Installation Instruction
================================
                      2019-04-24

In this example, suppose KOfam and KofamScan are installed
under $HOME/kofamscan.

% mkdir -p ~/kofamscan/db
% cd ~/kofamscan/db
% wget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz 
% wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz 
% gunzip ko_list.gz 
% tar xvzf profiles.tar.gz 
% mkdir -p ~/kofamscan/bin
% cd ~/kofamscan/bin
% wget ftp://ftp.genome.jp/pub/tools/kofamscan/kofamscan.tar.gz 
% tar xvzf kofamscan.tar.gz 

% cd ~/kofamscan 
% mkdir hmmer src 
% cd src 

Download here hmmer.tar.gz from hmmer.org.

% tar xvzf hmmer.tar.gz 
% cd hmmer-3.2.1 
% ./configure --prefix=$HOME/kofamscan/hmmer 
% make 
% make install 

If you already have ruby 2.4 or later, please skip the follwing
installation instruction of ruby.

  % cd ~/kofamscan 
  % mkdir ruby
  % cd src

  Download here the latest version of ruby from ruby-lang.org.

  % cd ~/kofamscan/src 
  % tar xvzf ruby-2.6.3.tar.gz 
  % cd ruby-2.6.3 
  % ./configure --prefix=$HOME/kofamscan/ruby 
  % make 
  % make install 
  % export PATH=$HOME/kofamscan/ruby/bin:$PATH 

If you already have parallel, please skip the following installation
instruction of parallel.

  % cd ~/kofamscan 
  % mkdir parallel
  % cd src 

  Download here parallel-latest.tar.bz2 from ftp.gnu.org/gnu/parallel/.

  % cd ~/kofamscan/src 
  % tar xvjf parallel-latest.tar.bz2 
  % cd parallel-20190322 
  % ./configure --prefix=$HOME/kofamscan/parallel 
  % make 
  % make install 

Edit config.yml.

% cd ~/kofamscan/bin/ 
% cp config-template.yml config.yml 

An example of config.yml is as follows: 
profile: /path/to/home/kofamscan/db/profiles 
ko_list: /path/to/home/kofamscan/db/ko_list 
hmmsearch: /path/to/home/kofamscan/hmmer/bin/hmmsearch 
parallel: /path/to/home/kofamscan/parallel/bin/parallel 
cpu: 8

If you already have parallel in /usr/bin/parallel,
parallel should be set as follows:

parallel: /usr/bin/parallel 


In this another example, suppose ruby, hmmer and parallel
are installed with Anaconda3, KOfam and KofamScan are
installed under $HOME/kofamscan.

% mkdir -p ~/kofamscan/db
% cd ~/kofamscan/db
% wget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz 
% wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz 
% gunzip ko_list.gz 
% tar xvzf profiles.tar.gz 
% mkdir -p ~/kofamscan/bin
% cd ~/kofamscan/bin
% wget ftp://ftp.genome.jp/pub/tools/kofamscan/kofamscan.tar.gz 
% tar xvzf kofamscan.tar.gz 

Download the appropriate installer of Anaconda3 for your system
from anaconda.com/distribution/.
The installer of Anaconda3 will create $HOME/anaconda3 by default.

% sh Anaconda3-2019.03-Linux-x86_64.sh
% export PATH=$HOME/anaconda3/bin:$PATH
% conda install ruby
% conda install -c bioconda hmmer
% conda install -c bioconda parallel

Edit config.yml.

% cd ~/kofamscan/bin/ 
% cp config-template.yml config.yml 

An example of config.yml is as follows: 
profile: /path/to/home/kofamscan/db/profiles
ko_list: /path/to/home/kofamscan/db/ko_list
hmmsearch: /path/to/home/anaconda3/bin/hmmsearch
parallel: /path/to/home/anaconda3/bin/parallel
cpu: 8