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root/taxinspector/README.txt
Revision: 1.2
Committed: Wed Jun 29 10:31:29 2005 UTC (14 years, 9 months ago) by tbooth
Branch: MAIN
CVS Tags: HEAD
Changes since 1.1: +11 -2 lines
Log Message:
better README

Line File contents
1 REDAME for TaxInspector
2
3 GENERAL
4
5 This is a browser for taxonomy databases originally designed to enable
6 taxonomy browsing as a plugin function for the Pedro tool (see links).
7
8 In the version 1.0 release, it browses the NCBI Taxonomy by loading the
9 tree from the flat files supplied by the NCBI into a local HSQLDB database.
10
11 INSTALLATION
12
13 This is handled by the IzPack installer. Simply run
14 java -jar TaxInspectorInstaller.jar
15
16 You will need Java installed, of course!
17
18 REQUIREMENTS
19
20 You need to be able to make direct FTP or HTTP connections to fetch the data
21 files.
22 You will need around 100MB of disk space to hold the populated
23 database of taxonomy entries.
24
25 CONFIGURATION
26
27 There are various options you can set in the taxinspector.conf file.
28 See the comments in the supplied default file for more information.
29
30 You can overrride these settings by having an alternate personal
31 configuration file named .taxinspector.conf in your home directory.
32
33 USING YOUR OWN DATABASE
34
35 Things can be speeded up by using MySQL as the database backend.
36
37 More info to come in this section.
38
39 WORKING WITHOUT A DIRECT NET CONNECTION
40
41 The is currently no support for FTP or HTTP proxies. If the application
42 cannot fetch the files, it is possible to download the taxdmp.zip
43 file manually and then tell the program to use the local copy. See the
44 taxinspector.conf file for details.
45
46 USING THE BROWSER AS A PEDRO PLUGIN
47
48 More info to come. See the NOTES.txt in the source directory.
49
50 CREDITS AND LINKS
51
52 This project is now hosted at bioinformatics.org
53 http://bioinformatics.org/groups/?group_id=504
54
55 The development of this program was funded by the Natural Environment
56 Research Council as part of the Environmental Genomics Thematic
57 Programme Datacentre
58 http://www.nerc.ac.uk
59 http://envgen.nox.ac.uk
60
61 The Pedro tool for creating input forms from XML schemata:
62 http://pedro.sf.net
63
64 IzPack is a free Java installer maker which is very nifty.
65 http://www.izforge.com/izpack
66
67 Kudos to Dave Hancock for suggesting the name of the tool.
68 http://www.davesweboflies.com