INSTALL

INSTALLATION INSTRUCTIONS FOR MacSyFinder and MacSyView
*******************************************************


1 - Requirements :
==================

for MacSyFinder :
-----------------
- Any machine running a unix-like Operating System.
- Python, (>=2.7 & <3.0)
- makeblastdb (>= 2.2.28) or formatdb (>=2.2.26)
   + makeblastdb is a distribute with blastdb 
     (http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
   + formatdb 
- hmmsearch 3.0 (http://hmmer.janelia.org/)

for MacSyView :
---------------
- chromium or firefox web browser.

2 - Archive overview:
=====================
bin => contain the executables (macsyfinder)
data => the hmm profiles and the systems definitions
doc => the documentation in html and pdf
etc => a template of macsyfinder configuration file
test => all needed for unit tests
macsypy => the macsyfinder python library
setup.py => the installation script

3 - Installation steps:
=======================

3.1 - Make sure every required dependence/software is present.
--------------------------------------------------------------
by default MacSyFinder will search if makeblastdb is on your PATH if not it will looking for formatdb.
if neither makeblastdb nor formatdb are in your path you have to set the absolute path toward one of 
these tools in the configuration file.
by default MacSyFinder will try to use hmmsearch in your PATH, if hmmsearch is not in the PATH, 
you have to set the absolute path to the hmmsearch in configuration.
If the tools are not in the path, some test will be skipped and a warning will be raised.


3.2 - Perform the installation.
-------------------------------

unpack the archive

tar -xzf macsyfinder-x.x.tar.gz
cd macsyfinder-x.x

macsyfinder installation follows classical "pythonic" installation procedure (see http://docs.python.org/2/install/):

 python setup.py build
 python setup.py test -vv
 python setup.py install

if you have not the privileges to perform a system wide installation, you can use virtualenv 
(http://www.virtualenv.org/en/latest/virtualenv.html).
or use the option --prefix
 
You can access all general cmd with  python setup.py --help
and specific options with python setup.py cmd --help


4 Configuration.
================
macsyfinder have some options that can be set in configuration file 
 + system wide $prefix/etc/macsyfinder/macsyfinder.conf
 + user wide ~/.macsyfinder/macsyfinder.conf
 + for project ./macsyfinder.conf
or on the command line.

for all options see documentation 
 + ($prefix or /usr)/share/doc/macsyfinder/html/index.html
 + ($prefix or /usr)/share/doc/macsyfinder/pdf/Macsyfinder.pdf
 
 
5 Uninstalation.
================

To uninstall MacSyFinder (the last version installed), run:
(sudo) python setup.py uninstall


To get started after installation, see the Running MacSyFinder section in the
 User's Guide (Userguide.pdf)