Mercurial > repos > devteam > table_annovar
comparison README @ 0:75b252cf390e
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| author | devteam |
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| date | Mon, 02 Dec 2013 15:29:39 -0500 |
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| -1:000000000000 | 0:75b252cf390e |
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| 1 ANNOVAR needs to be installed manually in the following way: | |
| 2 | |
| 3 1a) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of | |
| 4 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files) | |
| 5 | |
| 6 1b) If you do not have ANNOVAR installed, request annovar download and sign license here: | |
| 7 http://www.openbioinformatics.org/annovar/annovar_download_form.php | |
| 8 | |
| 9 i) Once downloaded, install annovar per the installation instructions and note the installation path. | |
| 10 | |
| 11 ii) Then download all desired databases for all desired builds as follows: | |
| 12 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb> | |
| 13 | |
| 14 where <humandb> is location where all database files should be stored | |
| 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) | |
| 16 and <build> can be hg18 or hg19 for humans, also other organisms available. | |
| 17 | |
| 18 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html | |
| 19 | |
| 20 iii) edit the tool-data/annovar.loc file to reflect location of humandb folder | |
| 21 | |
| 22 2) add the annovar scripts convert2annovar.pl and table_annovar.pl to your Galaxy user's path | |
| 23 | |
| 24 3) restart galaxy instance for changes in .loc file to take effect |