsnp": "bla",
"haplotypecaller": {
"stand_call_conf": 20,
"stand_emit_conf": 20
}
}
public/biopet-framework/examples/mapping.json deleted 100644 → 0
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{
"samtools": {"exe": "test"},
"reference": "/blabla/blabla.fa",
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"bwa": { "exe": "test" },
"flexiprep": {
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
"cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
"sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
}
}
public/biopet-framework/examples/sage.json deleted 100644 → 0
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{
"bedtools": {"exe": "test"},
"samtools": {"exe": "test"},
"reference": "/blabla/blabla.fa",
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"bwa": { "exe": "test" },
"flexiprep": {
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
"cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
"sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
},
"samples": {
"test": {
"libraries": {
"1": {
"R1": "test.fastq"
}
}
}
},
"bowtie": {"exe": "test"}
}
public/biopet-framework/examples/shark_apps.json deleted 100644 → 0
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{
"bwa": {
"exe": "/usr/local/bwa/bwa-0.7.10/bwa"
},
"seqtk": {
"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"
},
"sickle": {
"exe":"/data/DIV5/SASC/common/programs/sickle/sickle-1.33/sickle"
},
"clever": {
"exe": "/data/DIV5/SASC/common/programs/clever/clever-toolkit-v2.0rc3/bin/clever",
"version_exe": "/data/DIV5/SASC/common/programs/clever/clever-toolkit-v2.0rc3/bin/ctk-version"
},
"pindel": {
"exe": "/data/DIV5/SASC/common/programs/pindel/pindel-0.2.5/pindel"
},
"breakdancerconfig": {
"exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/lib/breakdancer-max1.4.4/bam2cfg.pl"
},
"breakdancercaller": {
"exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/bin/breakdancer-max"
},
"fastqc": {
"exe": "/usr/local/FastQC/FastQC_v0.10.1/fastqc"
},
"seqstat": {
"exe": "/data/DIV5/SASC/common/programs/dQual/fastq-seqstat"
},
"stampy": {
"exe": "/usr/local/stampy/stampy-1.0.23/stampy.py"
},
"sambamba": {
"exe": "/data/DIV5/SASC/common/programs/sambamba/sambamba-0.4.7/build/sambamba"
}
}
public/biopet-framework/examples/summaryformat.json deleted 100644 → 0
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{
"_meta": {},
"stats": {},
"resources": {
"res_key": {
"uri:": "",
"md5sum": "",
"sha256sum": "",
"adler32sum": ""
}
},
"samples" :{
"SampleID": {
"stats": {},
"resources": {},
"libraries": {
"libraryID": {
"stats": {},
"resources": {}
}
}
}, "SampleID2": {
"stats": {},
"resources": {},
"libraries": {
"libraryID": {
"stats": {},
"resources": {}
}
}
}
}
}
public/biopet-framework/pom.xml deleted 100644 → 0
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<!--
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">
<modelVersion>4.0.0</modelVersion>
<artifactId>BiopetFramework</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.5.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>BiopetFramework</name>
<repositories>
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.10.4</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue</artifactId>
<version>3.4</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue-extensions-public</artifactId>
<version>3.4</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-utils</artifactId>
<version>3.4</version>
<exclusions>
<exclusion>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gsalib</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.argonaut</groupId>
<artifactId>argonaut_2.10</artifactId>
<version>6.1-M4</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.1.0</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-sequencing</artifactId>
<version>3.1.0</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>18.0</version>
</dependency>
<dependency>
<groupId>com.github.scopt</groupId>
<artifactId>scopt_2.10</artifactId>
<version>3.3.0</version>
</dependency>
<dependency>
<groupId>org.scalatra.scalate</groupId>
<artifactId>scalate-core_2.10</artifactId>
<version>1.7.0</version>
</dependency>
<dependency>
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
<version>1.15</version>
</dependency>
</dependencies>
</project>
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