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annotate readme.rst @ 0:dfc5a344e2c2 draft

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author bgruening
date Thu, 15 Feb 2018 08:13:20 -0500
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1 ========================
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2 Galaxy deeptools wrapper
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3 ========================
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5 deepTools are user-friendly tools for the normalization and visualization of
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6 deep-sequencing data.
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7 They address the challenge of visualizing the large amounts of data that are now
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8 routinely generated from sequencing centers in a meaningful way.
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9 To do so, deepTools contain useful routines to process the mapped reads data
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10 through removal of duplicates and different filtering options to create coverage
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11 files in standard bedGraph and bigWig file formats. deepTools allow the creation
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12 of normalized coverage files or the comparison between two files
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13 (for example, treatment and control). Finally, using such normalized and
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14 standardized files, multiple visualizations can be created to identify
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15 enrichments with functional annotations of the genome.
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16 For a gallery of images that can be produced and a description
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17 of the tools see our poster_.
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19 .. _poster: http://f1000.com/posters/browse/summary/1094053
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21 deeptools is developed under here:
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23 https://github.com/deeptools/deepTools
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25 For support, questions, or feature requests contact: deeptools@googlegroups.com
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28 ============
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29 Installation
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30 ============
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32 Requirements: python-2.7
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34 Galaxy should be able to automatically install all other dependencies, such as numpy or scipy.
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36 For the best performance we recommend to install blas/lapack/atlas in your environment before
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37 installing deepTools from the Tool Shed.
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40 ========
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41 Citation
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42 ========
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44 deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools.
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47 =======
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48 History
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49 =======
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51 * v1.0: Initial public release
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52 * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version
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55 Licence (MIT)
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56 =============
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57
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58 Permission is hereby granted, free of charge, to any person obtaining a copy
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59 of this software and associated documentation files (the "Software"), to deal
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60 in the Software without restriction, including without limitation the rights
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61 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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62 copies of the Software, and to permit persons to whom the Software is
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63 furnished to do so, subject to the following conditions:
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64
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65 The above copyright notice and this permission notice shall be included in
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66 all copies or substantial portions of the Software.
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67
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68 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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69 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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70 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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71 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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72 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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73 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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74 THE SOFTWARE.