#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:
##For Ubuntu (tested with 14.04)
apt-get update && \
apt-get -y install \
build-essential zlib1g-dev libncurses5-dev libcurl4-gnutls-dev libssl-dev libexpat1-dev nettle-dev lsof libgoogle-perftools-dev &&\
apt-get clean
##For 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