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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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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_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