changed base image

Dockerfile

@@ -1,37 +1,5 @@
-FROM rocker/r-base:4.0.2
+FROM blcdsdockerregistry/docker-bb-base:latest
 
-RUN apt-get update && apt-get upgrade -y
-RUN apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
-RUN install2.r BiocManager
-RUN installBioc.r XML httr openssl BiocFileCache Rsamtools GenomicFeatures Rhtslib GenomicRanges SummarizedExperiment rtracklayer BSgenome GenomeInfoDb
-RUN installBioc.r devtools splines readr doParallel ggplot2 RColorBrewer gridExtra gtools parallel VariantAnnotation
-RUN installGithub.r Crick-CancerGenomics/ascat/ASCAT
-RUN installBioc.r VariantAnnotation
-RUN installGithub.r Wedge-lab/battenberg@dev
-RUN installBioc.r optparse
-
-RUN apt-get install -y curl default-jre
-
-RUN mkdir /tmp/downloads
-
-RUN curl -sSL -o tmp.tar.gz --retry 10 https://github.com/samtools/htslib/archive/1.7.tar.gz && \
-    mkdir /tmp/downloads/htslib && \
-    tar -C /tmp/downloads/htslib --strip-components 1 -zxf tmp.tar.gz && \
-    make -C /tmp/downloads/htslib && \
-    rm -f /tmp/downloads/tmp.tar.gz
-
-ENV HTSLIB /tmp/downloads/htslib
-
-RUN curl -sSL -o tmp.tar.gz --retry 10 https://github.com/cancerit/alleleCount/archive/v4.0.0.tar.gz && \
-    mkdir /tmp/downloads/alleleCount && \
-    tar -C /tmp/downloads/alleleCount --strip-components 1 -zxf tmp.tar.gz && \
-    cd /tmp/downloads/alleleCount/c && \
-    mkdir bin && \
-    make && \
-    cp /tmp/downloads/alleleCount/c/bin/alleleCounter /usr/local/bin/. && \
-    cd /tmp/downloads && \
-    rm -rf /tmp/downloads/alleleCount /tmp/downloads/tmp.tar.gz
-
-#COPY battenberg_wgs.R /usr/local/bin/battenberg_wgs.R
+RUN installGithub.r Wedge-lab/battenberg@9537a58369
 
 CMD ["/bin/bash"]

Dockerfile.bak

@@ -0,0 +1,38 @@
+FROM rocker/r-base:4.0.2
+
+RUN apt-get update && apt-get upgrade -y
+RUN apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
+RUN install2.r BiocManager
+RUN installBioc.r XML httr openssl BiocFileCache Rsamtools GenomicFeatures Rhtslib GenomicRanges SummarizedExperiment rtracklayer BSgenome GenomeInfoDb
+RUN installBioc.r devtools splines readr doParallel ggplot2 RColorBrewer gridExtra gtools parallel VariantAnnotation
+RUN installGithub.r Crick-CancerGenomics/ascat/ASCAT
+RUN installBioc.r VariantAnnotation
+#RUN installGithub.r Wedge-lab/battenberg@dev
+RUN installGithub.r Wedge-lab/battenberg@aa14170714
+RUN installBioc.r optparse
+
+RUN apt-get install -y curl default-jre
+
+RUN mkdir /tmp/downloads
+
+RUN curl -sSL -o tmp.tar.gz --retry 10 https://github.com/samtools/htslib/archive/1.7.tar.gz && \
+    mkdir /tmp/downloads/htslib && \
+    tar -C /tmp/downloads/htslib --strip-components 1 -zxf tmp.tar.gz && \
+    make -C /tmp/downloads/htslib && \
+    rm -f /tmp/downloads/tmp.tar.gz
+
+ENV HTSLIB /tmp/downloads/htslib
+
+RUN curl -sSL -o tmp.tar.gz --retry 10 https://github.com/cancerit/alleleCount/archive/v4.0.0.tar.gz && \
+    mkdir /tmp/downloads/alleleCount && \
+    tar -C /tmp/downloads/alleleCount --strip-components 1 -zxf tmp.tar.gz && \
+    cd /tmp/downloads/alleleCount/c && \
+    mkdir bin && \
+    make && \
+    cp /tmp/downloads/alleleCount/c/bin/alleleCounter /usr/local/bin/. && \
+    cd /tmp/downloads && \
+    rm -rf /tmp/downloads/alleleCount /tmp/downloads/tmp.tar.gz
+
+#COPY battenberg_wgs.R /usr/local/bin/battenberg_wgs.R
+
+CMD ["/bin/bash"]