# HG changeset patch
# User inra-sigenae-sarah-maman
# Date 1356107474 18000
# Node ID 12ab33cb35118bd1726c4612ffc9b03f21a54008
# Parent  574f84006256ce0609e12779b7336b981d3f7894
Uploaded

diff -r 574f84006256 -r 12ab33cb3511 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Dec 21 11:31:14 2012 -0500
@@ -0,0 +1,95 @@
+1 - For these tools, when you will unzip miRNA directory, 3 directories will be created under galaxy_dist/tools/ to house downloaded tools.
+sm_miRNA_qual
+sm_mirdeep2
+sm_miRNA_annotations
+
+
+2 - In the new directory, place the XML and any script file(s) which were contained in the archive.
+
+
+3 - If the tool includes binaries, you'll need to copy them to a directory on your $PATH. If the tool depends on C binaries but does not come with them (only source), you'll need to compile the source first.
+
+Tools which should be installed on your cluster : 
+fastqc : FastQC v0.10.0
+cutadapt : v1.0
+bowtie version 0.12.8
+bwa Version: 0.6.1-r104
+miRDeep2 : "2.0.0.5"
+samtools version: 0.1.18 (r982:295)
+
+sed -i -e "s|/usr/local/bioinfo/bin/bwa|/path/to/your/bwa|" sm_mirdeep2/sm_bwa.pl
+
+sed -i -e "s|/usr/local/bioinfo/bin/samtools|/path/to/your/samtools|" sm_mirdeep2/sm_bwa.pl
+
+sed -i -e "s|/usr/local/bioinfo/bin/samtools|/path/to/your/samtools|" sm_mirdeep2/sm_miRNA_filtrer_aln.pl
+ 
+sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_mirdeep2/mapper.pl|/path/to/mapper script|" sm_mirdeep2/sm_mapper.pl
+
+
+sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_mirdeep2/miRDeep2.pl|/path/to/miRDeep2 script|" sm_mirdeep2/sm_mirdeep2core.pl
+
+sed -i -e "s|:/usr/local/bioinfo/bin|/your/$ENV/path|" sm_mirdeep2/sm_mirdeep2core.pl
+
+
+sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_annotations/join.pl|/path/to/join script|" sm_miRNA_annotations/sm_join_matrice.pl
+
+sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_annotations/lists2venn.pl|/path/to/lists2venn script|" sm_miRNA_annotations/venn.pl
+
+sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/fastqnr.pl|/path/to/fastqnr script|" sm_miRNA_qual/sm_miRNA_fastqnr.pl
+
+sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/join.pl|/path/to/join script|" sm_miRNA_qual/sm_miRNA_join.pl
+
+sed -i -e "s|/usr/local/bioinfo/src/python/current/bin/cutadapt|/path/to/cutadapt script|" sm_miRNA_qual/sm_miRNA_qual.pl
+
+sed -i -e "s|/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/matrix.pl|/path/to/matrix script|" sm_miRNA_qual/sm_miRNA_matrix.pl
+
+sed -i -e "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/plot1.pl|/path/to/plot1 script|" sm_miRNA_qual/sm_miRNA_stats_qual.pl
+
+
+sed -i -e "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/sm_miRNA_qual/stat1_V2.pl|/path/to/stat1_V2 script|" sm_miRNA_qual/sm_miRNA_stats_qual.pl
+
+No dependancies for miRNA tools.
+
+
+
+4 - Add the tool to galaxy_dist/tool_conf.xml.
+
+<section name="Qualite / Nettoyage / Mirdeep2 / Annotation" id="mirdeep2">
+    <tool file="rgenetics/rgFastQC.xml" />
+    <tool file="sm_miRNA_qual/sm_miRNA_qual.xml" />
+    <tool file="sm_miRNA_qual/sm_miRNA_fastqnr.xml" />
+    <tool file="sm_miRNA_qual/sm_miRNA_join.xml" />
+    <tool file="sm_miRNA_qual/sm_miRNA_matrix.xml" />
+    <tool file="sm_miRNA_qual/sm_miRNA_stats_qual.xml" />
+    <tool file="sm_mirdeep2/sm_mapper.xml" />
+    <tool file="sm_mirdeep2/sm_mirdeep2core.xml" />
+    <tool file="sm_mirdeep2/sm_mirdeep2core_bed_to_fasta.xml" />
+    <tool file="sm_mirdeep2/sm_bwa.xml" />
+    <tool file="sm_miRNA_annotations/sm_miRNA_join_matrice.xml" />
+    <tool file="sm_miRNA_annotations/sm_miRNA_venn.xml" />
+</section> 
+
+5 - Restart your Galaxy server process.
+
+
+/***************************************************************
+*  Copyright notice
+*
+*  (c) 2012 PF bioinformatique de Toulouse <>
+*  All rights reserved
+*
+*  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 2 of the License, or
+*  (at your option) any later version.
+*
+*  The GNU General Public License can be found at
+*  http://www.gnu.org/copyleft/gpl.html.
+*
+*  This script 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.
+*
+*  This copyright notice MUST APPEAR in all copies of the script!
+***************************************************************/