Prok Functional AutoAnnotate Files

Full instructions are in the file doc/README, in doc.tar.gz .
NOTE: autoAnnotate.dbi calls wu-blastp.  A version of wu-blastp is available at
http://www.advbiocomp.com/blast/obsolete/
However, versions from that site have not been tested with autoAnnotate.
Neither has autoAnnotate been tested with NCBI blastp.


Quickstart to install JCVI autoAnnotate v2.5, August 27 2010, on Unix:


1. Install Perl modules from www.cpan.org.

To install DBD::File on Debian:

	apt-get install lib-dbd-file-perl

To install DBD::File using an installed cpan:

	perl -MCPAN -e shell

or

	cpan

then

	install DBD::File
	install DBD::SQLite

etc.

If these methods fail, download the packages from CPAN, untar them,
find the .pm files inside the packages (probably inside a lib directory),
them move them into src/lib, maintaining their directory structure
(e.g., for DBD::File, File.pm goes into src/lib/DBD/File.pm).

These are the Perl modules to install:

	Carp
	CDB_File
	Config::IniFiles
	Cwd
	DBD::File
	DBD::SQLite
	DBI
	English
	File::Basename
	File::Which
	FindBin
	Getopt::Long
	List::Util
	Log::Log4perl
	Pod::Usage
	Storable
	Text::CSV_XS
	threads       (optional)
	Thread::Queue (optional)
	Tree::Trie

These Perl modules are included in the src/lib directory, so you
shouldn't need to install them; but be aware that you may be using
a different version of them now:

	Algorithm::Diff
	Blast::BlastHitDataType
	DBD::CSV
	String::Diff

2. Download the software from sourceforge, gunzip and untar it.

3. Download panda from JCVI at ftp://ftp.jcvi.org/pub/data/panda
(login as user 'anonymous'), then gunzip and untar it into data/panda.

	cd data
	mkdir panda
	cd panda
	(get allgroupWithTables090810.tar.gz and indices-allgroup090810.tar.gz)
	tar xvf all*.tar.gz
	tar xvf ind*.tar.gz

You can alternately load allgroup.tar.gz and indices.tar.gz from SourceForge,
in the 2.4 directory.

4. Download bioname, if you would like to use it (via applyBioName.pl),
from https://sourceforge.net/projects/microbiomeutil/files/
into the src directory, then

	tar xvf bioname-06072009.tar.gz

5. Test autoAnnotate by doing this (in bash):

	./run.bash

This will run autoAnnotate.dbi on the organism jcvi_ann_small_test_1, produce an output file,
and diff it with out/sqlite-smalltest1.dat .  There should be no differences.

6. Note that, to run your own genomes, you'll probably want to figure out
some way to run hmmer2 and BLAST on a large compute grid.  If you
run autoAnnotate without generating the hmmer and BLAST output files
(and set -makedata), it will call blast and hmmpfam itself
(which you will need to install first).  This will take weeks or
months on a single machine.  NOTE: autoAnnotate.dbi calls wu-blastp,
which is no longer available anywhere.  It hasn't been tested with
NCBI blastp.

7. Download and install tmhmm.

8. Download and install signalp.

9. Download and install coils:
Once downloaded, compile coils with these commands:

	tar xvf ncoils.tar.gz
	cd coils
	cc -O2 -I. -o ncoils ncoils.c read_matrix.c -lm
	mv ncoils <somewhere on your executable path>
	cd ..

Now note that you are not moving the top-level coils directory, but only the
directory containing the source code and (what matters to us) the data files:

	mv coils <path>/anno/data/coils


Phil Goetz
pgoetz @ jcvi.org