PGP-UK/GenomeChronicler:latest

$ singularity pull shub://PGP-UK/GenomeChronicler:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:bionic

%runscript
echo "Starting the GenomeChronicler container [20-210]..."

echo "Running GenomeChronicler itself"
perl /GenomeChronicler/GenomeChronicler_mainDruid.pl "$@"

%post

apt-get -y update

apt-get install -y apt-transport-https software-properties-common
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
add-apt-repository ppa:linuxuprising/java

apt-get -y update

apt-get -y install openjdk-8-jdk


#apt-get -y update
apt-get -y install r-base-core

apt-get -y install tk-dev
apt-get -y install mesa-common-dev libglu1-mesa-dev #Satisfying dependencies for rgl that seems to be required below for RColorBrewer


# Installing perl modules

apt-get -y install wget
wget -O - http://cpanmin.us | perl - --self-upgrade #Attempting to automatically configure CPAN

cpan File::chdir
cpan Config::General
cpan Data::Dumper
cpan Excel::Writer::XLSX
cpan DBI
cpan DBD::SQLite


# Installing a couple of tools here from github releases

cd /usr/bin
wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
tar -vxjf htslib-1.9.tar.bz2
cd htslib-1.9
make

cd /usr/bin
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -vxjf samtools-1.9.tar.bz2
cd samtools-1.9
make

cd /usr/bin
wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
tar -vxjf bcftools-1.9.tar.bz2
cd bcftools-1.9
make

cd /


# Install required R packages
R --slave -e 'install.packages("RColorBrewer", dependencies=TRUE, repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("TeachingDemos", dependencies=TRUE, repos = "http://cran.us.r-project.org")'



# Installing LaTeX stuff
apt-get -y install texlive-latex-base texlive-fonts-recommended texlive-latex-extra lmodern


# Installing extra software
#apt-get -y install libssl
apt-get -y install libssl-dev
apt-get -y install libcurl4-openssl-dev
apt-get -y install git


# Getting GenomeChronicler Repo
git clone https://github.com/PGP-UK/GenomeChronicler.git


# Running GenomeChronicler Setup
cd /GenomeChronicler
bash SetupMeFirst.sh

chmod +x GenomeChronicler_mainDruid.pl


%apprun genomechronicler
    perl /GenomeChronicler/GenomeChronicler_mainDruid.pl "$@"

%apprun gc
    perl /GenomeChronicler/GenomeChronicler_mainDruid.pl "$@"

%environment
export LC_ALL=C
export PATH=$PATH:$PWD
export PATH="$PATH:/usr/bin/bcftools-1.9"
export PATH="$PATH:/usr/bin/samtools-1.9"
export PATH="$PATH:/usr/bin/htslib-1.9"
export PATH="$PATH:/GenomeChronicler"


#genomechronicler

Collection

• Name: PGP-UK/GenomeChronicler
• License: None

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