README

AXIOME
======

Tools for making QIIME easier to use. (Formerly AutoQIIME.)

To build AXIOME, you'll need:
	Vala <https://live.gnome.org/Vala>
	Gee <https://live.gnome.org/Libgee>
	libxml2 <http://xmlsoft.org/>
	file <http://www.darwinsys.com/file/>
	bzip2 <http://www.bzip.org/>

and their dependencies (zlib, glib).

On Debian/Ubuntu, you can install these using:
	apt-get install valac libgee-dev libxml2-dev libmagic-dev libbz2-dev

You'll need to install this package with:
	./autogen.sh && ./configure && make && make install

To run AXIOME, you'll additionally need:
	QIIME 1.3+ <http://qiime.org/>
	R
	GNU make <http://www.gnu.org/software/make/>
	Gawk

Some functions require:
	PANDAseq <http://github.com/neufeld/pandaseq>
	NCBI blast2 <http://blast.ncbi.nlm.nih.gov>

You will need to install several R packages which are dependencies. This can be done by calling:
	aq-inst-cran

NOTE: You will need to have a default CRAN mirror set in your Rprofile.site file for the aq-inst-cran script to work.

And then you should read sample.ax and man axiome

If you would like a printable manual, in this directory run:
	make AXIOMEManual.pdf
This requires GNU roff (groff).