srnapipe: README.rst annotate

annotate README.rst @ 68:a5a99218ef7a draft

planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62

author	brasset_jensen
date	Wed, 06 Feb 2019 04:03:15 -0500
parents	740884893563
children	fe3a93edb210

rev	line source
63 11708af40030 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a461e07471d3897046e14389171a2c03d09b912d pierre.pouchin parents: 61 diff changeset	1 .. image:: https://travis-ci.org/GReD-Clermont/sRNAPipe.svg?branch=master
11708af40030 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a461e07471d3897046e14389171a2c03d09b912d pierre.pouchin parents: 61 diff changeset	2 :target: https://travis-ci.org/GReD-Clermont/sRNAPipe
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	3
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	4 sRNAPipe
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	5 ========
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	6
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	7 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	8
68 a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	9
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	10 Description
67 740884893563 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit fa75629bca78685de0106390758c0e85f1ca0836 brasset_jensen parents: 64 diff changeset	11 -----------
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	12
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	13 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	14 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.
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68 a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	16
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	17 Prerequisites
67 740884893563 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit fa75629bca78685de0106390758c0e85f1ca0836 brasset_jensen parents: 64 diff changeset	18 -------------
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	19
64 967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d brasset_jensen parents: 63 diff changeset	20 1. Unix system with A Galaxy server (release 16.01 or later installed)
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	21
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	22 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	23
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	24
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	25 * 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	26 * 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	27 * 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	28
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	29 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	30
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	31 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
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68 a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	33
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	34 Installation
67 740884893563 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit fa75629bca78685de0106390758c0e85f1ca0836 brasset_jensen parents: 64 diff changeset	35 ------------
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	36
68 a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	37 sRNAPipe can be installed through the toolshed.
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	38 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	39
68 a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	40 You can also install the tool manually:
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	41
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	42 1. Download sRNAPipe
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	43 You can find sRNAPipe here: https://github.com/brassetjensen/sRNAPipe
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	44
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	45 2. Put the tool into Galaxy's tools directory
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	46 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	47
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	48 3. Make Galaxy aware of the new tool sRNAPipe
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	49 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	50 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	51
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	52 .. code-block:: xml
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	53
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	54 <section name="NewTools" id="mTools">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	55 <tool file="sRNAPipe.xml" />
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	56 </section>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	57
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	58 4. Start or Restart Galaxy to use it.
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	59
68 a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	60 5. Check that the dependencies are correctly installed through Conda in "Manage dependencies".
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a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	62
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	63 User Manual
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	64 ===========
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	65
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	66 .. raw:: html
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	67
63 11708af40030 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a461e07471d3897046e14389171a2c03d09b912d pierre.pouchin parents: 61 diff changeset	68 <object data="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px">
68 a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	69 <embed src="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">
a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	70 <p>This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p>
a5a99218ef7a planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit d00c3c72956fedbac3aec795b35c8d94d8297a62 brasset_jensen parents: 67 diff changeset	71 </embed>
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	72 </object>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: diff changeset	73

Mercurial > repos > brasset_jensen > srnapipe

annotate README.rst @ 68:a5a99218ef7a draft