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INSTALL.md

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Install

./setup.sh /install/to/here

'/install/to/here' is where you want the bin/lib folders to be created.

setup.sh will install

  • biobambam
  • bwa
  • samtools

NOTE:

bwa_aln.pl will only function when 0.6.x installed (you will need to make this available on path manually) bwa_mem.pl will only function when 0.7.x installed

Perl

Minimum version: 5.10.1 Tested version: 5.16.3

OS

This distribution will only work on *NIX type systems at present.

Other Software

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 libexpat1-dev nettle-dev libgoogle-perftools-dev &&\
apt-get clean

Ubuntu 16

Thanks to @jsmedmar

apt-get -yqq install \
    build-essential \
    libbz2-dev \
    libcurl4-gnutls-dev \
    libgnutls-dev \
    liblzma-dev \
    libncurses5-dev \
    libssl-dev \
    locales \
    nettle-dev \
    wget \
    zlib1g-dev \
    curl
    libexpat1-dev \
    libgoogle-perftools-dev \
    lsof \
    time \
    libgd-perl \
    psmisc \
    moreutils

Amazon Linux AMI

(2016.03.0 x86_64)

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

Should nettle-devel not exist Use the following

yum -q -y install autoconf
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