Creating zip file with minimal data required for reproduction of asse…

…mbly errors #260 #261

Dockerfile

@@ -9,21 +9,19 @@ RUN echo "deb http://mirror.aarnet.edu.au/ubuntu/ bionic-security universe multi
 RUN echo "deb http://mirror.aarnet.edu.au/ubuntu/ bionic-updates universe multiverse" >> /etc/apt/sources.list
 
 # CRAN ubuntu package repository for the latest version of R
-RUN apt-get update
-RUN apt-get install -y apt-transport-https software-properties-common
+RUN apt-get update ; apt-get install -y apt-transport-https software-properties-common ; apt-get clean ; rm -rf /var/lib/apt/lists/*
 RUN gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 RUN gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add -
 RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
 
-RUN apt-get update
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y openjdk-8-jre-headless samtools sambamba bwa time build-essential make r-base libssl-dev libcurl4-openssl-dev libxml2-dev
+RUN apt-get update ; DEBIAN_FRONTEND=noninteractive apt-get install -y openjdk-8-jre-headless samtools sambamba bwa time build-essential make r-base libssl-dev libcurl4-openssl-dev libxml2-dev ; rm -rf /var/lib/apt/lists/*
 
 # R packages used by GRIDSS and PURPLE
 ENV R_INSTALL_STAGED=false
 RUN Rscript -e 'options(Ncpus=16L, repos="https://cloud.r-project.org/");install.packages(c("tidyverse", "assertthat", "testthat", "NMF", "randomForest", "stringdist", "stringr", "argparser", "R.cache", "BiocManager", "Rcpp", "blob", "RSQLite"))'
 RUN Rscript -e 'options(Ncpus=16L, repos="https://cloud.r-project.org/");BiocManager::install(ask=FALSE, pkgs=c("copynumber", "StructuralVariantAnnotation", "VariantAnnotation", "rtracklayer", "BSgenome", "Rsamtools", "biomaRt", "org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Hsapiens.UCSC.hg38.knownGene"))'
 
-ENV GRIDSS_VERSION=2.6.2
+ENV GRIDSS_VERSION=2.6.3
 ENV GRIDSS_JAR=/opt/gridss/gridss-${GRIDSS_VERSION}-gridss-jar-with-dependencies.jar
 
 RUN mkdir /opt/gridss/

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>au.edu.wehi</groupId>
 	<artifactId>gridss</artifactId>
 	<packaging>jar</packaging>
-	<version>2.6.2-gridss</version>
+	<version>2.6.3-gridss</version>
 	<name>gridss</name>
 	<url>https://github.com/PapenfussLab/gridss</url>
 	<properties>