annotate README @ 0:525e6995fe44 draft default tip

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author devteam
date Mon, 09 Nov 2015 11:58:50 -0500
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 ANNOVAR needs to be installed manually in the following way:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 1a) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 1b) If you do not have ANNOVAR installed, request annovar download and sign license here:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 http://www.openbioinformatics.org/annovar/annovar_download_form.php
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 i) Once downloaded, install annovar per the installation instructions and note the installation path.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 ii) Then download all desired databases for all desired builds as follows:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 where <humandb> is location where all database files should be stored
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 and <database> is the database file to download, e.g. refGene (see bottom of document for all available database files at the time of writing this tool)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 and <build> can be hg18 or hg19 for humans, also other organisms available.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 iii) edit the tool-data/annovar.loc file to reflect location of humandb folder
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 2) add the annovar scripts convert2annovar.pl and table_annovar.pl to your Galaxy user's path
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 3) restart galaxy instance for changes in .loc file to take effect