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update included tools
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@nr23730
nr23730 committed Apr 19, 2024
1 parent 6db8451 commit 852bd11
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Showing 12 changed files with 54 additions and 24 deletions.
17 changes: 17 additions & 0 deletions .gitignore
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Expand Up @@ -15,7 +15,24 @@ assets/input/*
assets/output/*
!assets/output/.gitkeep

assets/references

docker/*.log

.idea
.vscode

tools/vep
tools/vcf2maf

databases/actionable_genes.txt
databases/cancerGeneList.tsv
databases/DGIdb_interactions.tsv
databases/fannsdb.tsv.gz*
databases/h.all.*
databases/hallmarksOfCancer_GeneSets.RData
databases/hg19all.wig.gz
databases/hotspots_v2.xls
databases/microsatellite_sites_hg19
databases/oncokb_biomarker_drug_associations.tsv
databases/vep/*
15 changes: 9 additions & 6 deletions RScripts/Report.Rnw
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Expand Up @@ -556,17 +556,20 @@ if(is.null(germ_all$muts_tab) || dim(germ_all$muts_tab)[1] == 0){

\subsection{Programmversionen}
\begin{itemize}
\item FastQC: 0.11.10.devel
\item FastQC: 0.12.1
\item Trimmomatic: 0.39
\item bwa-mem2: 2.2.1
\item bam-readcount: 0.8.0-unstable-7-625eea2
\item samtools 1.10
\item samtools 1.20
\item GATK: 4.2.4.0
\item picard-tools: 2.20.6
\item picard-tools: 3.1.1
\item VEP: 111.0
\item bedtools: 2.28.0
\item Control-FREEC: 11.6
\item Java: openjdk-8-hotspot
\item bedtools: 2.31.1
\item Control-FREEC: 11.6b
\item sequenza: 3.0.0
\item msisensor2: 0.1
\item MSIsensor-pro: 1.2.0
\item Java: 11.0.22+7-1
\end{itemize}

\subsection{VEP Datenbanken}
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15 changes: 9 additions & 6 deletions RScripts/Report_Panel.Rnw
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Expand Up @@ -439,17 +439,20 @@ if(is.null(som_all$muts_tab || )dim(som_all$muts_tab)[1] == 0) {

\subsection{Programmversionen}
\begin{itemize}
\item FastQC: 0.11.10.devel
\item FastQC: 0.12.1
\item Trimmomatic: 0.39
\item bwa-mem2: 2.2.1
\item bam-readcount: 0.8.0-unstable-7-625eea2
\item samtools 1.10
\item samtools 1.20
\item GATK: 4.2.4.0
\item picard-tools: 2.20.6
\item picard-tools: 3.1.1
\item VEP: 111.0
\item bedtools: 2.28.0
\item Control-FREEC: 11.6
\item Java: openjdk-8-hotspot
\item bedtools: 2.31.1
\item Control-FREEC: 11.6b
\item sequenza: 3.0.0
\item msisensor2: 0.1
\item MSIsensor-pro: 1.2.0
\item Java: 11.0.22+7-1
\end{itemize}

\subsection{VEP Datenbanken}
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15 changes: 9 additions & 6 deletions RScripts/Report_tumorOnly.Rnw
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Expand Up @@ -410,17 +410,20 @@ if(is.null(som_all$muts_tab) || dim(som_all$muts_tab)[1] == 0) {

\subsection{Programmversionen}
\begin{itemize}
\item FastQC: 0.11.10.devel
\item FastQC: 0.12.1
\item Trimmomatic: 0.39
\item bwa-mem2: 2.2.1
\item bam-readcount: 0.8.0-unstable-7-625eea2
\item samtools 1.10
\item samtools 1.20
\item GATK: 4.2.4.0
\item picard-tools: 2.20.6
\item picard-tools: 3.1.1
\item VEP: 111.0
\item bedtools: 2.28.0
\item Control-FREEC: 11.6
\item Java: openjdk-8-hotspot
\item bedtools: 2.31.1
\item Control-FREEC: 11.6b
\item sequenza: 3.0.0
\item msisensor2: 0.1
\item MSIsensor-pro: 1.2.0
\item Java: 11.0.22+7-1
\end{itemize}

\subsection{VEP Datenbanken}
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5 changes: 4 additions & 1 deletion databases/geneset_generation.R
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@@ -1,5 +1,8 @@
library(GSA)
gmt <- GSA.read.gmt('h.all.v7.0.entrez.gmt')

args <- commandArgs(trailingOnly = TRUE)
hallmarks <- args[1]
gmt <- GSA.read.gmt(hallmarks)
genesets <- gmt$genesets
names <- data.frame(Names = gmt$geneset.names, Descriptions = gmt$geneset.descriptions)
names(genesets) <- names$Names
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2 changes: 1 addition & 1 deletion tools/FastQC
Submodule FastQC updated 37 files
+13 −9 .classpath
+2 −1 Configuration/adapter_list.txt
+11 −0 Help/3 Analysis Modules/10 Adapter Content.html
+15 −21 Help/3 Analysis Modules/8 Duplicate Sequences.html
+3 −3 Help/3 Analysis Modules/9 Overrepresented Sequences.html
+617 −282 LICENSE
+60 −0 RELEASE_NOTES.txt
+2 −2 build.xml
+66 −9 fastqc
+ − htsjdk.jar
+ − sam-1.103.jar
+3 −3 uk/ac/babraham/FastQC/Analysis/OfflineRunner.java
+2 −2 uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel.java
+2 −2 uk/ac/babraham/FastQC/FastQCApplication.java
+20 −1 uk/ac/babraham/FastQC/FastQCConfig.java
+4 −1 uk/ac/babraham/FastQC/FileFilters/BAMFileFilter.java
+11 −1 uk/ac/babraham/FastQC/FileFilters/FastQFileFilter.java
+4 −1 uk/ac/babraham/FastQC/FileFilters/MappedBAMFileFilter.java
+20 −3 uk/ac/babraham/FastQC/Graphs/LineGraph.java
+46 −14 uk/ac/babraham/FastQC/Modules/AbstractQCModule.java
+59 −3 uk/ac/babraham/FastQC/Modules/BasicStats.java
+14 −17 uk/ac/babraham/FastQC/Modules/DuplicationLevel.java
+1 −1 uk/ac/babraham/FastQC/Modules/NContent.java
+11 −1 uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs.java
+30 −16 uk/ac/babraham/FastQC/Modules/PerTileQualityScores.java
+4 −0 uk/ac/babraham/FastQC/Report/HTMLReportArchive.java
+12 −10 uk/ac/babraham/FastQC/Sequence/BAMFile.java
+1 −1 uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
+15 −7 uk/ac/babraham/FastQC/Sequence/FastQFile.java
+2 −2 uk/ac/babraham/FastQC/Sequence/QualityEncoding/PhredEncoding.java
+1 −1 uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+3 −3 uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.java
+721 −0 uk/ac/babraham/FastQC/Utilities/ImageSaver/SVGGenerator.java
+44 −0 uk/ac/babraham/FastQC/Utilities/ImageSaver/SVGImageSaver.java
+20 −3 uk/ac/babraham/FastQC/Utilities/ImageToBase64.java
+8 −4 uk/ac/babraham/FastQC/Utilities/QualityCount.java
+3 −3 uk/ac/babraham/FastQC/Utilities/RGB.java
Empty file removed tools/annovar/.gitkeep
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2 changes: 1 addition & 1 deletion tools/bam-matcher
Submodule bam-matcher updated 1 files
+1 −1 .github/workflows/docker-image.yml
Empty file removed tools/gatk/.gitkeep
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2 changes: 1 addition & 1 deletion tools/htslib
Submodule htslib updated 219 files
3 changes: 2 additions & 1 deletion tools/install.sh
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Expand Up @@ -4,6 +4,7 @@
readonly VERSION_TRIMMOMATIC="0.39"
readonly VERSION_PICARD="3.1.1"
readonly VERSION_BEDTOOLS="2.31.1"
readonly VERSION_BWAMEM2="2.2.1"
readonly VERSION_VEP_MAJOR="111"
readonly VERSION_VEP="${VERSION_VEP_MAJOR}.0"

Expand Down Expand Up @@ -148,7 +149,7 @@ rm -rf ${DIR_SCRIPT}/bam-readcount/build
# bwa-mem2 #
#######
cd ${DIR_SCRIPT}
wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2 -O bwa-mem2.tar.bz2
wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v${VERSION_BWAMEM2}/bwa-mem2-${VERSION_BWAMEM2}_x64-linux.tar.bz2 -O bwa-mem2.tar.bz2
tar -xf bwa-mem2.tar.bz2
rm bwa-mem2*.tar.bz2
mv bwa-mem2* bwa-mem2
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2 changes: 1 addition & 1 deletion tools/samtools
Submodule samtools updated 165 files

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