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Singularity
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Singularity
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Bootstrap: shub
From: team113sanger/t113-singularity:r-3.6.0.base-1.0.0
IncludeCmd: no
%help
Help message
%labels
Maintainer Victoria Offord, Wellcome Sanger Institute
Version v1.0.0
R_Version 3.6.0
%environment
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
%post
yum install -y perl-core perl-App-cpanminus
rpm -Uvh http://repo.openfusion.net/centos7-x86_64/openfusion-release-0.7-1.of.el7.noarch.rpm
yum install -y perl-Dist-Zilla
yum -y install epel-release
yum -y install haskell-platform
yum -y install pandoc
Rscript -e "install.packages('BiocManager', repos='https://www.stats.bris.ac.uk/R/', dependencies=TRUE, clean = TRUE)"
Rscript -e "BiocManager::install(c('DESeq2', 'genefilter', 'GenomicRanges', 'graph', 'limma', 'S4Vectors', 'SummarizedExperiment', 'topGO'))"
Rscript -e "library(devtools); install_github('vaofford/deago')"
git clone https://github.com/sanger-pathogens/Bio-Deago.git
cd Bio-Deago
cpanm aliased File::pushd
dzil authordeps --missing | cpanm --notest -f
cpanm CPAN::Meta::Requirements
dzil listdeps --missing | cpanm
dzil test
dzil install
cp -r ./markdown_templates /usr/local/share/