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AXIOME - Automation, Extension, and Integration Of Microbial Ecology: Helper tools to make managing numerical ecology pipelines easier
Vala C R Shell Python Perl Awk
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build-aux Converted to GNU autotools
debian
plugins
.gitignore Update .gitignore for built version of betadisper
.tarball-version
AUTHORS
COPYING
Makefile.am
NEWS
README
README.developers
aq-base
aq-base.1 The great renaming
aq-betadisper.in
aq-biplot
aq-biplot.1
aq-bubbleplot
aq-bubbleplot.1
aq-cmplibs
aq-cmplibs.1
aq-count-n.1
aq-demux-illumina.1
aq-duleg.1
aq-duleg.in
aq-dulegplot
aq-dulegplot.1
aq-estimateq.1
aq-fasta-length
aq-fasta-length.1
aq-fastq2oldillumina.1
aq-filter-fastq-known.1
aq-inst-cran.1
aq-inst-cran.in
aq-joinn.1
aq-libcontrib
aq-libcontrib.1
aq-marry-illumina-index.1
aq-marry-otu-names.1
aq-mkrepset.1
aq-module.vala
aq-mothur-alpha
aq-mothur-alpha.1
aq-mothur-base
aq-mrpp-unifrac
aq-mrpp-unifrac.1
aq-mrpp.1
aq-mrpp.in
aq-nmf-concordance.1
aq-nmf-concordance.in
aq-nmf.1 Overdue documentation update
aq-nmf.in
aq-oldillumina2fastq
aq-oldillumina2fastq.1
aq-orderotu Made orderotu play nice with converted OTU table
aq-orderotu.1
aq-otu2lnotu
aq-otu2lnotu.1
aq-otu2pcord
aq-otu2pcord.1
aq-otubinner
aq-otubinner.1
aq-otudulegmerge.1
aq-otuhistogram
aq-otuhistogram.1
aq-otunolineage
aq-otunolineage.1
aq-otuplothistogram
aq-otuplothistogram.1
aq-otusum
aq-otusum.1
aq-otutop
aq-otutop.1
aq-otuwithseqs.1
aq-pca.1
aq-pca.in
aq-pcoa.1
aq-pcoa.in
aq-pretendsummarize
aq-pretendsummarize.1
aq-qiime-base
aq-qualhisto.1
aq-qualityanal Put all R library() commands in quotes
aq-qualityanal.1
aq-rareotuwithlineage
aq-rareotuwithlineage.1
aq-sort-fasta
aq-sort-fasta.1
aq-syntheticfastq.1
aq-venn
aq-venn.1
aqxs.1
aqxs.in
autogen.sh
autoqiime.1
axiome.1.in
axiome.deps.in
axiome.spec Add in sample data to docs directory
axiome.vala
biom.R
config.vapi
configure.ac
count-n.c
cover.ps.in
demux-illumina.c
estimateq.c
fasta.vala
fastq2oldillumina.c Removed unnecessary dependency on math
filter-fastq-known.c Removed unnecessary dependency on math
fmap.vala
hmmb.ax.in
hmmb.fasta.gz
joinn.vala
kseq.h
marry-illumina-index.c
marry-otu.vala Updated documentation and usage messages.
mkrepset.vala
nmf.R
otudulegmerge.vala
otuwithseqs.vala
parser.c
parser.h
primers.lst Converted to GNU autotools
qualhisto.c
sample.ax.in
syntheticfastq.c

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).
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