Mercurial > repos > inra-sigenae-sarah-maman > mirna_mirdeep2
changeset 3:12ab33cb3511 draft
Uploaded
author | inra-sigenae-sarah-maman |
---|---|
date | Fri, 21 Dec 2012 11:31:14 -0500 |
parents | 574f84006256 |
children | 526494efcaf5 |
files | README |
diffstat | 1 files changed, 95 insertions(+), 0 deletions(-) [+] |
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--- /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! +***************************************************************/