#
# Pyrocleaner 
# Copyright (C) 2009 INRA
# 
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#

1. WHAT IS PYROCLEANER

PyroCleaner is intended to clean reads coming from pyrosequencing in order to ease the assembly process. 
It enables filtering sequences on multiple copy reads and other criteria such as length, complexity and 
number of undetermined bases which has been proven to correlate with pour quality. It also permits to 
clean sff files of paired-end sequences and generates on one side a sff with the validated paired-ends 
and on the other the shotgun reads.


2. DEPENDENCIES

Pyrocleaner has some dependencies :
  - BioPython, http://www.biopython.org/wiki/Download
  - NCBI_blast (megablast and formatdb), http://www.ncbi.nlm.nih.gov/BLAST/download.shtml
  - sff_extract.py, http://bioinf.comav.upv.es/sff_extract/index.html
  - cross_match from the Phrap package, this software is only used with the pairends cleaning option.
  - sfffile from Newbler provided by Roche. This software is only used to return a sff file as output. If this one is not installed into your output will be generated in fastq format. 


3. INSTALLATION GUIDELINES

# Download the source from the svn repository 
svn checkout svn://scm.mulcyber.toulouse.inra.fr/svnroot/pyrocleaner

# Then to make sure your installation succeed, the pyrocleaner help should be displayed when typing the following command :
python pyrocleaner.py 


4. GALAXY

If you're using the galaxy tool, when pyrocleaner.py is installed, add the shebang flag as following:

#!/usr/bin/python
# Pyrocleaner 
# Copyright (C) 2009 INRA
...

# Then make a symbolic link to the script file in a PATH directory without the .py extension so it can be called by the galaxy wrapper:
ln -s /path/to/pyrocleaner.py /path/to/bin/dir/pyrocleaner


5. ERGATIS

If you're using the ergatis component, when pyrocleaner.py is installed, add the shebang flag as following:

#!/usr/bin/python
# Pyrocleaner 
# Copyright (C) 2009 INRA
...

# Then make a symbolic link to the script file in a PATH directory without the .py extension so it can be called by the ergatis component:
ln -s /path/to/pyrocleaner.py /path/to/bin/dir/pyrocleaner

# Edit the ergatis config file (/path/to/ergatis/software.config) and add the following lines:
[component pyrocleaner]
$;PYROCLEANER_EXEC$;=/path/to/pyrocleaner

# To iter througth multiple file, the script create_2files_iterator_list.pl is required. Copy this file into the ergatis bin dir and create it's wrapper:
cp create_2files_iterator_list.pl /path/to/ergatis/bin/