Commit ea2bd360 authored by mmassaviol's avatar mmassaviol
Browse files

Add base container recipe

parent ce641642
Bootstrap: docker
From: rocker/r-ver:3.5.3
%environment
export PATH=/opt/biotools/bin:$PATH
export ROOTSYS=/opt/biotools/root
export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'
%post
if [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi
if [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi
apt-get update
apt-get install -y curl wget git nano
apt-get install -y build-essential checkinstall make cmake software-properties-common
apt-get install -y libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev liblzma-dev
apt-get install -y libxml2-dev libcurl4-openssl-dev
# Python and Snakemake
apt-get install -y python3-pip
cd /usr/bin && ln python3 python && cd -
pip3 install snakemake==5.4.0 oyaml
pip3 install multiqc==1.7
fic=$(find /usr/ -name stacks.py) && sed -i 's/out_dict\[s_name\] = cdict/out_dict\[content\[0\]\] = cdict/' $fic
apt install -y fastqc=0.11.5+dfsg-6
apt-get install -y graphviz pandoc
Rscript -e 'install.packages("BiocManager",Ncpus=8, repos="https://cloud.r-project.org/", clean=TRUE)'
Rscript -e 'install.packages("devtools",Ncpus=8, clean=TRUE)'
Rscript -e 'install.packages(c("shiny","shinydashboard","shinyjs","shinyFiles"),Ncpus=8, repos="https://cloud.r-project.org/", clean=TRUE)'
Rscript -e 'install.packages(c("DT","yaml","tidyverse","gplots"),Ncpus=8, repos="https://cloud.r-project.org/", clean=TRUE)'
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