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1 ANNOVAR needs to be installed manually in the following way:
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2
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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
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4 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files)
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5
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6 1b) If you do not have ANNOVAR installed, request annovar download and sign license here:
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7 http://www.openbioinformatics.org/annovar/annovar_download_form.php
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8
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9 i) Once downloaded, install annovar per the installation instructions and note the installation path.
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10
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11 ii) Then download all desired databases for all desired builds as follows:
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12 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
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13
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14 where <humandb> is location where all database files should be stored
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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)
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16 and <build> can be hg18 or hg19 for humans, also other organisms available.
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17
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18 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html
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19
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20 iii) edit the tool-data/annovar.loc file to reflect location of humandb folder
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21
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22 2) add the annovar scripts convert2annovar.pl and table_annovar.pl to your Galaxy user's path
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23
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24 3) restart galaxy instance for changes in .loc file to take effect |
