INSTALL-UBUNTU20+

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


### Install openjdk.
sudo apt install openjdk-8-jdk # can possibly work with higher versions


### Install Ruby.
sudo apt install ruby


### Install R
sudo apt install r-base


### Perl modules.
sudo apt install libtie-ixhash-perl libclass-dbi-mysql-perl libxml-parser-perl libxml-libxml-perl libdbd-sqlite3-perl
sudo cpan Linux::MemInfo


### Python modules.
sudo apt install python3-pip python3-dev python3-scipy python3-matplotlib python3-numpy python3-pandas libgsl-dev

sudo -H python3 -m pip install cython dendropy pysam biopython scikit-learn nose


### 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")
# if this fails try
# source("https://bioconductor.org/biocLite.R")
# BiocInstaller::biocLite("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


### Optional: install concoct (if you want to runing along with or instead of maxbin/metabat)
cd <installpath>/SqueezeMeta/bin/bin/CONCOCT-1.1.0
sudo python3 setup.py install


### 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/