From 405222b6eaa1670fb6ee5fef975f192173a9b27e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 13 Sep 2015 20:15:17 +0200
Subject: [PATCH] Remove framework files
---
public/biopet-framework/.gitignore | 1 -
public/biopet-framework/README.md | 9 --
.../examples/bam-metrics.json | 6 -
.../examples/biopet-defaults.json | 22 ----
.../biopet-framework/examples/flexiprep.json | 8 --
.../examples/gatk-benchmark-genotyping.json | 9 --
.../examples/gatk-genotypeing.json | 8 --
.../examples/gatk-pipeline.json | 40 ------
.../examples/gatk-variantcalling.json | 9 --
.../examples/gatk-vcf-sample-compare.json | 9 --
public/biopet-framework/examples/mapping.json | 12 --
public/biopet-framework/examples/sage.json | 23 ----
.../biopet-framework/examples/shark_apps.json | 36 -----
.../examples/summaryformat.json | 33 -----
public/biopet-framework/pom.xml | 123 ------------------
15 files changed, 348 deletions(-)
delete mode 100644 public/biopet-framework/.gitignore
delete mode 100644 public/biopet-framework/README.md
delete mode 100644 public/biopet-framework/examples/bam-metrics.json
delete mode 100644 public/biopet-framework/examples/biopet-defaults.json
delete mode 100644 public/biopet-framework/examples/flexiprep.json
delete mode 100644 public/biopet-framework/examples/gatk-benchmark-genotyping.json
delete mode 100644 public/biopet-framework/examples/gatk-genotypeing.json
delete mode 100644 public/biopet-framework/examples/gatk-pipeline.json
delete mode 100644 public/biopet-framework/examples/gatk-variantcalling.json
delete mode 100644 public/biopet-framework/examples/gatk-vcf-sample-compare.json
delete mode 100644 public/biopet-framework/examples/mapping.json
delete mode 100644 public/biopet-framework/examples/sage.json
delete mode 100644 public/biopet-framework/examples/shark_apps.json
delete mode 100644 public/biopet-framework/examples/summaryformat.json
delete mode 100644 public/biopet-framework/pom.xml
diff --git a/public/biopet-framework/.gitignore b/public/biopet-framework/.gitignore
deleted file mode 100644
index a6f89c2da..000000000
--- a/public/biopet-framework/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/target/
\ No newline at end of file
diff --git a/public/biopet-framework/README.md b/public/biopet-framework/README.md
deleted file mode 100644
index 3dc04d5cb..000000000
--- a/public/biopet-framework/README.md
+++ /dev/null
@@ -1,9 +0,0 @@
-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.
diff --git a/public/biopet-framework/examples/bam-metrics.json b/public/biopet-framework/examples/bam-metrics.json
deleted file mode 100644
index 87ee73e04..000000000
--- a/public/biopet-framework/examples/bam-metrics.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "reference": "bla",
- "bedtools": { "exe": "test"},
- "samtools": { "exe": "test"},
- "targetBed": ["target_1", "target_2"]
-}
diff --git a/public/biopet-framework/examples/biopet-defaults.json b/public/biopet-framework/examples/biopet-defaults.json
deleted file mode 100644
index 1f505ce90..000000000
--- a/public/biopet-framework/examples/biopet-defaults.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
- "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 }
- }
-}
diff --git a/public/biopet-framework/examples/flexiprep.json b/public/biopet-framework/examples/flexiprep.json
deleted file mode 100644
index 177cfdd25..000000000
--- a/public/biopet-framework/examples/flexiprep.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "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"}
- }
-}
diff --git a/public/biopet-framework/examples/gatk-benchmark-genotyping.json b/public/biopet-framework/examples/gatk-benchmark-genotyping.json
deleted file mode 100644
index 89d0d7d92..000000000
--- a/public/biopet-framework/examples/gatk-benchmark-genotyping.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "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
- }
-}
diff --git a/public/biopet-framework/examples/gatk-genotypeing.json b/public/biopet-framework/examples/gatk-genotypeing.json
deleted file mode 100644
index 083b93825..000000000
--- a/public/biopet-framework/examples/gatk-genotypeing.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "dbsnp": "bla",
- "haplotypecaller": {
- "stand_call_conf": 20,
- "stand_emit_conf": 20
- }
-}
diff --git a/public/biopet-framework/examples/gatk-pipeline.json b/public/biopet-framework/examples/gatk-pipeline.json
deleted file mode 100644
index b9b1ef2b6..000000000
--- a/public/biopet-framework/examples/gatk-pipeline.json
+++ /dev/null
@@ -1,40 +0,0 @@
-{
- "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
-}
diff --git a/public/biopet-framework/examples/gatk-variantcalling.json b/public/biopet-framework/examples/gatk-variantcalling.json
deleted file mode 100644
index 0cab6e62f..000000000
--- a/public/biopet-framework/examples/gatk-variantcalling.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "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
-}
diff --git a/public/biopet-framework/examples/gatk-vcf-sample-compare.json b/public/biopet-framework/examples/gatk-vcf-sample-compare.json
deleted file mode 100644
index 89d0d7d92..000000000
--- a/public/biopet-framework/examples/gatk-vcf-sample-compare.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "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
- }
-}
diff --git a/public/biopet-framework/examples/mapping.json b/public/biopet-framework/examples/mapping.json
deleted file mode 100644
index 5b675451a..000000000
--- a/public/biopet-framework/examples/mapping.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
- "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"}
- }
-}
diff --git a/public/biopet-framework/examples/sage.json b/public/biopet-framework/examples/sage.json
deleted file mode 100644
index 44d57a292..000000000
--- a/public/biopet-framework/examples/sage.json
+++ /dev/null
@@ -1,23 +0,0 @@
-{
- "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"}
-}
diff --git a/public/biopet-framework/examples/shark_apps.json b/public/biopet-framework/examples/shark_apps.json
deleted file mode 100644
index d5bd63e02..000000000
--- a/public/biopet-framework/examples/shark_apps.json
+++ /dev/null
@@ -1,36 +0,0 @@
-{
- "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"
- }
-}
diff --git a/public/biopet-framework/examples/summaryformat.json b/public/biopet-framework/examples/summaryformat.json
deleted file mode 100644
index be47260b2..000000000
--- a/public/biopet-framework/examples/summaryformat.json
+++ /dev/null
@@ -1,33 +0,0 @@
-{
- "_meta": {},
- "stats": {},
- "resources": {
- "res_key": {
- "uri:": "",
- "md5sum": "",
- "sha256sum": "",
- "adler32sum": ""
- }
- },
- "samples" :{
- "SampleID": {
- "stats": {},
- "resources": {},
- "libraries": {
- "libraryID": {
- "stats": {},
- "resources": {}
- }
- }
- }, "SampleID2": {
- "stats": {},
- "resources": {},
- "libraries": {
- "libraryID": {
- "stats": {},
- "resources": {}
- }
- }
- }
- }
-}
diff --git a/public/biopet-framework/pom.xml b/public/biopet-framework/pom.xml
deleted file mode 100644
index 2517acae3..000000000
--- a/public/biopet-framework/pom.xml
+++ /dev/null
@@ -1,123 +0,0 @@
-<!--
-
- 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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