zayed/genomemusic repository overview

#Dockerfile
FROM ubuntu:trusty
MAINTAINER Kai Yu, "http://readline.net" #modified by Zayed Albertyn

# Replace apt-get source and install wget
#ADD sources.list /etc/apt/sources.list
RUN apt-get update
RUN apt-get install --yes wget build-essential
RUN apt-get install --yes  liblog-dispatch-filerotate-perl 
RUN apt-get install --yes libdatetime-perl



# Install genome-music
ADD install.sh /opt/install.sh
RUN sh /opt/install.sh
RUN genome install --yes genome-music
RUN rm /opt/install.sh

#! /bin/bash
#save in same folder as dockerfile 

die () {
  echo "$@"
  exit 1
}

APT_URL=http://apt.genome.wustl.edu/ubuntu
KEY_URL=http://apt.genome.wustl.edu/ubuntu/files/genome-institute.asc
DIST=lucid-genome
APT_LIST=/etc/apt/sources.list.d/genome.list


PKG=genome
[ -n "$PKG" ] || \
  die "Please specify the package to install (eg. genome-music)."

[ -d /etc/apt/sources.list.d ] || \
  die "/etc/apt/sources.list.d is not a directory. It looks like this host does not use apt."

APT_PREF="\
# $DIST
Package: *
Pin: release n=$DIST
Pin-Priority: 990"
APT_PREF_FILE="/etc/apt/preferences.d/$DIST.pref"
echo "$APT_PREF" > "$APT_PREF_FILE"

LINE="deb $APT_URL $DIST main"
grep -q "$LINE" "$APT_LIST" 2>/dev/null || \
{
  echo "Adding Genome Institute apt repository to $APT_LIST"
  cat > $APT_LIST <<EOF || die "Cannot write to $APT_LIST."
$LINE
EOF
}

apt-key list 2>/dev/null | grep -q "[email protected]" || \
{
  echo "Adding Genome Institute apt key to keyring"
  wget -q -O - 2>/dev/null $KEY_URL | \
    apt-key add - >/dev/null 2>&1 || \
    die "There was an error importing GPG key with apt-key."
  echo Success
}

apt-get -q2 update || \
  die "There was an error running apt-get update."

echo "Installing $PKG..."
apt-get -y install "$PKG" || \
  die "There was an error installing $PKG."

echo "Success!"
echo "To install genome modules, now run:"
echo "genome install --yes \$MODULENAME"

docker build -t imagename

#!/bin/bash

#WAshU Genome MuSic install
######### INSTALL STUFF
sudo apt-get install  -y curl gcc make pdl libpdl-stats-perl  git samtools libbam-dev bedtools r-base-core libexpat1-dev libnumber-compare-perl  libtext-glob-perl  zlib1g-dev tabix

curl -LO https://github.com/samtools/samtools/archive/0.1.19.tar.gz
tar -zxf 0.1.19.tar.gz
export SAMDIR=$PWD/samtools-0.1.19
cd samtools-0.1.19
make;
cd ..

git clone https://github.com/ding-lab/calc-roi-covg.git
cd  calc-roi-covg; make
sudo mv calcRoiCovg /usr/local/bin/
cd ..


#Install some R packages that enable parallelization across cores:
sudo apt-get install -y r-cran-domc

curl -L http://cpanmin.us | sudo perl - --self-upgrade
#Install some prerequisite Perl modules:

sudo `which cpanm` -n Text::CSV_XS Statistics::Distributions Statistics::Descriptive  Module::Build Regexp::Common Time::HiRes IPC::Cmd LWP::Simple List::MoreUtils Set::Scalar Bit::Vector UR
sudo `which cpanm` -n http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome/genome_0.80.1-3.tar.gz
#Install MuSiC:

sudo `which cpanm` -n http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome-music/genome-music_0.4.1-1.tar.gz

############################# INSTALLATION DONE ###################