INSTALL-CENTOS7

#### NOTE THAT SUPPORT FOR CENTOS7 HAS BEEN DISCONTINUED. SOME BINARIES (e.g. related to the metabat2 pipeline) WILL NOT WORK UNLESS RE-COMPILED IN YOUR ENVIRONMENT
###   WE ARE LEAVING THE INFO BELOW AS A REFERENCE IF YOU ARE A (sorta) POWER USER AND REALLY WANT TO MAKE SQUEEZEMETA RUN IN YOUR SYSTEM

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


### Install git and system libraries
sudo yum -y install gcc ncurses-devel git zlib-devel bzip2-devel xz-devel libxml2-devel libcurl-devel openssl-devel tree libjpeg-turbo-devel gsl-devel


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


### Install Perl modules.
sudo yum -y install cpan perl-Tie-IxHash perl-DBI perl-DBD-mysql perl-XML-LibXML perl-XML-Parser perl-DBD-SQLite perl-Time-Piece
sudo cpan DBD::SQLite::Constants
sudo cpan Linux::MemInfo
sudo cpan Term::ANSIColor


###Install Python modules.
sudo yum -y install python3 python36-scipy python3-devel
sudo python3 -m pip install future cython
sudo python3 -m pip install pandas
sudo python3 -m pip install matplotlib dendropy pysam
sudo python3 -m pip install biopython sklearn nose


### 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.
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


### 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/