INSTALL-CENTOS7

### Enable Extended Packages for Enterprise Linux.
sudo yum -y install epel-release


### Install ncurses-devel and git
sudo yum -y install ncurses-devel git


### Install Ruby.
sudo yum -y install ruby


### Install Perl modules.
sudo yum -y install perl-Tie-IxHash perl-DBI perl-DBD-mysql perl-XML-LibXML perl-XML-Parser perl-DBD-SQLite perl-Time-Piece


###Install Python modules.
sudo yum -y install python-pip scipy python-matplotlib python34 python34-numpy
sudo python -m pip install dendropy pysam

sudo ln -s /usr/bin/python3.4 /usr/bin/python3 # Only if python3 is not already in your path!


### Install R.
sudo yum -y install R


### Download SqueezeMeta.
## You can download the latest release of SqueezeMeta from https://github.com/jtamames/SqueezeM/releases/latest
## Alternatively you can clone the github repository.
##     git clone http://github.com/jtamames/SqueezeMeta


### Install R packages for DAS tool.
sudo R
install.packages("doMC")
install.packages("ggplot2")
install.packages("data.table")
quit(save='no')
sudo R CMD INSTALL <installpath>/SqueezeMeta/bin/DAS_Tool/package/DASTool_1.1.1.tar.gz


### Install the SQMtools R package for downstream analysis of SqueezeMeta results.
sudo R
install.packages("reshape2")
quit(save='no')
sudo R CMD INSTALL <installpath>/SqueezeMeta/lib/SQMtools


### Install databases and test data.
# This will occupy around 200Gb.
<installpath>/SqueezeMeta/scripts/preparing_databases/download_databases.pl <datapath>


### Run SqueezeMeta on test data.
cd <datapath>/test
perl <installpath>/SqueezeMeta/scripts/SqueezeMeta.pl -m merged -p Hadza -s test.samples -f raw/