File	Date	Author	Commit
TestData	2014-05-16	Marnix Medema	[bd8028] - Update documentation
lib	2014-03-11	Marnix Medema	[cf4da1] - add RiPP_aa.txt
LICENSE.txt	2013-10-02	Marnix Medema	[f9113b] - Linux line breaks
NRP_aa.txt	2013-10-02	Marnix Medema	[f9113b] - Linux line breaks
Pep2Path_Documentation.pdf	2014-05-16	Marnix Medema	[bd8028] - Update documentation
README.txt	2013-10-02	Marnix Medema	[f9113b] - Linux line breaks
RiPP_aa.txt	2014-03-11	Marnix Medema	[cf4da1] - add RiPP_aa.txt
genbank.ppd	2013-10-02	Marnix Medema	[403a33] - fixed genbank.ppd for faulty taxonomy lines w...
makedb.py	2014-03-11	Marnix Medema	[e75cb8] - update Pep2Path to Nrp2Path
mergedb.py	2014-03-11	Marnix Medema	[94c4b1] - update mergedb
norine_peptides.txt	2013-10-02	Marnix Medema	[f9113b] - Linux line breaks
nrp2path.py	2014-05-15	Marnix Medema	[00187c] - fix issue with wrong minimal score
pep2path.cfg	2014-01-23	Marnix Medema	[89caf3] - add number of small bug fixes
ripp2path.py	2014-03-19	Marnix Medema	[eb5225] - bug fix for running antiSMASH parsing with FA...

Read Me

# Copyright (C) 2013 Marnix H. Medema
# University of Groningen
# Department of Microbial Physiology / Groningen Bioinformatics Centre
#
# License: GNU General Public License v3 or later
# A copy of GNU GPL v3 should have been included in this software 
# package in LICENSE.txt.


#########################################################################
PREPREQUISITES FOR PEP2PATH

antiSMASH 2.* must be installed for the makedb program of Pep2Path to
work, and the path to the antiSMASH installation directory should be
indicated in the pep2path.cfg file.

If one only uses the supplied genbank.ppd file, it is not necessary to
install antiSMASH2.

#########################################################################
PREPREQUISITES FOR ANTISMASH 2

To be able to run antiSMASH2 on Windows, you will need to install the
following packages:
- Microsoft Visual C++ 2008 Redistributable Package:
  http://www.microsoft.com/en-us/download/details.aspx?id=29
- Java
  http://www.java.com/en/download/index.jsp
- Python 2.7.X (32-bits version)
  http://www.python.org/ftp/python/2.7.3/python-2.7.3.msi

To be able to run antiSMASH on Mac OS X, you will need to install Cairo
and libxml2.

These can be acquired by first installing MacPorts.
Then, to get Cairo, type 'sudo port install cairo' in the terminal.
To get libxml2, type 'sudo port install libxml2' in the terminal.

If using a version of OS X older than 10.8, make sure that Python 2.7.3
is installed too.

For more information, see the antiSMASH README file.

#########################################################################
INSTALLING PEP2PATH WITHOUT INSTALLING THE ANTISMASH DATABASES

It is possible to install and run Pep2Path without installing the
antiSMASH2 ClusterBlast and Pfam databases.

In such a case, one can edit the run_antismash.py file and delete the
following lines:

"""
    #Check prerequisites
    if check_prereqs(plugins, options) > 0:
        logging.error("Not all prerequisites met")
        sys.exit(1)
"""


#######################################################################
TROUBLESHOOTING

If you have problems running Pep2Path on your system, please contact us
by sending an e-mail to marnixmedema@gmail.com