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+++ b/pyrocleaner_galaxy_tool_V1.2/README	Thu Jun 09 06:09:09 2011 -0400
@@ -0,0 +1,77 @@
+#
+# 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/