Mercurial > repos > iuc > gemini_qc
annotate readme.rst @ 2:9872131c2377 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author | iuc |
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date | Thu, 09 Nov 2017 13:17:27 -0500 |
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a875f940d8fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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1 ========================= |
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2 Galaxy wrapper for GEMINI |
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3 ========================= |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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4 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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6 GEMINI: a flexible framework for exploring genome variation |
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7 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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8 GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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9 the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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10 and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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11 powerful system for exploring genetic variation for for disease and population genetics. |
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12 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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13 Using the GEMINI framework begins by loading a VCF file into a database. Each variant is automatically |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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14 annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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15 OMIM, dbSNP, KEGG, and HPRD. All of this information is stored in portable SQLite database that allows |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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16 one to explore and interpret both coding and non-coding variation using “off-the-shelf” tools or an |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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17 enhanced SQL engine. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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18 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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19 Please also see the original [manuscript](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153). |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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20 |
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21 |
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22 ============ |
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23 Installation |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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24 ============ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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25 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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26 It is recommended to install this wrapper via the `Galaxy Tool Shed`. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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27 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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28 .. _`Galaxy Tool Shed`: https://testtoolshed.g2.bx.psu.edu/view/iuc/gemini |
a875f940d8fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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29 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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30 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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31 ======= |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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32 History |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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33 ======= |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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34 - 0.9.1: Initial public release |
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35 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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36 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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37 ==================== |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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38 Detailed description |
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39 ==================== |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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40 |
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41 View the original GEMINI documentation: http://gemini.readthedocs.org/en/latest/index.html |
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42 |
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43 |
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44 =============================== |
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45 Wrapper Licence (MIT/BSD style) |
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46 =============================== |
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47 |
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48 Permission to use, copy, modify, and distribute this software and its |
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49 documentation with or without modifications and for any purpose and |
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50 without fee is hereby granted, provided that any copyright notices |
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51 appear in all copies and that both those copyright notices and this |
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52 permission notice appear in supporting documentation, and that the |
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53 names of the contributors or copyright holders not be used in |
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54 advertising or publicity pertaining to distribution of the software |
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55 without specific prior permission. |
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56 |
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57 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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58 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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59 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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60 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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61 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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62 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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63 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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64 OR PERFORMANCE OF THIS SOFTWARE. |
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65 |