RIPELINE is the R-based sequence analysis pipeline

***HOW TO INSTALL RIPELINE***

All platforms:
=============

You will need:

R with working Rscript command (check it by typing in the terminal window
"Rscript", there should come some short instructions of how to use it)

shipunov R package; after installation load it and type in R window
"Rresults()"; this will output the instruction of how to install
"Rresults" command. In principle, Ripeline works with basic "Rscript"
(without "Rresults") but in that case you will need to modify "make_*"
shell scripts

The following R packages: ips, ape, kmer

MrBayes installation which contains "mb-mpi" executable working in the
terminal (check it by typing "mb-mpi" in the terminal window).

RAxML installation; type "raxmlHPC" in terminal to see if this executable
works

MUSCLE installation (optionally also MAFFT and ClustalO); type "muscle"
in terminal to see if it works

NOTE (especially Windows users): if for any reason "mb-mpi" and
"raxmlHPC" do not work, the Ripeline will still run (probably, with some
messages) but Bayesian and RAxML trees will not appear. If you have RAxML
and MrBayes installed, please change names of executable files by editing
corresponding R scripts (they are simple text files). However, Ripeline
will _not_ work without "muscle".

ANOTHER NOTE: all scripts are simple text files, so on Windows and
(probably) on macOS you will need the simple text editor to work with
them. There are many, but few are fully cross-platform and at the same
time feature rich and simple enough for non-programmers; examples of the
latter are "Kate" and "Geany".

Windows:
========

Install bash UNIX shell, e.g. from https://cygwin.com/install.html

(Optional) Install the good terminal application, e.g., ConEmu or cmder (please
google these names)

macOS and Linux:
================

No additional installations required

***HOW TO USE RIPELINE***

Run the example:
================

In the terminal, make Ripeline directory current, e.g., enter in
the terminal window something like "cd ~/some/dir/ripeline"

Then run the shell script "make_all", e.g., enter in the terminal window
"bash ./make_all"

All paramaters (like bootstrap replicates) are set to minimal values so
on the Intel Core i5 with SSD and 8 Gb memory it runs approximately 2 min

Check phylogeny trees which will appear in the directory names "99_trees"

Now change the DNA database (file "_kubricks_dna_txt"): for example,
uncomment (remove "#") in the beginning of last line, then new sequence
start to be available for Ripeline

Run "make_all" again

Check out new phylogeny trees, compare with old ones

Play with this example as long as you like, e.g., add some data, comment
(with "#") some data etc., run "make_all" and observe new phylogeny trees

Run with your data:
===================

The best way is to replace the example databases with your own database
made _in the same way_ (same set of text tables, same column names), and
run again