source: trunk/config/dist/base.config @ 3719

Last change on this file since 3719 was 3719, checked in by Nicklas Nordborg, 14 years ago

References #411: Most of the basic functionality is now in place and has been documented
On major issue is that the Affymetrix Fusion SDK will not work with compressed files since
it expects direct access to the java.io.File object. I will try to solve this by modifying the
Affymetric Fusion SDK to work with InputStream:s instead. This would be better than to decompress
CEL and CDF files everytime they are needed. In most cases we only scan the headers anyway, so
it would be good if we can avoid copying the entire 40+ MB file(s) each time.

File size: 5.0 KB
Line 
1# $Id: base.config.in 2932 2006-11-17 11:29:27Z nicklas $
2#
3# Copyright (C) 2006 Nicklas Nordborg
4# Copyright (C) 2007 Nicklas Nordborg, Martin Svensson
5#
6# This file is part of BASE - BioArray Software Environment.
7# Available at http://base.thep.lu.se/
8#
9# BASE is free software; you can redistribute it and/or
10# modify it under the terms of the GNU General Public License
11# as published by the Free Software Foundation; either version 2
12# of the License, or (at your option) any later version.
13#
14# BASE is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program; if not, write to the Free Software
21# Foundation, Inc., 59 Temple Place - Suite 330,
22# Boston, MA  02111-1307, USA.
23# ----------------------------------------
24
25# =======================
26# Database driver section
27# =======================
28
29# -----
30# MySQL
31# -----
32db.dialect          = org.hibernate.dialect.MySQLInnoDBDialect
33db.driver           = com.mysql.jdbc.Driver
34db.url              = jdbc:mysql://localhost/base2?useCursorFetch=true&defaultFetchSize=100
35db.dynamic.catalog  = base2dynamic
36db.queries          = /mysql-queries.xml
37#export.max.items    = 20000
38
39# --------
40# Postgres
41# --------
42#db.dialect          = org.hibernate.dialect.PostgreSQLDialect
43#db.driver           = org.postgresql.Driver
44#db.url              = jdbc:postgresql:base2
45#db.dynamic.catalog  = base2
46#db.dynamic.schema   = dynamic
47#db.queries          = /postgres-queries.xml
48#export.max.items    = 0
49
50# -------------
51# Common to all
52# -------------
53db.username            = base2user
54db.password            = password
55db.extended-properties = /extended-properties.xml
56db.raw-data-types      = /raw-data-types.xml
57db.batch-size          = 50
58
59
60# ======================
61# Authentication section
62# ======================
63
64# ----------------
65# POP3 mail server
66# ----------------
67#auth.driver         = net.sf.basedb.core.authentication.POP3Authenticator
68#auth.init           = mail.example.com
69#auth.synchronize    = 0
70#auth.cachepasswords = 0
71#auth.daystocache    = 0
72
73
74# ==========================
75# Internal job queue section
76# ==========================
77# If the internal job queue should be enabled or not
78jobqueue.internal.enabled            = true
79#jobqueue.internal.maxthreadpriority  = 4
80
81# Number of seconds between checks to the job queue
82jobqueue.internal.checkinterval      = 30
83
84# NOTE! A quick job may use threads from any of the "slower" pools
85# if there is place for another thread
86# Number of threads to reserved for jobs that takes < 1 minute to execute
87jobqueue.internal.shortest.threads   = 1
88#jobqueue.internal.shortest.threadpriority = 4
89
90# Number of threads to reserved for jobs that takes < 10 minutes to execute
91jobqueue.internal.short.threads      = 1
92#jobqueue.internal.short.threadpriority = 4
93
94# Number of threads to reserved for jobs that takes < 1 hour to execute
95jobqueue.internal.medium.threads     = 2
96#jobqueue.internal.medium.threadpriority = 3
97
98# Number of threads to reserved for jobs that takes > 1 hour to execute
99jobqueue.internal.long.threads       = 4
100#jobqueue.internal.long.threadpriority = 3
101
102# ==========================
103# External job agent section
104# ==========================
105
106# Number of seconds to cache information from a job agent before it
107# is reloaded. The default value is 60 seconds.
108agent.maxage=60
109
110# The timeout in milliseconds to use when connecting to job agents to
111# get information. The default value is 1000 milliseconds.
112agent.connection.timeout=1000
113
114
115# =========================
116# Secondary storage section
117# =========================
118# The classname of the driver; leave empty to disable secondary storage
119# secondary.storage.driver   = net.sf.basedb.core.InternalStorageController
120
121# Initialisation options to the seconday storage controller
122# The internal implementation wants a path to the secondary directory
123# secondary.storage.init     = /usr/local/base2/secondary
124
125# The interval (in seconds) between checks for new files to move
126# secondary.storage.interval = 3600
127
128# Comma-separated list of time values (hours:minutes) when the controller
129# should be executed; overrides the interval setting if present
130# secondary.storage.time = 18:15,07:30
131
132# ===============
133# General section
134# ===============
135
136# The path to the directory where uploaded files are stored
137userfiles = /usr/local/base2/files
138
139# The path to the directory where external plugins are installed
140plugin.dir=/usr/local/base2/plugins
141
142# Number of minutes to keep permission information for the logged
143# in user in memory before it is reloaded from the database.
144permission.timeout = 10
145
146# Number of minutes to keep SessionControl object in the cache
147# after the last use
148cache.timeout = 20
149
150#Overwrite the existing help texts when updating the program
151helptext.update = true
152
153# Set to 1 to disable auto-compression of uploaded files
154autocompress.disable = 0
155
156
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