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Installation

./setup.sh /path/to/installation

/path/to/installation is where you want the bin, lib directories to be created. The following tools will be installed: bwjoin, bwcat, bam2bw, bam2bwbases, bg2bw and bam2bedgraph

⚠️ This distribution will only work on *NIX type systems.

System Dependencies

For installation to proceed you require the following packages:

Ubuntu 14.04

apt-get update && \
apt-get -y install \

            build-essential \
            zlib1g-dev \
            libncurses5-dev \
            libcurl4-gnutls-dev \
            libssl-dev \
            nettle-dev \
            libbz2-dev \
            liblzma-dev \
            &&\

apt-get clean

Ubuntu 16.04

apt-get update && \
apt-get -y install \

            build-essential \
            libbz2-dev \
            libcurl4-gnutls-dev \
            libgnutls-dev \
            liblzma-dev \
            libncurses5-dev \
            libssl-dev \
            nettle-dev \
            zlib1g-dev \
            libp11-kit-dev \
            libtasn1-dev \
            && \            

apt-get clean

Amazon Linux AMI (2016.03.3 x86_64)

yum -q -y update && \
yum -y install \
          make  \
          glibc-devel \
          gcc \
          patch \
          ncurses-devel \
          openssl-devel \
          libcurl-devel \
          gnutls-devel \
          libtasn1-devel \
          p11-kit-devel \
          gmp-devel \
          nettle-devel \
          libbz2-devel \
          liblzma-devel

Should nettle-devel not exist

yum -q -y install autoconf ghostscript texinfo-tex
wget https://git.lysator.liu.se/nettle/nettle/repository/archive.tar.gz?ref=nettle_3.2_release_20160128 -O nettle.tar.gz
mkdir -p nettle
tar --strip-components 1 -C nettle -zxf nettle.tar.gz
cd nettle
./.bootstrap
./configure --disable-pic --disable-shared && \
sudo make && \
sudo make check && \
sudo make install && \
cd .. && \
rm -rf nettle nettle.tar.gz

OSX

In order for cgpBigWig to install you may need the following packages installed

brew install gnutls
# fixes gnutls include
export LIBRARY_PATH="$HOME/homebrew/lib"
export LDFLAGS="-L$HOME/homebrew/opt/libffi/lib"
export PKG_CONFIG_PATH="$HOME/homebrew/opt/libffi/lib/pkgconfig"
brew install libffi
# from https://p11-glue.freedesktop.org/doc/p11-kit/devel-building.html
wget https://p11-glue.freedesktop.org/releases/p11-kit-0.23.2.tar.gz
tar zxf p11-kit-0.23.2.tar.gz
cd p11-kit-0.23.2
./configure --prefix=$HOME/local --without-trust-paths
make