0
+ − 1 ANNOVAR needs to be installed manually in the following way:
+ − 2
+ − 3
+ − 4 1) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of
+ − 5 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files)
+ − 6 1b) Restart galaxy instance for changes in .loc file to take effect
+ − 7
+ − 8
+ − 9 2) If you do not have ANNOVAR installed, request annovar download and sign license here:
+ − 10 http://www.openbioinformatics.org/annovar/annovar_download_form.php
+ − 11
+ − 12 3) Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts.
+ − 13 tool uses annotate_variation.pl and convert2annovar.pl
+ − 14
+ − 15 4) Then download all desired databases for all desired builds as follows:
+ − 16 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
+ − 17
+ − 18 where <humandb> is location where all database files should be stored
+ − 19 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)
+ − 20 and <build> can be hg18 or hg19 for humans, also other organisms available.
+ − 21
+ − 22 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html
+ − 23
+ − 24 5) edit the tool-data/annovar.loc file to reflect location of humandb folder
+ − 25 5b) restart galaxy instance for changes in .loc file to take effect
+ − 26
+ − 27 6) Tool uses cgatools join for combining of files, this should be installed automatically with repository. If not, get a copy from Complete Genomics directly:
+ − 28 wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
+ − 29 tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
+ − 30
+ − 31 and place the "cgatools" binary found in bin/ directory on your $PATH
+ − 32
+ − 33
+ − 34 list of files in my own humandb folder:
+ − 35
+ − 36 hg18_ALL.sites.2012_04.txt
+ − 37 hg18_ALL.sites.2012_04.txt.idx
+ − 38 hg18_avsift.txt
+ − 39 hg18_avsift.txt.idx
+ − 40 hg18_CEU.sites.2010_07.txt
+ − 41 hg18_CEU.sites.2010_07.txt.idx
+ − 42 hg18_cg46.txt
+ − 43 hg18_cg46.txt.idx
+ − 44 hg18_cg69.txt
+ − 45 hg18_cg69.txt.idx
+ − 46 hg18_cytoBand.txt
+ − 47 hg18_dgv.txt
+ − 48 hg18_ensGeneMrna.fa
+ − 49 hg18_ensGene.txt
+ − 50 hg18_esp5400_aa.txt
+ − 51 hg18_esp5400_aa.txt.idx
+ − 52 hg18_esp5400_all.txt
+ − 53 hg18_esp5400_all.txt.idx
+ − 54 hg18_esp5400_ea.txt
+ − 55 hg18_esp5400_ea.txt.idx
+ − 56 hg18_esp6500_aa.txt
+ − 57 hg18_esp6500_aa.txt.idx
+ − 58 hg18_esp6500_all.txt
+ − 59 hg18_esp6500_all.txt.idx
+ − 60 hg18_esp6500_ea.txt
+ − 61 hg18_esp6500_ea.txt.idx
+ − 62 hg18_esp6500si_aa.txt
+ − 63 hg18_esp6500si_aa.txt.idx
+ − 64 hg18_esp6500si_all.txt
+ − 65 hg18_esp6500si_all.txt.idx
+ − 66 hg18_esp6500si_ea.txt
+ − 67 hg18_esp6500si_ea.txt.idx
+ − 68 hg18_example_db_generic.txt
+ − 69 hg18_example_db_gff3.txt
+ − 70 hg18_genomicSuperDups.txt
+ − 71 hg18_gerp++gt2.txt
+ − 72 hg18_gerp++gt2.txt.idx
+ − 73 hg18_gwasCatalog.txt
+ − 74 hg18_JPTCHB.sites.2010_07.txt
+ − 75 hg18_JPTCHB.sites.2010_07.txt.idx
+ − 76 hg18_keggMapDesc.txt
+ − 77 hg18_keggPathway.txt
+ − 78 hg18_kgXref.txt
+ − 79 hg18_knownGeneMrna.fa
+ − 80 hg18_knownGene.txt
+ − 81 hg18_ljb_all.txt
+ − 82 hg18_ljb_all.txt.idx
+ − 83 hg18_ljb_lrt.txt
+ − 84 hg18_ljb_lrt.txt.idx
+ − 85 hg18_ljb_mt.txt
+ − 86 hg18_ljb_mt.txt.idx
+ − 87 hg18_ljb_phylop.txt
+ − 88 hg18_ljb_phylop.txt.idx
+ − 89 hg18_ljb_pp2.txt
+ − 90 hg18_ljb_pp2.txt.idx
+ − 91 hg18_ljb_sift.txt
+ − 92 hg18_ljb_sift.txt.idx
+ − 93 hg18_phastConsElements44way.txt
+ − 94 hg18_refGeneMrna.fa
+ − 95 hg18_refGene.txt
+ − 96 hg18_refLink.txt
+ − 97 hg18_snp128NonFlagged.txt
+ − 98 hg18_snp128NonFlagged.txt.idx
+ − 99 hg18_snp128.txt
+ − 100 hg18_snp128.txt.idx
+ − 101 hg18_snp129NonFlagged.txt
+ − 102 hg18_snp129NonFlagged.txt.idx
+ − 103 hg18_snp129.txt
+ − 104 hg18_snp129.txt.idx
+ − 105 hg18_snp130NonFlagged.txt
+ − 106 hg18_snp130NonFlagged.txt.idx
+ − 107 hg18_snp130.txt
+ − 108 hg18_snp130.txt.idx
+ − 109 hg18_snp131NonFlagged.txt
+ − 110 hg18_snp131NonFlagged.txt.idx
+ − 111 hg18_snp131.txt
+ − 112 hg18_snp131.txt.idx
+ − 113 hg18_snp132NonFlagged.txt
+ − 114 hg18_snp132NonFlagged.txt.idx
+ − 115 hg18_snp132.txt
+ − 116 hg18_snp132.txt.idx
+ − 117 hg18_tfbsConsSites.txt
+ − 118 hg18_YRI.sites.2010_07.txt
+ − 119 hg18_YRI.sites.2010_07.txt.idx
+ − 120 hg19_AFR.sites.2012_04.txt
+ − 121 hg19_AFR.sites.2012_04.txt.idx
+ − 122 hg19_ALL.sites.2010_11.txt
+ − 123 hg19_ALL.sites.2010_11.txt.idx
+ − 124 hg19_ALL.sites.2012_02.txt
+ − 125 hg19_ALL.sites.2012_02.txt.idx
+ − 126 hg19_ALL.sites.2012_04.txt
+ − 127 hg19_ALL.sites.2012_04.txt.idx
+ − 128 hg19_AMR.sites.2012_04.txt
+ − 129 hg19_AMR.sites.2012_04.txt.idx
+ − 130 hg19_ASN.sites.2012_04.txt
+ − 131 hg19_ASN.sites.2012_04.txt.idx
+ − 132 hg19_avsift.txt
+ − 133 hg19_avsift.txt.idx
+ − 134 hg19_cg46.txt
+ − 135 hg19_cg46.txt.idx
+ − 136 hg19_cg69.txt
+ − 137 hg19_cg69.txt.idx
+ − 138 hg19_cosmic61.txt
+ − 139 hg19_cosmic61.txt.idx
+ − 140 hg19_cosmic63.txt
+ − 141 hg19_cosmic63.txt.idx
+ − 142 hg19_cosmic64.txt
+ − 143 hg19_cosmic64.txt.idx
+ − 144 hg19_cosmic65.txt
+ − 145 hg19_cosmic65.txt.idx
+ − 146 hg19_cytoBand.txt
+ − 147 hg19_dgv.txt
+ − 148 hg19_ensGeneMrna.fa
+ − 149 hg19_ensGene.txt
+ − 150 hg19_esp5400_aa.txt
+ − 151 hg19_esp5400_aa.txt.idx
+ − 152 hg19_esp5400_all.txt
+ − 153 hg19_esp5400_all.txt.idx
+ − 154 hg19_esp5400_ea.txt
+ − 155 hg19_esp5400_ea.txt.idx
+ − 156 hg19_esp6500_aa.txt
+ − 157 hg19_esp6500_aa.txt.idx
+ − 158 hg19_esp6500_all.txt
+ − 159 hg19_esp6500_all.txt.idx
+ − 160 hg19_esp6500_ea.txt
+ − 161 hg19_esp6500_ea.txt.idx
+ − 162 hg19_esp6500si_aa.txt
+ − 163 hg19_esp6500si_aa.txt.idx
+ − 164 hg19_esp6500si_all.txt
+ − 165 hg19_esp6500si_all.txt.idx
+ − 166 hg19_esp6500si_ea.txt
+ − 167 hg19_esp6500si_ea.txt.idx
+ − 168 hg19_EUR.sites.2012_04.txt
+ − 169 hg19_EUR.sites.2012_04.txt.idx
+ − 170 hg19_genomicSuperDups.txt
+ − 171 hg19_gerp++gt2.txt
+ − 172 hg19_gerp++gt2.txt.idx
+ − 173 hg19_gwasCatalog.txt
+ − 174 hg19_keggMapDesc.txt
+ − 175 hg19_keggPathway.txt
+ − 176 hg19_kgXref.txt
+ − 177 hg19_knownGeneMrna.fa
+ − 178 hg19_knownGene.txt
+ − 179 hg19_ljb_all.txt
+ − 180 hg19_ljb_all.txt.idx
+ − 181 hg19_ljb_lrt.txt
+ − 182 hg19_ljb_lrt.txt.idx
+ − 183 hg19_ljb_mt.txt
+ − 184 hg19_ljb_mt.txt.idx
+ − 185 hg19_ljb_phylop.txt
+ − 186 hg19_ljb_phylop.txt.idx
+ − 187 hg19_ljb_pp2.txt
+ − 188 hg19_ljb_pp2.txt.idx
+ − 189 hg19_ljb_sift.txt
+ − 190 hg19_ljb_sift.txt.idx
+ − 191 hg19_phastConsElements46way.txt
+ − 192 hg19_refGeneMrna.fa
+ − 193 hg19_refGene.txt
+ − 194 hg19_refLink.txt
+ − 195 hg19_snp130NonFlagged.txt
+ − 196 hg19_snp130NonFlagged.txt.idx
+ − 197 hg19_snp130.txt
+ − 198 hg19_snp130.txt.idx
+ − 199 hg19_snp131NonFlagged.txt
+ − 200 hg19_snp131NonFlagged.txt.idx
+ − 201 hg19_snp131.txt
+ − 202 hg19_snp132NonFlagged.txt
+ − 203 hg19_snp132NonFlagged.txt.idx
+ − 204 hg19_snp132.txt
+ − 205 hg19_snp132.txt.idx
+ − 206 hg19_snp135NonFlagged.txt
+ − 207 hg19_snp135NonFlagged.txt.idx
+ − 208 hg19_snp135.txt
+ − 209 hg19_snp137NonFlagged.txt
+ − 210 hg19_snp137NonFlagged.txt.idx
+ − 211 hg19_snp137.txt
+ − 212 hg19_tfbsConsSites.txt
+ − 213
