INSTALL-UBUNTU14+

### Install openjdk.
# If you are using Ubuntu 14 first add the openjdk repository.
sudo add-apt-repository ppa:openjdk-r/ppa
sudo apt-get update
# If you are using Ubuntu 16 or above, just start from here.
sudo apt-get install openjdk-8-jdk
### Install Ruby.
sudo apt-get install ruby


### Install R 3.2.3 or higher.
# If you are using Ubuntu 14 first add the cran repository:
sudo gedit /etc/apt/sources.list
# add "deb https://cloud.r-project.org/bin/linux/ubuntu trusty-cran35/"
#  (without the quotes) to the last line of the file.
sudo apt-get update
# If you are using Ubuntu 16 or above, just start from here.
sudo apt-get install r-base-core


### System libraries.
sudo apt-get install git sqlite3 libxml2-dev libcurl4-openssl-dev


### Perl modules.
sudo apt-get install libtie-ixhash-perl libclass-dbi-mysql-perl libxml-parser-perl libxml-libxml-perl libdbd-sqlite3-perl
sudo cpan Linux::MemInfo
sudo cpan Term::ANSIColor
# If using Ubuntu 14, install DBD::SQLite::Constants with cpan. Not needed for Ubuntu 16+
sudo cpan DBD::SQLite::Constants


### Python modules.
sudo apt-get install python3-pip python3-dev python3-scipy python3-matplotlib python3-numpy python3-pandas
sudo -H python3 -m pip install future cython 
sudo -H python3 -m pip install dendropy pysam


### 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.
sudo R
install.packages("doMC")
install.packages("ggplot2")
install.packages("data.table")
install.packages("reshape2")
install.packages("BiocManager")
BiocManager::install("pathview")
quit(save="no")
sudo R CMD INSTALL <installpath>/SqueezeMeta/bin/DAS_Tool/package/DASTool_1.1.1.tar.gz
sudo R CMD INSTALL <installpath>/SqueezeMeta/lib/SQMtools


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


### Test that all the dependencies can be located in this environment.
<installpath>/SqueezeMeta/utils/install_utils/test_install.pl


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