Mercurial > repos > brasset_jensen > srnapipe

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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 fa794d2a5aaf
files README.rst
diffstat 1 files changed, 11 insertions(+), 3 deletions(-) [+]
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--- a/README.rst	Thu Jan 31 16:10:58 2019 -0500
+++ b/README.rst	Wed Feb 06 04:03:15 2019 -0500
@@ -6,12 +6,14 @@
 
 A GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data
 
+
 Description
 -----------
 
 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.
 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.
 
+
 Prerequisites
 -------------
 
@@ -28,11 +30,14 @@
 
 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
 
+
 Installation
 ------------
 
+sRNAPipe can be installed through the toolshed.
 The process has to be completed by an administrator of your Galaxy server to install sRNAPipe.
 
+You can also install the tool manually:
 
 1. Download sRNAPipe
    You can find sRNAPipe here: https://github.com/brassetjensen/sRNAPipe
@@ -52,14 +57,17 @@
 
 4. Start or Restart Galaxy to use it.
 
+5. Check that the dependencies are correctly installed through Conda in "Manage dependencies".
+
+
 User Manual
 ===========
 
    .. raw:: html
 
       <object data="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px">
-      <embed src="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">
-          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>
-      </embed>
+        <embed src="https://github.com/GReD-Clermont/sRNAPipe/raw/master/sRNAPipe_User_Manual.pdf">
+          <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>
+        </embed>
       </object>