.. _installing_software:

.. role:: comment

=====================
Software installation
=====================

Here we detail how to install all Linux command-line software used in these resources. Note that if you are setting up a server from scratch, for example if you are using a :ref:`cloud server<cloud_servers>`, you should also ensure that you perform any necessary administration tasks and install and configure any necessary security software you need.

These commands are written for Ubuntu Linux. They will probably work fine on any Ubuntu or Debian machine, and on most Linux machines with the appropriate package manager changes.

We supply these instructions with absolutely no guarantee or warranty. If you break a machine following these instructions, it's not our fault. If you fail to properly secure a cloud server and have it compromised and used to spam people or launch crippling viruses, it's not our fault. If in doubt, seek expert advice.

These commands use the most recent software versions as of December 2020, where the code points to a specific version you should make sure to look up the most recent version and edit accordingly.

Setup
=====

The following commands install some general purpose Linux tools and some libraries that are required for installing one or more software tools detailed below.

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	:class: codebg
	
	:comment:`# Set up directories`
	sudo mkdir /usr/local/deb/
	
	:comment:`# Update installed packages`
	sudo apt update && sudo apt upgrade -y
	
	:comment:`# Install some useful tools`
	sudo apt install rename zip unzip -y
	
	:comment:`# Install tools for building source packages`
	sudo apt install build-essential pkg-config autoconf -y
	
	:comment:`# Install useful language packages`
	sudo apt install python3-pip perl-doc default-jre -y


.. warning::
	
	You should make sure to run all of the above commands before installing any software in this section.


.. _alan:

ALAN
----

Commandline alignment viewer, github `here <https://github.com/mpdunne/alan>`_.

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	sudo wget -P /usr/local/bin/ \https://raw.githubusercontent.com/mpdunne/alan/master/alan
	sudo chmod a+x /usr/local/bin/alan


.. _blast:

BLAST
-----

Widely used sequence searching software, documentation and installation instructions `here <https://www.ncbi.nlm.nih.gov/books/NBK279690/>`_.

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	cd /usr/local/src/
	
	BLAST_VERSION="2.11.0" :comment:`# Change as appropriate`
	sudo wget "\ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
	sudo tar -zxf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
	sudo cp ncbi-blast-${BLAST_VERSION}+/bin/\* /usr/local/bin/


.. _bPTP:

bPTP
----

Bayesian phylogeny-based species delimitation, github `here <https://github.com/zhangjiajie/PTP>`_.

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	:class: codebg
	
	cd /usr/local/src
	sudo git clone \https://github.com/zhangjiajie/PTP
	cd PTP
	sudo -H python3 -m pip install -r requirements.txt
	cd /PTP/bin
	:comment:`# Patch the python version`
	for f in \*.py; do sed -i "1s/python$/python3/" $f; done
	:comment:`# Patch for running on headless server`
	sudo sed -i -e "14s/^$/\nos.environ['QT_QPA_PLATFORM'] = 'offscreen'\n/" bPTP.py
	sudo ln -s /usr/local/src/PTP/bin/bPTP.py /usr/local/bin/bPTP
	sudo ln -s /usr/local/src/PTP/bin/PTP.py /usr/local/bin/PTP


.. _catfasta2phyml:

catfasta2phyml
--------------

Script for concatenating alignments into a supermatrix, github `here <https://github.com/nylander/catfasta2phyml>`_.

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	:class: codebg
	
	sudo wget -O /usr/local/bin/ \https://raw.githubusercontent.com/nylander/catfasta2phyml/master/catfasta2phyml.pl
	sudo chmod a+x /usr/local/bin/catfasta2phyml.pl

Installation not necessary: you could simply download it to your working directory and run it using ``perl``:

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	:class: codebg

	wget /usr/local/bin/ \https://raw.githubusercontent.com/nylander/catfasta2phyml/master/catfasta2phyml.pl
	perl catfasta2phyml.pl


.. _crop:

CROP
----

Bayesian OTU delimitation, github `here <https://github.com/tingchenlab/CROP>`_.

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	sudo apt install libgsl-dev
	
	cd /usr/local/src
	sudo git clone \https://github.com/zhangjiajie/PTP
	cd PTP
	sudo -H python3 -m pip install -r requirements.txt
	sudo -H python3 -m pip install python-nexus
	sudo sed -i "1s/python$/python3/" bin/bPTP.py
	sudo ln -s /usr/local/src/PTP/bin/bPTP.py /usr/local/bin/bPTP


.. _cutadapt:

Cutadapt
--------

Versatile adapter sequence removal, documentation `here <https://cutadapt.readthedocs.io/en/stable/>`_.

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	sudo -H python3 -m pip install cutadapt


.. _extract_genes:

extract_genes
-------------

Script for extracting individual gene sequences from GenBank files, github `here <https://github.com/tjcreedy/biotools>`_.

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	sudo apt install bioperl libarray-utils-perl
	
	sudo wget -O /usr/local/bin/ \https://raw.githubusercontent.com/tjcreedy/biotools/master/extract_genes.pl
	sudo chmod a+x /usr/local/bin/extract_genes.pl

Installation not necessary: you coul simply download it to your working directory and run it using ``perl``:

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	:class: codebg
	
	wget \https://raw.githubusercontent.com/tjcreedy/biotools/master/extract_genes.pl
	perl extract_genes.pl


.. _fasttree:

FastTree
--------

Fast maximum likelihood phylogenetic inference, website `here <http://www.microbesonline.org/fasttree/>`_.

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	cd /usr/local/bin/
	sudo wget \http://www.microbesonline.org/fasttree/FastTree
	sudo wget \http://www.microbesonline.org/fasttree/FastTreeMP
	sudo chmod a+x FastTree\*


.. _fastqc:

FastQC
------

Raw sequence quality assessment, website `here <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_.

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	:class: codebg
	
	cd /usr/local/src/ 
	sudo wget \https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
	sudo unzip fastqc_v0.11.9.zip
	sudo chmod a+x FastQC/fastqc
	sudo ln -s /usr/local/src/FastQC/fastqc /usr/local/bin/fastqc


.. _fastx_toolkit:

FASTX Toolkit
-------------

Various handy tools for dealing with FASTA and FASTQ files. A little out of date though, requires patching to work in modern Ubuntu (all done in the below commands). Website `here <http://hannonlab.cshl.edu/fastx_toolkit/index.html>`_.

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	:class: codebg
	
	cd /usr/local/src/
	
	sudo wget \https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz
	sudo tar -xzf libgtextutils-0.7.tar.gz
	cd libgtextutils-0.7
	sudo sed -i '47s/input_stream/static_cast<bool>(input_stream)/' src/gtextutils/text_line_reader.cpp
	sudo ./configure
	sudo make
	sudo make install
	cd ../
	
	sudo wget \https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
	sudo tar -xjf fastx_toolkit-0.0.14.tar.bz2
	cd fastx_toolkit-0.0.14
	sudo wget \https://github.com/agordon/fastx_toolkit/files/1182724/fastx-toolkit-gcc7-patch.txt
	sudo patch -p1 < fastx-toolkit-gcc7-patch.txt
	sudo ./configure
	sudo make
	sudo make install
	cd ../


.. _mafft:

MAFFT
-----

Sequence alignment software, website `here <https://mafft.cbrc.jp/alignment/software/>`_.

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	sudo wget -P /usr/local/deb/ \https://mafft.cbrc.jp/alignment/software/mafft_7.475-1_amd64.deb
	sudo apt install /usr/local/deb/mafft_7.475-1_amd64.deb


.. _metamate_install:

metaMATE
--------

Tool for exploring detailed read frequency filtering thresholds, github `here <https://github.com/tjcreedy/metaMATE>`_. Requires :ref:`BLAST<blast>`, :ref:`MAFFT<mafft>` and :ref:`R<r>`

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	:class: codebg
	
	sudo -H python3 -m pip install metaMATE
	sudo Rscript -e "install.packages(c('getopt', 'ape', 'fastcluster'), repos = '\https://cloud.r-project.org')"


.. _pairfq:

Pairfq
------

Ensures paired read files are syncronised, github `here <https://github.com/sestaton/Pairfq>`_.

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	sudo apt install libdbd-sqlite3-perl
	
	sudo curl -sL cpanmin.us | sudo perl - \git://github.com/sestaton/Pairfq.git


.. _pear:

PEAR
----

Paired end read merger, website `here <http://www.exelixis-lab.org/pear>`_. You must sign up for a PEAR academic licence on that website and you will receive an email with a link to download the installation files. The command here assumes you've downloaded the file to your home directory.

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	:class: codebg
	
	cd /usr/local/src/
	sudo cp ~/pear-0.9.11-linux-x86_64.tar.gz ./   :comment:`# Change the source path if necessary`
	sudo tar -xzf pear-0.9.11-linux-x86_64.tar.gz
	cd pear-0.9.11-linux-x86_64
	sudo cp bin/pear /usr/local/bin/
	sudo gzip man/pear.1
	sudo cp man/pear.1.gz /usr/share/man/man1/


.. _phylostuff:

phylostuff
----------

A set of scripts for doing stuff with phylogenies, including relabelling and inferring taxonomy. Github `here <https://github.com/tjcreedy/phylostuff>`_. Requires :ref:`R<r>`.

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	sudo apt install libxml2-dev libssl-dev libcurl4-openssl-dev
	
	cd /usr/local/src
	sudo git clone \https://github.com/tjcreedy/phylostuff.git
	cd phylostuff
	sudo ./install.sh

Or just open them in Rstudio and use them as a guide!


.. _r:

R
-

Versatile data handling language, website `here <https://cran.r-project.org>`_.

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	:class: codebg
	
	sudo apt install apt-transport-https
	sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
	sudo add-apt-repository 'deb \https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
	sudo apt install r-base


.. _swarm:

swarm
-----

Linkage-based OTU delimitation, github `here <https://github.com/torognes/swarm>`_.

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	cd /usr/local/src

	sudo git clone \https://github.com/torognes/swarm.git
	cd swarm/
	sudo make
	sudo cp bin/swarm /usr/local/bin/

	cd ~/
	gzip -c /usr/local/src/man/swarm.1 > swarm.1.gz
	sudo mv swarm.1.gz /usr/share/man/man1/


.. _vsearch:

VSEARCH
-------

Open-source implementation of USEARCH with more versatility. VSEARCH is a software package specifically designed for metabarcoding, based on the USEARCH package but completely free and open source. Github `here <https://github.com/torognes/vsearch>`_.

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	:class: codebg
	
	sudo apt install autoconf groff
	
	cd /usr/local/src
	
	sudo wget \https://github.com/torognes/vsearch/archive/v2.15.1.tar.gz
	sudo tar xzf v2.15.1.tar.gz
	cd vsearch-2.15.1
	sudo ./autogen.sh
	sudo ./configure
	sudo make
	sudo make install
	cd ../