Mercurial > repos > brasset_jensen > srnapipe

annotate README.rst @ 62:e6c4f3e96e47 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 87e0c95b4d0d1954e81247c31a8f74c5d87c7f9e
author pierre.pouchin
date Thu, 17 Jan 2019 09:56:52 -0500
parents 9185ca0a7b43
children 11708af40030
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
61
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
1
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
2 sRNAPipe
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
3 ========
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
4
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
5 A GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
6
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
7 Description
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
8 ===========
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
9
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
10 The field of small RNA is one of the most investigated research areas since they were shown to regulate gene expression and play essential roles in fundamental biological processes.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
11 sRNAPipe a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: microRNAs, gene transcripts, small nuclear RNAs, ribosomal RNAs, transfer RNAs and transposable elements. It also provides individual mapping and counting for chromosomes, gene transcripts and transposable elements, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5’-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing numbers of overlaps and corresponding z-scores.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
12
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
13 Prerequisites
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
14 =============
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
15
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
16 1. Unix system with A Galaxy server (release july 2014 or later installed)
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
17
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
18 2. Some tools are used by sRNAPipe and must be installed and added to the Path.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
19
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
20
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
21 * Bwa aligner: you can obtain it here: https://sourceforge.net/projects/bio-bwa/files/ . Please download version 0.7.12-r1039 or higher
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
22 * BedTools powerful toolset for genome arithmetic is also needed. It should be found here: http://bedtools.readthedocs.io/en/latest/ . We recommend to use v2.24.0 or higher.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
23 * Samtools : you can obtain it here : https://sourceforge.net/projects/samtools/files/samtools/1.5/. Please download version 1.5
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
24
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
25 3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random", "File::Copy::Recursive" and "Math::CDF" installed.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
26
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
27 4. R project version higher than 3.1 is needed with libraries "plotrix", "bioconductor-sushi", "RColorBrewer" and "ggplot2" installed. You can find respectively these libraries here: https://cran.r-project.org/web/packages/plotrix/index.html and https://bioconductor.org/packages/release/bioc/html/Sushi.html and https://cran.r-project.org/web/packages/RColorBrewer/index.html and https://cran.r-project.org/web/packages/ggplot2/index.html
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
28
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
29 Installation
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
30 ============
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
31
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
32 The process has to be completed by an administrator of your Galaxy server to install sRNAPipe.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
33
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
34
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
35 1. Download sRNAPipe
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
36 You can find sRNAPipe here: https://github.com/brassetjensen/sRNAPipe
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
37
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
38 2. Put the tool into Galaxy's tools directory
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
39 You need to add files into tools/ directory , where all tool-related files are stored, within your Galaxy installation.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
40
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
41 3. Make Galaxy aware of the new tool sRNAPipe
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
42 Now that the tool and its definition file are ready, the final step is to make Galaxy aware of the new files.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
43 Galaxy recognizes installed tools by reading the tool_conf.xml tool configuration file. Thus, letting Galaxy know about the new tool is as easy as adding a few lines to the tool_conf.xml file located in the config/ directory of the Galaxy installation. New tools can either be added to existing sections or added to new sections defined in the following way:
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
44
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
45 .. code-block:: xml
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
46
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
47 <section name="NewTools" id="mTools">
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
48 <tool file="sRNAPipe.xml" />
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
49 </section>
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
50
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
51 4. Start or Restart Galaxy to use it.
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
52
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
53 User Manual
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
54 ===========
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
55
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
56 .. raw:: html
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
57
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
58 <object data="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px">
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
59 <embed src="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf">
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
60 This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p>
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
61 </embed>
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
62 </object>
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
parents:
diff changeset
63