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