commit 3

Singularity.mapping

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+Bootstrap: docker
+From: continuumio/miniconda3
+
+%labels
+Maintainer Chaetognatha
+Hisat2
+
+%post
+	opt/conda/bin/conda install -c conda-forge -c bioconda hisat2

Singularity.renv

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+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+Maintainer Chaetognatha
+DESeq2
+
+%environment
+R_VERSION=3.6.1
+export R_VERSION
+R_CONFIG_DIR=/etc/R/
+export R_CONFIG_DIR
+export LC_ALL=C
+export PATH=$PATH
+
+%apprun R
+exec R "$@"
+
+%apprun Rscript
+exec Rscript "$@"
+
+%runscript
+exec R "$@"
+
+%post
+  apt-get update
+  apt-get install -y apt-transport-https apt-utils software-properties-common
+  apt-get install -y add-apt-key
+  # set noninteractive installation
+  export DEBIAN_FRONTEND=noninteractive
+  #install tzdata package
+  apt-get install -y tzdata
+  # set your timezone
+  ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
+  dpkg-reconfigure --frontend noninteractive tzdata
+
+  #add CRAN/Ubuntu repo, add key, then refresh
+  apt-get update
+  apt-get install -y wget
+  apt-get install -y r-base r-base-dev
+
+  R --version
+
+  # installing packages from cran
+  R --slave -e 'install.packages("gplots",repos="https://cran.rstudio.com/")'
+  R --slave -e 'install.packages("RColorBrewer",repos="https://cran.rstudio.com/")'
+
+  # installing from bioc
+  R --slave -e 'if (!requireNamespace("BiocManager",quietly=TRUE)) install.packages("BiocManager")'
+  R --slave -e 'BiocManager::install()'
+  R --slave -e 'BiocManager::install("DESeq2",ask=FALSE)'