comparison README~ @ 0:d3a72e55deca draft

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author saskia-hiltemann
date Wed, 18 Sep 2013 10:51:20 -0400
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children 565c0e690238
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1 ANNOVAR needs to be installed manually in the following way:
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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
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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
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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.
13 tool uses annotate_variation.pl and convert2annovar.pl
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15 4) Then download all desired databases for all desired builds as follows:
16 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
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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.
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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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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
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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:
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
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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_cytoBand.txt
145 hg19_dgv.txt
146 hg19_ensGeneMrna.fa
147 hg19_ensGene.txt
148 hg19_esp5400_aa.txt
149 hg19_esp5400_aa.txt.idx
150 hg19_esp5400_all.txt
151 hg19_esp5400_all.txt.idx
152 hg19_esp5400_ea.txt
153 hg19_esp5400_ea.txt.idx
154 hg19_esp6500_aa.txt
155 hg19_esp6500_aa.txt.idx
156 hg19_esp6500_all.txt
157 hg19_esp6500_all.txt.idx
158 hg19_esp6500_ea.txt
159 hg19_esp6500_ea.txt.idx
160 hg19_esp6500si_aa.txt
161 hg19_esp6500si_aa.txt.idx
162 hg19_esp6500si_all.txt
163 hg19_esp6500si_all.txt.idx
164 hg19_esp6500si_ea.txt
165 hg19_esp6500si_ea.txt.idx
166 hg19_EUR.sites.2012_04.txt
167 hg19_EUR.sites.2012_04.txt.idx
168 hg19_genomicSuperDups.txt
169 hg19_gerp++gt2.txt
170 hg19_gerp++gt2.txt.idx
171 hg19_gwasCatalog.txt
172 hg19_keggMapDesc.txt
173 hg19_keggPathway.txt
174 hg19_kgXref.txt
175 hg19_knownGeneMrna.fa
176 hg19_knownGene.txt
177 hg19_ljb_all.txt
178 hg19_ljb_all.txt.idx
179 hg19_ljb_lrt.txt
180 hg19_ljb_lrt.txt.idx
181 hg19_ljb_mt.txt
182 hg19_ljb_mt.txt.idx
183 hg19_ljb_phylop.txt
184 hg19_ljb_phylop.txt.idx
185 hg19_ljb_pp2.txt
186 hg19_ljb_pp2.txt.idx
187 hg19_ljb_sift.txt
188 hg19_ljb_sift.txt.idx
189 hg19_phastConsElements46way.txt
190 hg19_refGeneMrna.fa
191 hg19_refGene.txt
192 hg19_refLink.txt
193 hg19_snp130NonFlagged.txt
194 hg19_snp130NonFlagged.txt.idx
195 hg19_snp130.txt
196 hg19_snp130.txt.idx
197 hg19_snp131NonFlagged.txt
198 hg19_snp131NonFlagged.txt.idx
199 hg19_snp131.txt
200 hg19_snp132NonFlagged.txt
201 hg19_snp132NonFlagged.txt.idx
202 hg19_snp132.txt
203 hg19_snp132.txt.idx
204 hg19_snp135NonFlagged.txt
205 hg19_snp135NonFlagged.txt.idx
206 hg19_snp135.txt
207 hg19_snp137NonFlagged.txt
208 hg19_snp137NonFlagged.txt.idx
209 hg19_snp137.txt
210 hg19_tfbsConsSites.txt
211