Revision 84c81131
| b/AcNPV/dataset | ||
|---|---|---|
| 1 |
mock images/mock.png Mock data set \N Just a mock data set... |
|
| b/AcNPV/decorInfo | ||
|---|---|---|
| 1 |
gene genes \N 2 0 1 http://www.ncbi.nlm.nih.gov/gene/?term= |
|
| 2 |
CDS CDS (genes) gene 2 0 0 \N |
|
| 3 |
repeat_region repeats \N 2 0 0 \N |
|
| 4 |
gc5Base GC percent \N 5 14 1 \N |
|
| b/AcNPV/makeDb.sql | ||
|---|---|---|
| 1 |
drop table if exists config; |
|
| 2 |
create table config ( |
|
| 3 |
bbiPath text not null, |
|
| 4 |
seqPath text null, |
|
| 5 |
defaultTracks text null, |
|
| 6 |
defaultMdcategory varchar(255) not null, |
|
| 7 |
defaultGenelist text null, |
|
| 8 |
defaultCustomtracks text null, |
|
| 9 |
defaultPosition varchar(255) not null, |
|
| 10 |
defaultDataset varchar(255) not null, |
|
| 11 |
defaultDecor text null, |
|
| 12 |
defaultScaffold text not null, |
|
| 13 |
ideogram_wiggle1 varchar(255) null, |
|
| 14 |
ideogram_wiggle2 varchar(255) null, |
|
| 15 |
hasGene boolean not null, |
|
| 16 |
allowJuxtaposition boolean not null, |
|
| 17 |
keggSpeciesCode varchar(255) null, |
|
| 18 |
information text not null, |
|
| 19 |
runmode tinyint not null, |
|
| 20 |
initmatplot boolean not null |
|
| 21 |
); |
|
| 22 |
INSERT INTO `config` VALUES ( |
|
| 23 |
'/srv/epgg/data/data/subtleKnife/AcNPV/', |
|
| 24 |
'/srv/epgg/data/data/subtleKnife/seq/AcNPV.gz', |
|
| 25 |
NULL, |
|
| 26 |
'Sample', |
|
| 27 |
NULL, |
|
| 28 |
NULL, |
|
| 29 |
'NC_001623.1,0,NC_001623.1,10000', |
|
| 30 |
'mock', |
|
| 31 |
'gene,gc5Base', |
|
| 32 |
'NC_001623.1', |
|
| 33 |
NULL, |
|
| 34 |
NULL, |
|
| 35 |
1, |
|
| 36 |
1, |
|
| 37 |
'AcNPV', |
|
| 38 |
'Assembly version|08-MAR-1999|Sequence source|<a href=http://www.ncbi.nlm.nih.gov/nuccore/NC_001623 target=_blank>NCBI</a>|Reference|<a href=http://www.ncbi.nlm.nih.gov/pubmed/8030224 target=_blank>Virology. 1994 Aug 1;202(2):586-605.</a>|Date parsed|September 16, 2013|Chromosomes|1|Misc|0|Total bases|133,894|Logo art|<a href=http://viralzone.expasy.org/all_by_protein/537.html target=_blank>link</a>', |
|
| 39 |
0, |
|
| 40 |
0); |
|
| 41 |
|
|
| 42 |
|
|
| 43 |
-- grouping types on genomic features |
|
| 44 |
-- table name defined in macro: TBN_GF_GRP |
|
| 45 |
drop table if exists gfGrouping; |
|
| 46 |
create table gfGrouping ( |
|
| 47 |
id TINYINT not null primary key, |
|
| 48 |
name char(50) not null |
|
| 49 |
); |
|
| 50 |
insert into gfGrouping values (2, "Genes"); |
|
| 51 |
-- insert into gfGrouping values (3, "non-coding RNA"); |
|
| 52 |
-- insert into gfGrouping values (4, "RepeatMasker"); |
|
| 53 |
-- insert into gfGrouping values (6, "Sequence conservation"); |
|
| 54 |
insert into gfGrouping values (5, "Others"); |
|
| 55 |
|
|
| 56 |
|
|
| 57 |
|
|
| 58 |
drop table if exists decorInfo; |
|
| 59 |
create table decorInfo ( |
|
| 60 |
name char(50) not null primary key, |
|
| 61 |
printname char(100) not null, |
|
| 62 |
parent char(50) null, |
|
| 63 |
grp tinyint not null, |
|
| 64 |
fileType tinyint not null, |
|
| 65 |
hasStruct tinyint null, |
|
| 66 |
queryUrl varchar(255) null |
|
| 67 |
); |
|
| 68 |
load data local infile 'decorInfo' into table decorInfo; |
|
| 69 |
|
|
| 70 |
drop table if exists track2Label; |
|
| 71 |
create table track2Label ( |
|
| 72 |
name varchar(255) not null primary key, |
|
| 73 |
label text null |
|
| 74 |
); |
|
| 75 |
load data local infile 'track2Label' into table track2Label; |
|
| 76 |
|
|
| 77 |
drop table if exists track2ProcessInfo; |
|
| 78 |
create table track2ProcessInfo ( |
|
| 79 |
name varchar(255) not null primary key, |
|
| 80 |
detail text null |
|
| 81 |
); |
|
| 82 |
load data local infile 'track2ProcessInfo' into table track2ProcessInfo; |
|
| 83 |
|
|
| 84 |
drop table if exists track2BamInfo; |
|
| 85 |
create table track2BamInfo ( |
|
| 86 |
name varchar(255) not null, |
|
| 87 |
bamfile varchar(255) not null, |
|
| 88 |
bamfilelabel varchar(255) not null |
|
| 89 |
); |
|
| 90 |
load data local infile "track2BamInfo" into table track2BamInfo; |
|
| 91 |
|
|
| 92 |
drop table if exists track2Detail; |
|
| 93 |
create table track2Detail ( |
|
| 94 |
name varchar(255) not null primary key, |
|
| 95 |
detail text null |
|
| 96 |
); |
|
| 97 |
load data local infile 'track2Detail' into table track2Detail; |
|
| 98 |
load data local infile 'track2Detail_decor' into table track2Detail; |
|
| 99 |
|
|
| 100 |
drop table if exists track2GEO; |
|
| 101 |
create table track2GEO ( |
|
| 102 |
name varchar(255) not null primary key, |
|
| 103 |
geo char(20) not null |
|
| 104 |
); |
|
| 105 |
load data local infile 'track2GEO' into table track2GEO; |
|
| 106 |
|
|
| 107 |
drop table if exists track2Categorical; |
|
| 108 |
create table track2Categorical ( |
|
| 109 |
name varchar(255) not null primary key, |
|
| 110 |
info text not null |
|
| 111 |
); |
|
| 112 |
load data local infile 'track2Categorical' into table track2Categorical; |
|
| 113 |
|
|
| 114 |
|
|
| 115 |
drop table if exists track2VersionInfo; |
|
| 116 |
create table track2VersionInfo ( |
|
| 117 |
name varchar(255) not null primary key, |
|
| 118 |
info varchar(255) not null |
|
| 119 |
); |
|
| 120 |
load data local infile 'track2VersionInfo' into table track2VersionInfo; |
|
| 121 |
|
|
| 122 |
|
|
| 123 |
drop table if exists track2Annotation; |
|
| 124 |
create table track2Annotation ( |
|
| 125 |
name varchar(255) not null primary key, |
|
| 126 |
attridx varchar(255) not null |
|
| 127 |
); |
|
| 128 |
load data local infile "track2Annotation" into table track2Annotation; |
|
| 129 |
|
|
| 130 |
drop table if exists track2Ft; |
|
| 131 |
create table track2Ft ( |
|
| 132 |
name varchar(255) not null primary key, |
|
| 133 |
ft tinyint not null |
|
| 134 |
); |
|
| 135 |
load data local infile "track2Ft" into table track2Ft; |
|
| 136 |
|
|
| 137 |
drop table if exists track2Style; |
|
| 138 |
create table track2Style ( |
|
| 139 |
name varchar(255) not null primary key, |
|
| 140 |
style text not null |
|
| 141 |
); |
|
| 142 |
load data local infile "track2Style" into table track2Style; |
|
| 143 |
|
|
| 144 |
drop table if exists track2Regions; |
|
| 145 |
create table track2Regions ( |
|
| 146 |
name varchar(255) not null primary key, |
|
| 147 |
regionname varchar(255) not null, |
|
| 148 |
regions text not null |
|
| 149 |
); |
|
| 150 |
|
|
| 151 |
|
|
| 152 |
drop table if exists metadataVocabulary; |
|
| 153 |
create table metadataVocabulary ( |
|
| 154 |
child varchar(255) not null, |
|
| 155 |
parent varchar(255) not null |
|
| 156 |
); |
|
| 157 |
load data local infile "metadataVocabulary" into table metadataVocabulary; |
|
| 158 |
|
|
| 159 |
drop table if exists trackAttr2idx; |
|
| 160 |
create table trackAttr2idx ( |
|
| 161 |
idx varchar(255) not null primary key, |
|
| 162 |
attr varchar(255) not null, |
|
| 163 |
note varchar(255) null, |
|
| 164 |
description text null |
|
| 165 |
); |
|
| 166 |
load data local infile "trackAttr2idx" into table trackAttr2idx; |
|
| 167 |
|
|
| 168 |
|
|
| 169 |
drop table if exists tempURL; |
|
| 170 |
create table tempURL ( |
|
| 171 |
session varchar(100) not null, |
|
| 172 |
offset INT unsigned not null, |
|
| 173 |
urlpiece text not null |
|
| 174 |
); |
|
| 175 |
|
|
| 176 |
|
|
| 177 |
drop table if exists dataset; |
|
| 178 |
create table dataset ( |
|
| 179 |
tablename varchar(255) not null, |
|
| 180 |
logo varchar(255) null, |
|
| 181 |
name varchar(255) not null, |
|
| 182 |
url varchar(255) null, |
|
| 183 |
description text not null |
|
| 184 |
); |
|
| 185 |
-- load data local infile "dataset" into table dataset; |
|
| 186 |
|
|
| 187 |
drop table if exists mock; |
|
| 188 |
create table mock ( |
|
| 189 |
tkname varchar(255) not null |
|
| 190 |
); |
|
| 191 |
load data local infile "mock" into table mock; |
|
| 192 |
|
|
| 193 |
|
|
| 194 |
drop table if exists scaffoldInfo; |
|
| 195 |
create table scaffoldInfo ( |
|
| 196 |
parent varchar(255) not null, |
|
| 197 |
child varchar(255) not null, |
|
| 198 |
childLength int unsigned not null |
|
| 199 |
); |
|
| 200 |
load data local infile "scaffoldInfo" into table scaffoldInfo; |
|
| 201 |
|
|
| 202 |
|
|
| 203 |
drop table if exists cytoband; |
|
| 204 |
create table cytoband ( |
|
| 205 |
id int null auto_increment primary key, |
|
| 206 |
chrom char(20) not null, |
|
| 207 |
start int not null, |
|
| 208 |
stop int not null, |
|
| 209 |
name char(20) not null, |
|
| 210 |
colorIdx int not null |
|
| 211 |
); |
|
| 212 |
/* |
|
| 213 |
load data local infile "cytoband" into table cytoband; |
|
| 214 |
|
|
| 215 |
DROP TABLE IF EXISTS `rmsk`; |
|
| 216 |
CREATE TABLE `rmsk` ( |
|
| 217 |
`bin` smallint(5) unsigned NOT NULL default '0', |
|
| 218 |
`swScore` int(10) unsigned NOT NULL default '0', |
|
| 219 |
`milliDiv` int(10) unsigned NOT NULL default '0', |
|
| 220 |
`milliDel` int(10) unsigned NOT NULL default '0', |
|
| 221 |
`milliIns` int(10) unsigned NOT NULL default '0', |
|
| 222 |
`genoName` varchar(255) NOT NULL default '', |
|
| 223 |
`genoStart` int(10) unsigned NOT NULL default '0', |
|
| 224 |
`genoEnd` int(10) unsigned NOT NULL default '0', |
|
| 225 |
`genoLeft` int(11) NOT NULL default '0', |
|
| 226 |
`strand` char(1) NOT NULL default '', |
|
| 227 |
`repName` varchar(255) NOT NULL default '', |
|
| 228 |
`repClass` varchar(255) NOT NULL default '', |
|
| 229 |
`repFamily` varchar(255) NOT NULL default '', |
|
| 230 |
`repStart` int(11) NOT NULL default '0', |
|
| 231 |
`repEnd` int(11) NOT NULL default '0', |
|
| 232 |
`repLeft` int(11) NOT NULL default '0', |
|
| 233 |
`id` char(1) NOT NULL default '', |
|
| 234 |
KEY `genoName` (`genoName`(14),`bin`) |
|
| 235 |
); |
|
| 236 |
load data local infile 'rmsk.txt' into table rmsk; |
|
| 237 |
*/ |
|
| 238 |
|
|
| 239 |
|
|
| 240 |
drop table if exists genestruct; |
|
| 241 |
create table genestruct ( |
|
| 242 |
id int unsigned not null primary key, |
|
| 243 |
chrom varchar(255) not null, |
|
| 244 |
strand char(1) not null, |
|
| 245 |
txStart int unsigned not null, |
|
| 246 |
txEnd int unsigned not null, |
|
| 247 |
cdsStart int unsigned not null, |
|
| 248 |
cdsEnd int unsigned not null, |
|
| 249 |
exonCount int unsigned not null, |
|
| 250 |
exonStarts text not null, |
|
| 251 |
exonEnds text not null, |
|
| 252 |
name varchar(255) not null |
|
| 253 |
); |
|
| 254 |
load data local infile 'geneStruct' into table genestruct; |
|
| 255 |
|
|
| 256 |
|
|
| 257 |
drop table if exists genesymbol; |
|
| 258 |
create table genesymbol ( |
|
| 259 |
name varchar(255) not null, |
|
| 260 |
symbol varchar(255) null, |
|
| 261 |
description text null, |
|
| 262 |
id int unsigned not null primary key, |
|
| 263 |
index(name) |
|
| 264 |
); |
|
| 265 |
-- load data local infile 'geneSymbol' into table genesymbol; |
|
| 266 |
|
|
| b/AcNPV/metadataVocabulary | ||
|---|---|---|
| 1 |
mock term Sample |
|
| 2 |
11 mock term |
|
| 3 |
12 mock term |
|
| 4 |
13 mock term |
|
| 5 |
14 mock term |
|
| 6 |
15 mock term |
|
| 7 |
16 mock term |
|
| 8 |
17 mock term |
|
| 9 |
18 mock term |
|
| 10 |
19 mock term |
|
| 11 |
20 mock term |
|
| 12 |
21 mock term |
|
| 13 |
22 mock term |
|
| 14 |
23 mock term |
|
| 15 |
24 mock term |
|
| 16 |
25 mock term |
|
| 17 |
26 mock term |
|
| 18 |
27 mock term |
|
| 19 |
28 mock term |
|
| 20 |
29 mock term |
|
| 21 |
30 mock term |
|
| b/AcNPV/mock | ||
|---|---|---|
| 1 |
mock1 |
|
| 2 |
mock2 |
|
| 3 |
mock3 |
|
| 4 |
mock4 |
|
| 5 |
mock5 |
|
| 6 |
mock6 |
|
| 7 |
mock7 |
|
| 8 |
mock8 |
|
| 9 |
mock9 |
|
| 10 |
mock10 |
|
| 11 |
mock11 |
|
| 12 |
mock12 |
|
| 13 |
mock13 |
|
| 14 |
mock14 |
|
| 15 |
mock15 |
|
| 16 |
mock16 |
|
| 17 |
mock17 |
|
| 18 |
mock18 |
|
| 19 |
mock19 |
|
| 20 |
mock20 |
|
| b/AcNPV/scaffoldInfo | ||
|---|---|---|
| 1 |
ROOT chromosome 0 |
|
| 2 |
ROOT other 0 |
|
| 3 |
chromosome NC_001623.1 133894 |
|
| b/AcNPV/track2Annotation | ||
|---|---|---|
| 1 |
mock1 11 |
|
| 2 |
mock2 12 |
|
| 3 |
mock3 13 |
|
| 4 |
mock4 14 |
|
| 5 |
mock5 15 |
|
| 6 |
mock6 16 |
|
| 7 |
mock7 17 |
|
| 8 |
mock8 18 |
|
| 9 |
mock9 19 |
|
| 10 |
mock10 20 |
|
| 11 |
mock11 21 |
|
| 12 |
mock12 22 |
|
| 13 |
mock13 23 |
|
| 14 |
mock14 24 |
|
| 15 |
mock15 25 |
|
| 16 |
mock16 26 |
|
| 17 |
mock17 27 |
|
| 18 |
mock18 28 |
|
| 19 |
mock19 29 |
|
| 20 |
mock20 30 |
|
| b/AcNPV/track2Detail | ||
|---|---|---|
| 1 |
mock20 \N |
|
| 2 |
mock19 \N |
|
| 3 |
mock18 \N |
|
| 4 |
mock13 \N |
|
| 5 |
mock12 \N |
|
| 6 |
mock11 \N |
|
| 7 |
mock10 \N |
|
| 8 |
mock17 \N |
|
| 9 |
mock16 \N |
|
| 10 |
mock15 \N |
|
| 11 |
mock14 \N |
|
| 12 |
mock9 \N |
|
| 13 |
mock8 \N |
|
| 14 |
mock3 \N |
|
| 15 |
mock2 \N |
|
| 16 |
mock1 \N |
|
| 17 |
mock7 \N |
|
| 18 |
mock6 \N |
|
| 19 |
mock5 \N |
|
| 20 |
mock4 \N |
|
| b/AcNPV/track2Detail_decor | ||
|---|---|---|
| 1 |
gene Download date=Sep-16-2013; Parsed by=in house script; Download from=http://www.ncbi.nlm.nih.gov/nuccore/NC_001623 |
|
| 2 |
CDS Download date=Sep-16-2013; Parsed by=in house script; Download from=http://www.ncbi.nlm.nih.gov/nuccore/NC_001623 |
|
| 3 |
repeat_region Download date=Sep-16-2013; Parsed by=in house script; Download from=http://www.ncbi.nlm.nih.gov/nuccore/NC_001623 |
|
| 4 |
gc5Base Download date=Sep-16-2013; Parsed by=hgGcPercent in Kent utils |
|
| b/AcNPV/track2Ft | ||
|---|---|---|
| 1 |
mock1 2 |
|
| 2 |
mock2 2 |
|
| 3 |
mock3 2 |
|
| 4 |
mock4 2 |
|
| 5 |
mock5 2 |
|
| 6 |
mock6 2 |
|
| 7 |
mock7 2 |
|
| 8 |
mock8 2 |
|
| 9 |
mock9 2 |
|
| 10 |
mock10 2 |
|
| 11 |
mock11 2 |
|
| 12 |
mock12 2 |
|
| 13 |
mock13 2 |
|
| 14 |
mock14 2 |
|
| 15 |
mock15 2 |
|
| 16 |
mock16 2 |
|
| 17 |
mock17 2 |
|
| 18 |
mock18 2 |
|
| 19 |
mock19 2 |
|
| 20 |
mock20 2 |
|
| b/AcNPV/track2Label | ||
|---|---|---|
| 1 |
mock20 mock20 |
|
| 2 |
mock19 mock19 |
|
| 3 |
mock18 mock18 |
|
| 4 |
mock13 mock13 |
|
| 5 |
mock12 mock12 |
|
| 6 |
mock11 mock11 |
|
| 7 |
mock10 mock10 |
|
| 8 |
mock17 mock17 |
|
| 9 |
mock16 mock16 |
|
| 10 |
mock15 mock15 |
|
| 11 |
mock14 mock14 |
|
| 12 |
mock9 mock9 |
|
| 13 |
mock8 mock8 |
|
| 14 |
mock3 mock3 |
|
| 15 |
mock2 mock2 |
|
| 16 |
mock1 mock1 |
|
| 17 |
mock7 mock7 |
|
| 18 |
mock6 mock6 |
|
| 19 |
mock5 mock5 |
|
| 20 |
mock4 mock4 |
|
| b/AcNPV/track2Style | ||
|---|---|---|
| 1 |
gene 'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)' |
|
| 2 |
CDS 'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)' |
|
| 3 |
repeat_region 'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)' |
|
| 4 |
gc5Base \N |
|
| b/AcNPV/trackAttr2idx | ||
|---|---|---|
| 1 |
11 1 mock |
|
| 2 |
12 2 mock |
|
| 3 |
13 3 mock |
|
| 4 |
14 4 mock |
|
| 5 |
15 5 mock |
|
| 6 |
16 6 mock |
|
| 7 |
17 7 mock |
|
| 8 |
18 8 mock |
|
| 9 |
19 9 mock |
|
| 10 |
20 10 mock |
|
| 11 |
21 11 mock |
|
| 12 |
22 12 mock |
|
| 13 |
23 13 mock |
|
| 14 |
24 14 mock |
|
| 15 |
25 15 mock |
|
| 16 |
26 16 mock |
|
| 17 |
27 17 mock |
|
| 18 |
28 18 mock |
|
| 19 |
29 19 mock |
|
| 20 |
30 20 mock |
|
| b/hg18/publichub.json | ||
|---|---|---|
| 1 |
[ |
|
| 2 |
{
|
|
| 3 |
id:'mm1s', |
|
| 4 |
name:'Multiple Myeloma cell line with JQ1 treatment', |
|
| 5 |
logo:'http://bradner.dfci.harvard.edu/images/generegulationchemistry.jpg', |
|
| 6 |
url:'http://vizhub.wustl.edu/public/hg18/mm1s/hub', |
|
| 7 |
institution:['<a href=http://younglab.wi.mit.edu target=_blank>Richard Young at Whitehead Institute</a>', |
|
| 8 |
'<a href=http://bradner.dfci.harvard.edu/ target=_blank>James E. Bradner at Harvard Medical School</a>'], |
|
| 9 |
desc:'This collection of genome-wide sequencing results is from multiple myeloma 1S cell line under JQ1 treatment. The experiments systematically characterized response to JQ1 treatment from many aspects: histone protein modifications, oncogene transcription regulator binding of DNA, and gene transcription. Data are available as sequencing reads aligned to the reference genome.', |
|
| 10 |
cite:['Lin C. et. al., Cell. 2012 Sept 28;151(1):56-67','Loven J et. al., Cell. 2013 Apr 11;153(2):320-34'], |
|
| 11 |
}, |
|
| 12 |
] |
|
| b/hg19/publichub.json | ||
|---|---|---|
| 1 |
[ |
|
| 2 |
{
|
|
| 3 |
id:'ec', |
|
| 4 |
name:'Endometrioid Cancer Methylome from Wang Lab', |
|
| 5 |
logo:'http://cgs.wustl.edu/~dli/labwebsite_dev/img/wang_logo.png', |
|
| 6 |
url:'http://wangftp.wustl.edu/~bzhang/CNV_EC/DataHub_EC_CNV', |
|
| 7 |
institution:['<a href=http://wang.wustl.edu/ target=_blank>Wang Lab at Washington University in St. Louis</a>'], |
|
| 8 |
desc:'The methylMnM software is used to identify DMRs by integrating MeDIP-Seq and MRE-Seq assay results.', |
|
| 9 |
}, |
|
| 10 |
{
|
|
| 11 |
id:'gbm', |
|
| 12 |
name:'Glioblastoma Methylome from Wang Lab', |
|
| 13 |
logo:'http://cgs.wustl.edu/~dli/labwebsite_dev/img/wang_logo.png', |
|
| 14 |
url:'http://wangftp.wustl.edu/~bzhang/CNV_GBM/DataHub_GBM_CNV', |
|
| 15 |
institution:['<a href=http://wang.wustl.edu/ target=_blank>Wang Lab at Washington University in St. Louis</a>'], |
|
| 16 |
desc:'The methylMnM software is used to identify DMRs by integrating MeDIP-Seq and MRE-Seq assay results.', |
|
| 17 |
}, |
|
| 18 |
] |
|
| b/rapa1_1/dataset | ||
|---|---|---|
| 1 |
mock images/mock.png Mock data set \N Just a mock data set... |
|
| b/rapa1_1/decorInfo | ||
|---|---|---|
| 1 |
gene BRAD genes \N 2 0 1 http://brassicadb.org/cgi-bin/gbrowse/Brassica/?name= |
|
| 2 |
mRNA BRAD mRNA gene 2 0 0 \N |
|
| 3 |
exon exons (BRAD genes) gene 2 0 0 \N |
|
| 4 |
CDS CDS (BRAD genes) gene 2 0 0 \N |
|
| 5 |
gc5Base GC percent \N 5 14 1 \N |
|
| b/rapa1_1/makeDb.sql | ||
|---|---|---|
| 1 |
drop table if exists config; |
|
| 2 |
create table config ( |
|
| 3 |
bbiPath text not null, |
|
| 4 |
seqPath text null, |
|
| 5 |
defaultTracks text null, |
|
| 6 |
defaultMdcategory varchar(255) not null, |
|
| 7 |
defaultGenelist text null, |
|
| 8 |
defaultCustomtracks text null, |
|
| 9 |
defaultPosition varchar(255) not null, |
|
| 10 |
defaultDataset varchar(255) not null, |
|
| 11 |
defaultDecor text null, |
|
| 12 |
defaultScaffold text not null, |
|
| 13 |
ideogram_wiggle1 varchar(255) null, |
|
| 14 |
ideogram_wiggle2 varchar(255) null, |
|
| 15 |
hasGene boolean not null, |
|
| 16 |
allowJuxtaposition boolean not null, |
|
| 17 |
keggSpeciesCode varchar(255) null, |
|
| 18 |
information text not null, |
|
| 19 |
runmode tinyint not null, |
|
| 20 |
initmatplot boolean not null |
|
| 21 |
); |
|
| 22 |
insert into config values( |
|
| 23 |
"/srv/epgg/data/data/subtleKnife/rapa1.1/", |
|
| 24 |
"/srv/epgg/data/data/subtleKnife/seq/rapa1.1.gz", |
|
| 25 |
\N, |
|
| 26 |
"Sample", |
|
| 27 |
\N, |
|
| 28 |
\N, |
|
| 29 |
"A01,14668689,A01,14684661", |
|
| 30 |
"mock", |
|
| 31 |
"gene,gc5Base", |
|
| 32 |
"A01,A02,A03,A04,A05,A06,A07,A08,A09,A10", |
|
| 33 |
\N,\N, |
|
| 34 |
true, |
|
| 35 |
true, |
|
| 36 |
"Brapa", |
|
| 37 |
"Assembly version|v1.1|Sequence source|<a href=http://brassicadb.org/brad/ target=_blank>BRAD</a>|Reference|<a href=http://www.biomedcentral.com/1471-2229/11/136 target=_blank>Cheng et. al, BMC Plant Biol. 2011</a>|Date parsed|August 25, 2013|Chromosomes|10|Misc|0|Total bases|256,258,763|Logo art|<a href=http://www.gardensonline.com.au/GardenShed/PlantFinder/Show_2691.aspx target=_blank>link</a>", |
|
| 38 |
0, |
|
| 39 |
false |
|
| 40 |
); |
|
| 41 |
|
|
| 42 |
|
|
| 43 |
-- grouping types on genomic features |
|
| 44 |
-- table name defined in macro: TBN_GF_GRP |
|
| 45 |
drop table if exists gfGrouping; |
|
| 46 |
create table gfGrouping ( |
|
| 47 |
id TINYINT not null primary key, |
|
| 48 |
name char(50) not null |
|
| 49 |
); |
|
| 50 |
insert into gfGrouping values (2, "Genes"); |
|
| 51 |
-- insert into gfGrouping values (3, "non-coding RNA"); |
|
| 52 |
-- insert into gfGrouping values (4, "RepeatMasker"); |
|
| 53 |
-- insert into gfGrouping values (6, "Sequence conservation"); |
|
| 54 |
insert into gfGrouping values (5, "Others"); |
|
| 55 |
|
|
| 56 |
|
|
| 57 |
|
|
| 58 |
drop table if exists decorInfo; |
|
| 59 |
create table decorInfo ( |
|
| 60 |
name char(50) not null primary key, |
|
| 61 |
printname char(100) not null, |
|
| 62 |
parent char(50) null, |
|
| 63 |
grp tinyint not null, |
|
| 64 |
fileType tinyint not null, |
|
| 65 |
hasStruct tinyint null, |
|
| 66 |
queryUrl varchar(255) null |
|
| 67 |
); |
|
| 68 |
load data local infile 'decorInfo' into table decorInfo; |
|
| 69 |
|
|
| 70 |
drop table if exists track2Label; |
|
| 71 |
create table track2Label ( |
|
| 72 |
name varchar(255) not null primary key, |
|
| 73 |
label text null |
|
| 74 |
); |
|
| 75 |
load data local infile 'track2Label' into table track2Label; |
|
| 76 |
|
|
| 77 |
drop table if exists track2ProcessInfo; |
|
| 78 |
create table track2ProcessInfo ( |
|
| 79 |
name varchar(255) not null primary key, |
|
| 80 |
detail text null |
|
| 81 |
); |
|
| 82 |
load data local infile 'track2ProcessInfo' into table track2ProcessInfo; |
|
| 83 |
|
|
| 84 |
drop table if exists track2BamInfo; |
|
| 85 |
create table track2BamInfo ( |
|
| 86 |
name varchar(255) not null, |
|
| 87 |
bamfile varchar(255) not null, |
|
| 88 |
bamfilelabel varchar(255) not null |
|
| 89 |
); |
|
| 90 |
load data local infile "track2BamInfo" into table track2BamInfo; |
|
| 91 |
|
|
| 92 |
drop table if exists track2Detail; |
|
| 93 |
create table track2Detail ( |
|
| 94 |
name varchar(255) not null primary key, |
|
| 95 |
detail text null |
|
| 96 |
); |
|
| 97 |
load data local infile 'track2Detail' into table track2Detail; |
|
| 98 |
load data local infile 'track2Detail_decor' into table track2Detail; |
|
| 99 |
|
|
| 100 |
drop table if exists track2GEO; |
|
| 101 |
create table track2GEO ( |
|
| 102 |
name varchar(255) not null primary key, |
|
| 103 |
geo char(20) not null |
|
| 104 |
); |
|
| 105 |
load data local infile 'track2GEO' into table track2GEO; |
|
| 106 |
|
|
| 107 |
drop table if exists track2Categorical; |
|
| 108 |
create table track2Categorical ( |
|
| 109 |
name varchar(255) not null primary key, |
|
| 110 |
info text not null |
|
| 111 |
); |
|
| 112 |
load data local infile 'track2Categorical' into table track2Categorical; |
|
| 113 |
|
|
| 114 |
|
|
| 115 |
drop table if exists track2VersionInfo; |
|
| 116 |
create table track2VersionInfo ( |
|
| 117 |
name varchar(255) not null primary key, |
|
| 118 |
info varchar(255) not null |
|
| 119 |
); |
|
| 120 |
load data local infile 'track2VersionInfo' into table track2VersionInfo; |
|
| 121 |
|
|
| 122 |
|
|
| 123 |
drop table if exists track2Annotation; |
|
| 124 |
create table track2Annotation ( |
|
| 125 |
name varchar(255) not null primary key, |
|
| 126 |
attridx varchar(255) not null |
|
| 127 |
); |
|
| 128 |
load data local infile "track2Annotation" into table track2Annotation; |
|
| 129 |
|
|
| 130 |
drop table if exists track2Ft; |
|
| 131 |
create table track2Ft ( |
|
| 132 |
name varchar(255) not null primary key, |
|
| 133 |
ft tinyint not null |
|
| 134 |
); |
|
| 135 |
load data local infile "track2Ft" into table track2Ft; |
|
| 136 |
|
|
| 137 |
drop table if exists track2Style; |
|
| 138 |
create table track2Style ( |
|
| 139 |
name varchar(255) not null primary key, |
|
| 140 |
style text not null |
|
| 141 |
); |
|
| 142 |
load data local infile "track2Style" into table track2Style; |
|
| 143 |
|
|
| 144 |
drop table if exists track2Regions; |
|
| 145 |
create table track2Regions ( |
|
| 146 |
name varchar(255) not null primary key, |
|
| 147 |
regionname varchar(255) not null, |
|
| 148 |
regions text not null |
|
| 149 |
); |
|
| 150 |
|
|
| 151 |
|
|
| 152 |
drop table if exists metadataVocabulary; |
|
| 153 |
create table metadataVocabulary ( |
|
| 154 |
child varchar(255) not null, |
|
| 155 |
parent varchar(255) not null |
|
| 156 |
); |
|
| 157 |
load data local infile "metadataVocabulary" into table metadataVocabulary; |
|
| 158 |
|
|
| 159 |
drop table if exists trackAttr2idx; |
|
| 160 |
create table trackAttr2idx ( |
|
| 161 |
idx varchar(255) not null primary key, |
|
| 162 |
attr varchar(255) not null, |
|
| 163 |
note varchar(255) null, |
|
| 164 |
description text null |
|
| 165 |
); |
|
| 166 |
load data local infile "trackAttr2idx" into table trackAttr2idx; |
|
| 167 |
|
|
| 168 |
|
|
| 169 |
drop table if exists tempURL; |
|
| 170 |
create table tempURL ( |
|
| 171 |
session varchar(100) not null, |
|
| 172 |
offset INT unsigned not null, |
|
| 173 |
urlpiece text not null |
|
| 174 |
); |
|
| 175 |
|
|
| 176 |
|
|
| 177 |
drop table if exists dataset; |
|
| 178 |
create table dataset ( |
|
| 179 |
tablename varchar(255) not null, |
|
| 180 |
logo varchar(255) null, |
|
| 181 |
name varchar(255) not null, |
|
| 182 |
url varchar(255) null, |
|
| 183 |
description text not null |
|
| 184 |
); |
|
| 185 |
-- load data local infile "dataset" into table dataset; |
|
| 186 |
|
|
| 187 |
drop table if exists mock; |
|
| 188 |
create table mock ( |
|
| 189 |
tkname varchar(255) not null |
|
| 190 |
); |
|
| 191 |
load data local infile "mock" into table mock; |
|
| 192 |
|
|
| 193 |
|
|
| 194 |
drop table if exists scaffoldInfo; |
|
| 195 |
create table scaffoldInfo ( |
|
| 196 |
parent varchar(255) not null, |
|
| 197 |
child varchar(255) not null, |
|
| 198 |
childLength int unsigned not null |
|
| 199 |
); |
|
| 200 |
load data local infile "scaffoldInfo" into table scaffoldInfo; |
|
| 201 |
|
|
| 202 |
|
|
| 203 |
drop table if exists cytoband; |
|
| 204 |
create table cytoband ( |
|
| 205 |
id int null auto_increment primary key, |
|
| 206 |
chrom char(20) not null, |
|
| 207 |
start int not null, |
|
| 208 |
stop int not null, |
|
| 209 |
name char(20) not null, |
|
| 210 |
colorIdx int not null |
|
| 211 |
); |
|
| 212 |
/* |
|
| 213 |
load data local infile "cytoband" into table cytoband; |
|
| 214 |
|
|
| 215 |
DROP TABLE IF EXISTS `rmsk`; |
|
| 216 |
CREATE TABLE `rmsk` ( |
|
| 217 |
`bin` smallint(5) unsigned NOT NULL default '0', |
|
| 218 |
`swScore` int(10) unsigned NOT NULL default '0', |
|
| 219 |
`milliDiv` int(10) unsigned NOT NULL default '0', |
|
| 220 |
`milliDel` int(10) unsigned NOT NULL default '0', |
|
| 221 |
`milliIns` int(10) unsigned NOT NULL default '0', |
|
| 222 |
`genoName` varchar(255) NOT NULL default '', |
|
| 223 |
`genoStart` int(10) unsigned NOT NULL default '0', |
|
| 224 |
`genoEnd` int(10) unsigned NOT NULL default '0', |
|
| 225 |
`genoLeft` int(11) NOT NULL default '0', |
|
| 226 |
`strand` char(1) NOT NULL default '', |
|
| 227 |
`repName` varchar(255) NOT NULL default '', |
|
| 228 |
`repClass` varchar(255) NOT NULL default '', |
|
| 229 |
`repFamily` varchar(255) NOT NULL default '', |
|
| 230 |
`repStart` int(11) NOT NULL default '0', |
|
| 231 |
`repEnd` int(11) NOT NULL default '0', |
|
| 232 |
`repLeft` int(11) NOT NULL default '0', |
|
| 233 |
`id` char(1) NOT NULL default '', |
|
| 234 |
KEY `genoName` (`genoName`(14),`bin`) |
|
| 235 |
); |
|
| 236 |
load data local infile 'rmsk.txt' into table rmsk; |
|
| 237 |
*/ |
|
| 238 |
|
|
| 239 |
/* |
|
| 240 |
|
|
| 241 |
drop table if exists genestruct; |
|
| 242 |
create table genestruct ( |
|
| 243 |
id int unsigned not null primary key, |
|
| 244 |
chrom varchar(255) not null, |
|
| 245 |
strand char(1) not null, |
|
| 246 |
txStart int unsigned not null, |
|
| 247 |
txEnd int unsigned not null, |
|
| 248 |
cdsStart int unsigned not null, |
|
| 249 |
cdsEnd int unsigned not null, |
|
| 250 |
exonCount int unsigned not null, |
|
| 251 |
exonStarts text not null, |
|
| 252 |
exonEnds text not null, |
|
| 253 |
name varchar(255) not null |
|
| 254 |
); |
|
| 255 |
load data local infile 'geneStruct' into table genestruct; |
|
| 256 |
|
|
| 257 |
|
|
| 258 |
drop table if exists genesymbol; |
|
| 259 |
create table genesymbol ( |
|
| 260 |
name varchar(255) not null, |
|
| 261 |
symbol varchar(255) null, |
|
| 262 |
description text null, |
|
| 263 |
id int unsigned not null primary key, |
|
| 264 |
index(name) |
|
| 265 |
); |
|
| 266 |
load data local infile 'geneSymbol' into table genesymbol; |
|
| 267 |
*/ |
|
| 268 |
|
|
| b/rapa1_1/metadataVocabulary | ||
|---|---|---|
| 1 |
mock term Sample |
|
| 2 |
11 mock term |
|
| 3 |
12 mock term |
|
| 4 |
13 mock term |
|
| 5 |
14 mock term |
|
| 6 |
15 mock term |
|
| 7 |
16 mock term |
|
| 8 |
17 mock term |
|
| 9 |
18 mock term |
|
| 10 |
19 mock term |
|
| 11 |
20 mock term |
|
| 12 |
21 mock term |
|
| 13 |
22 mock term |
|
| 14 |
23 mock term |
|
| 15 |
24 mock term |
|
| 16 |
25 mock term |
|
| 17 |
26 mock term |
|
| 18 |
27 mock term |
|
| 19 |
28 mock term |
|
| 20 |
29 mock term |
|
| 21 |
30 mock term |
|
| b/rapa1_1/mock | ||
|---|---|---|
| 1 |
mock1 |
|
| 2 |
mock2 |
|
| 3 |
mock3 |
|
| 4 |
mock4 |
|
| 5 |
mock5 |
|
| 6 |
mock6 |
|
| 7 |
mock7 |
|
| 8 |
mock8 |
|
| 9 |
mock9 |
|
| 10 |
mock10 |
|
| 11 |
mock11 |
|
| 12 |
mock12 |
|
| 13 |
mock13 |
|
| 14 |
mock14 |
|
| 15 |
mock15 |
|
| 16 |
mock16 |
|
| 17 |
mock17 |
|
| 18 |
mock18 |
|
| 19 |
mock19 |
|
| 20 |
mock20 |
|
| b/rapa1_1/publichub.json | ||
|---|---|---|
| 1 |
[ |
|
| 2 |
{
|
|
| 3 |
id:'ykhe', |
|
| 4 |
name:'Re-sequencing two subspecies of B. rapa', |
|
| 5 |
url:'http://vizhub.wustl.edu/public/rapa1_1/ykHE/hub', |
|
| 6 |
institution:['<a href=http://sippe.ac.cn/hyk/ target=_blank>He Yuke laboratory, SIPPE, SIBS, CAS</a>'], |
|
| 7 |
desc:'The two collection of genome-wide sequencing results are from Heading Chinese cabbage (B. rapa ssp. pekinensis. cv Bre) and non-heading Chinese cabbage (B. rapa ssp. chinensis. cv Wut) respectively. Four RNA sequencing data are from the seedling (3 weeks-old) and inflorescence apices (IA) (2 month-old) of Bre and Wut, respectively. Data are available as sequencing reads aligned to the reference genome.', |
|
| 8 |
}, |
|
| 9 |
] |
|
| b/rapa1_1/scaffoldInfo | ||
|---|---|---|
| 1 |
ROOT chromosome 0 |
|
| 2 |
ROOT other 0 |
|
| 3 |
chromosome A01 28608137 |
|
| 4 |
chromosome A02 27848129 |
|
| 5 |
chromosome A03 31716688 |
|
| 6 |
chromosome A04 18967243 |
|
| 7 |
chromosome A05 23941934 |
|
| 8 |
chromosome A06 26273242 |
|
| 9 |
chromosome A07 22587824 |
|
| 10 |
chromosome A08 21596550 |
|
| 11 |
chromosome A09 37123981 |
|
| 12 |
chromosome A10 17595035 |
|
| b/rapa1_1/track2Annotation | ||
|---|---|---|
| 1 |
mock1 11 |
|
| 2 |
mock2 12 |
|
| 3 |
mock3 13 |
|
| 4 |
mock4 14 |
|
| 5 |
mock5 15 |
|
| 6 |
mock6 16 |
|
| 7 |
mock7 17 |
|
| 8 |
mock8 18 |
|
| 9 |
mock9 19 |
|
| 10 |
mock10 20 |
|
| 11 |
mock11 21 |
|
| 12 |
mock12 22 |
|
| 13 |
mock13 23 |
|
| 14 |
mock14 24 |
|
| 15 |
mock15 25 |
|
| 16 |
mock16 26 |
|
| 17 |
mock17 27 |
|
| 18 |
mock18 28 |
|
| 19 |
mock19 29 |
|
| 20 |
mock20 30 |
|
| b/rapa1_1/track2Detail | ||
|---|---|---|
| 1 |
mock20 \N |
|
| 2 |
mock19 \N |
|
| 3 |
mock18 \N |
|
| 4 |
mock13 \N |
|
| 5 |
mock12 \N |
|
| 6 |
mock11 \N |
|
| 7 |
mock10 \N |
|
| 8 |
mock17 \N |
|
| 9 |
mock16 \N |
|
| 10 |
mock15 \N |
|
| 11 |
mock14 \N |
|
| 12 |
mock9 \N |
|
| 13 |
mock8 \N |
|
| 14 |
mock3 \N |
|
| 15 |
mock2 \N |
|
| 16 |
mock1 \N |
|
| 17 |
mock7 \N |
|
| 18 |
mock6 \N |
|
| 19 |
mock5 \N |
|
| 20 |
mock4 \N |
|
| b/rapa1_1/track2Detail_decor | ||
|---|---|---|
| 1 |
gene Download date=Aug-25-2013; Parsed by=in house script; Download from=http://brassicadb.org/brad/downloadOverview.php |
|
| 2 |
mRNA Download date=Aug-25-2013; Parsed by=in house script; Download from=http://brassicadb.org/brad/downloadOverview.php |
|
| 3 |
exon Download date=Aug-25-2013; Parsed by=in house script; Download from=http://brassicadb.org/brad/downloadOverview.php |
|
| 4 |
CDS Download date=Aug-25-2013; Parsed by=in house script; Download from=http://brassicadb.org/brad/downloadOverview.php |
|
| 5 |
gc5Base Download date=Aug-25-2013; Parsed by=hgGcPercent in Kent utils |
|
| b/rapa1_1/track2Ft | ||
|---|---|---|
| 1 |
mock1 2 |
|
| 2 |
mock2 2 |
|
| 3 |
mock3 2 |
|
| 4 |
mock4 2 |
|
| 5 |
mock5 2 |
|
| 6 |
mock6 2 |
|
| 7 |
mock7 2 |
|
| 8 |
mock8 2 |
|
| 9 |
mock9 2 |
|
| 10 |
mock10 2 |
|
| 11 |
mock11 2 |
|
| 12 |
mock12 2 |
|
| 13 |
mock13 2 |
|
| 14 |
mock14 2 |
|
| 15 |
mock15 2 |
|
| 16 |
mock16 2 |
|
| 17 |
mock17 2 |
|
| 18 |
mock18 2 |
|
| 19 |
mock19 2 |
|
| 20 |
mock20 2 |
|
| b/rapa1_1/track2Label | ||
|---|---|---|
| 1 |
mock20 mock20 |
|
| 2 |
mock19 mock19 |
|
| 3 |
mock18 mock18 |
|
| 4 |
mock13 mock13 |
|
| 5 |
mock12 mock12 |
|
| 6 |
mock11 mock11 |
|
| 7 |
mock10 mock10 |
|
| 8 |
mock17 mock17 |
|
| 9 |
mock16 mock16 |
|
| 10 |
mock15 mock15 |
|
| 11 |
mock14 mock14 |
|
| 12 |
mock9 mock9 |
|
| 13 |
mock8 mock8 |
|
| 14 |
mock3 mock3 |
|
| 15 |
mock2 mock2 |
|
| 16 |
mock1 mock1 |
|
| 17 |
mock7 mock7 |
|
| 18 |
mock6 mock6 |
|
| 19 |
mock5 mock5 |
|
| 20 |
mock4 mock4 |
|
| b/rapa1_1/track2Style | ||
|---|---|---|
| 1 |
gene 'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)' |
|
| 2 |
mRNA 'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)' |
|
| 3 |
exon 'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)' |
|
| 4 |
CDS 'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)' |
|
| 5 |
gc5Base \N |
|
| b/rapa1_1/trackAttr2idx | ||
|---|---|---|
| 1 |
11 1 mock |
|
| 2 |
12 2 mock |
|
| 3 |
13 3 mock |
|
| 4 |
14 4 mock |
|
| 5 |
15 5 mock |
|
| 6 |
16 6 mock |
|
| 7 |
17 7 mock |
|
| 8 |
18 8 mock |
|
| 9 |
19 9 mock |
|
| 10 |
20 10 mock |
|
| 11 |
21 11 mock |
|
| 12 |
22 12 mock |
|
| 13 |
23 13 mock |
|
| 14 |
24 14 mock |
|
| 15 |
25 15 mock |
|
| 16 |
26 16 mock |
|
| 17 |
27 17 mock |
|
| 18 |
28 18 mock |
|
| 19 |
29 19 mock |
|
| 20 |
30 20 mock |
|
Also available in: Unified diff