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change GenomeIntervals to genomeIntervals in Dockerfile
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JocelynSP committed May 30, 2024
1 parent 6158425 commit effa748
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2 changes: 1 addition & 1 deletion Docker/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ RUN echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" >> /
RUN apt-get install libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libcurl4-openssl-dev libssl-dev -y && apt-get clean
# install R + bioconductor packages
RUN MAKE="make -j" Rscript -e 'install.packages(c("BiocManager", "devtools", "tidyverse", "argparser", "stringr", "readr", "scales", "gridExtra", "stringdist", "R6", "ggplot2"), repos="https://cloud.r-project.org/")'
RUN MAKE="make -j" Rscript -e 'BiocManager::install(c("biobase", "biocparallel", "QDNAseq", "VariantAnnotation", "GenomeInfoDb", "SparseArray", "GenomicAlignments", "GenomeIntervals", "StructuralVariantAnnotation", "rtracklayer")); devtools::install_github("Bioconductor/BSgenome@e89b08b590039643f8fe9f030c1948233de4f50f")'
RUN MAKE="make -j" Rscript -e 'BiocManager::install(c("biobase", "biocparallel", "QDNAseq", "VariantAnnotation", "GenomeInfoDb", "SparseArray", "GenomicAlignments", "genomeIntervals", "StructuralVariantAnnotation", "rtracklayer")); devtools::install_github("Bioconductor/BSgenome@e89b08b590039643f8fe9f030c1948233de4f50f")'

COPY BSgenome.Pfalciparum3D7.PlasmoDB.52.tar.gz /tmp/BSgenome.Pfalciparum3D7.PlasmoDB.52.tar.gz
COPY BSgenome.PfalciparumDd2.PlasmoDB.57.tar.gz /tmp/BSgenome.PfalciparumDd2.PlasmoDB.57.tar.gz
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