diff readme.rst @ 26:2ad3b027dfcd draft

Uploaded
author bgruening
date Thu, 06 Feb 2014 06:40:05 -0500
parents d2898b81b912
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--- a/readme.rst	Tue Feb 04 13:45:17 2014 -0500
+++ b/readme.rst	Thu Feb 06 06:40:05 2014 -0500
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-This package contains a collection of Galaxy workflows utilising deepTools.
+========================
+Galaxy deeptools wrapper
+========================
 
-See http://www.galaxyproject.org for information about the Galaxy Project.
+deepTools are user-friendly tools for the normalization and visualization of 
+deep-sequencing data.
+They address the challenge of visualizing the large amounts of data that are now
+routinely generated from sequencing centers in a meaningful way. 
+To do so, deepTools contain useful routines to process the mapped reads data 
+through removal of duplicates and different filtering options to create coverage
+files in standard bedGraph and bigWig file formats. deepTools allow the creation
+of normalized coverage files or the comparison between two files 
+(for example, treatment and control). Finally, using such normalized and 
+standardized files, multiple visualizations can be created to identify 
+enrichments with functional annotations of the genome. 
+For a gallery of images that can be produced and a description 
+of the tools see our poster_.
+
+.. _poster: http://f1000.com/posters/browse/summary/1094053
+
+deeptools is developed under here:
+
+    https://github.com/fidelram/deepTools
+
+For support, questions, or feature requests contact: deeptools@googlegroups.com
 
 
-Sample Data
-===========
-
-Sample data can be obtained from http://deeptools.ie-freiburg.mpg.de/library or you
-can use aligned reads in BAM or SAM format.
-
-
-
+========
 Citation
 ========
 
-If you use this workflow directly, or a derivative of it, or the associated
-deepTools wrappers for Galaxy, in work leading to a scientific publication,
-please cite:
+deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
+
 
-{publication under review}
+=======
+History
+=======
+
+- v1.0: Initial public release
 
 
-Availability
-============
+Licence (MIT)
+=============
 
-This workflow is available on the main Galaxy Tool Shed:
-
-http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows
-
-Development is being done on github:
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-https://github.com/fidelram/deepTools
-
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-Dependencies
-============
-
-These dependencies should be resolved automatically via the Galaxy Tool Shed:
-
-* http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.