-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathGBrowse.conf
239 lines (197 loc) · 8.16 KB
/
GBrowse.conf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
# This is the global configuration for gbrowse
# It contains setting common to all data sources as well
# as the various constants formerly scattered amongst scripts and libraries
[GENERAL]
config_base = /var/www/conf # overridden by environment variable GBROWSE_CONF
htdocs_base = /var/www/html/gbrowse2
url_base = /gbrowse2
db_base = /var/www/html/gbrowse2/databases
tmp_base = /var/tmp/gbrowse2
# These paths are relative to the url base
buttons = images/buttons
balloons = images/balloons
openid = images/openid
gbrowse_help = .
js = js
# These paths are relative to the config base
plugin_path = plugins
language_path = languages
templates_path = templates
moby_path = MobyServices
# session settings
session lock type = default
# If no session driver is set, then GBrowse will pick one for you.
# It will use db_file for the driver and storable for the serializer
# if available; otherwise falling back to the file driver and default serializer.
# Override driver guessing by setting these options
# The safest, but slowest session driver...
#session driver = driver:file;serializer:default
#session args = Directory /var/tmp/gbrowse2/sessions
# to use the berkeley DB driver comment out the previous
# line and uncomment these two
#session driver = driver:db_file;serializer:default
#session args = FileName /var/tmp/gbrowse2/sessions.db
# DBI backend to use for uploaded userdata
# if this option is commented out, then GBrowse will
# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
# backend. For the DBI::mysql adaptor to work, you must give the web user
# permission to create databases named userdata_% using the following
# mysql command:
# mysql> grant create on `userdata\_%`.* to 'www-data'@localhost;
# note the backquotes around the database name.
userdb_adaptor = DBI::SQLite
# Debug settings
debug = 0
debug_external = 0
debug_plugins = 0
# Performance settings
renderfarm = 1
slave_timeout = 30
global_timeout = 30
# Clean up settings (used by the gbrowse_clean script)
expire session = 1M # expire unused sessions after a month
expire cache = 2h # expire cached data if unmodified for >2 hours
expire uploads = 6w # expire uploaded data if unused for >6 weeks
# Appearance settings
truecolor = 1 # better appearance at the expense of larger image files
generate pdf = 1
# The #include line following this one defines a transparent theme.
# Replace "transparent_colors" with "solid_gray_colors"
# or "warm_colors" for different themes.
#include "themes/solid_gray_colors"
balloon tips = 1
titles are balloons = 1
plugins = FastaDumper RestrictionAnnotator SequenceDumper TrackFinder #UcscNet UcscChain UcscConservation MotifFinder
overview grid = 0
region grid = 0
detail grid = 1
image widths = 450 640 800 1024
default width = 800
pad_left = 60
pad_right = 30
too many landmarks = 100
# Loads more details image data than can fit on the screen. This lets the user drag and drop the details
# tracks, without loading more data from the server. A value of 1 is default (no drag and drop). A value
# of 3 loads one full width on each side.
details multiplier = 3.0
# where to link to when user clicks in detailed view
link = AUTO
# HTML to insert inside the <head></head> section
head =
# At the top of the HTML...
header =
# At the footer
footer = <hr />
<table style="font-size:small" border=0>
<tr>
<td>
Generic Genome Browser version 2.40 For questions about the data
at this site, please contact modENCODE help desk <a href="mailto:[email protected]">[email protected]</a>. For support of the
browser software <i>only</i>, send email to
<a href="mailto:[email protected]">[email protected]</a>
or visit the <a href="http://www.gmod.org">GMOD Project</a> web pages.
</td>
<td width = 100 align = "right">
<a href="http://gmod.org/">
<img src="http://gmod.org/w/images/e/e3/PoweredByGMOD80.png" alt="Powered by GMOD" style="border-width: 0" /></a>
</td></tr>
</table>
# Various places where you can insert your own HTML -- see configuration docs
html1 =
#sub {
# require CGI;
# my $url = $ENV{'REQUEST_URI'};
# my $org = $url =~ /worm/ ? 'worm' : 'fly';
# my $href = $url =~ /fgb2/ ? "http://mod1.modencode.org/gb2/gbrowse/$org" : "http://modencode.oicr.on.ca/cgi-bin/gb2/gbrowse/$org";
# my $mirror = $href;
# $mirror =~ s!http://(.+?)/.*$!$1!;
# my $msg = CGI::h2("A mirror of this site is also available at ",
# CGI::a({-href=>$href},"$mirror"));
# return CGI::table({-width => '99%',-align => 'center', -bgcolor => 'lightsteelblue'}, CGI::Tr(CGI::td({-align=>'center'},$msg)));
# }
html2 =
html3 =
html4 =
html5 =
html6 =
# Limits on genomic regions (can be overridden in datasource config files)
region segment = 200000
max segment = 5000000
default segment = 5000
zoom levels = 100 200 1000 2000 5000 10000 20000 50000 100000 200000 5000000 1000000
region sizes = 1000 5000 10000 20000
default region = 5000
fine zoom = 10%
# keyword search maxima
max keyword results = 1000
###### Authorization ######
# uncomment this to use the PAM authentication plugin
# authentication plugin = PamAuthenticate
####### User Account Registration Database ######
# If no authentication plugin is defined, and
# "user_accounts" is true, then GBrowse
# will attempt to use its internal user accounts database
# to authenticate and/or register users.
user_accounts = 1
user_accounts_registration = 1
user_accounts_openid = 1
# Path to the database -- you will need to create this database and grant all
# privileges on it to the indicated user.
# user_account_db = DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse
user_account_db = DBI:SQLite:/var/www/conf/user_accounts/user_accounts_db
# What email gateway to use for outgoing registration confirmation messages.
# The full format is
# <smtp.server.com>:<port>:<encryption>:<username>:<password>
# Only the first field, the server name, is required.
# The port is assumed to be 25 unless ssl encryption is specified, in
# which case it defaults to 465.
# protocol is either "clear" or "ssl", "plain" assumed.
# username and password may be required by the gateway for authentication
smtp_gateway = mr.oicr.on.ca
# These values are used in the login confirmation message sent during
# user registration. You may customize
application_name = GBrowse
application_name_long = The Generic Genome Browser
email_address = [email protected]
###############################################################################################
#
# One stanza for each configured data source
#
###############################################################################################
default source = fly
[fly]
description = D. melanogaster Genomic Browser
path = fly.conf
[worm]
description = C. elegans Genomic Browser
path = worm.conf
[brenneri]
description = modENCODE C.brenneri DB
path = worm_brenneri.conf
[briggsae]
description = modENCODE C.briggsae DB
path = worm_briggsae.conf
[remanei]
description = modENCODE C.remanei DB
path = worm_remanei.conf
[japonica]
description = modENCODE C.japonica DB
path = worm_japonica.conf
[fly_dp]
description = modENCODE D.pseudoobscura DB
path = fly_dp.conf
[fly_dmoj]
description = modENCODE D.mojavensis DB
path = fly_dmoj.conf
[fly_ananas]
description = modENCODE D.ananassae DB
path = fly_ananas.conf
[fly_virilis]
description = modENCODE D.virilis DB
path = fly_virilis.conf
[fly_yakuba]
description = modENCODE D.yakuba DB
path = fly_yakuba.conf
[fly_simul]
description = modENCODE D.simulans DB
path = fly_simulans.conf