ViewVC Help
View File | Revision Log | Show Annotations | Root Listing
root/msatfinder/README.txt
Revision: 1.1.1.1 (vendor branch)
Committed: Mon Mar 7 15:34:42 2005 UTC (11 years, 5 months ago) by knirirr
Branch: MAIN
CVS Tags: HEAD, HEAD
Changes since 1.1: +0 -0 lines
Log Message:
First import

Line File contents
1 Msatminer README, Last Updated March 2004
2 Authors: Milo Thurston (mith@ceh.ac.uk) and Dawn Field
3 (dfield@ceh.ac.uk)
4 The latest version of this software is available at
5 http://www.genomics.ceh.ac.uk/msatminer/#download
6
7 This file describes the installation and usage of the msatminer package
8 for the detection of microsatellite repeats. For full instructions,
9 please see the msatminer user manual. Please send comments, suggestions,
10 or bug reports to the authors.
11
12
13 INSTALLATION
14
15 1. Download the latest version of the MsatMiner tarball and unpack
16 it.
17
18 <user> tar zxvf msatminer-latest.tar.gz
19 <user> cd msatminer-1.2.5
20
21 2. Move into the msatminer directory and run the install.sh script
22 as root. This will install Msatminer into /usr/local/.
23
24 <msatminer-1.2.5> ./install.sh
25
26 Note: You can install msatminer into any location using the -p flag.
27 For example, to install into your own account (say, if you don't have
28 root access) by typing:
29
30 <msatminer-1.2.5> ./install.sh -p /home/user/
31
32 3. Make sure that ../msatminer/bin is on your PATH.
33
34 4. Create these two environmental variables
35
36 PERL5LIB="/usr/local/msatminer/lib"
37 MSATMINER_HOME="/usr/local/msatminer"
38
39 5. Make sure the following dependencies are installed and configured on
40 your system:
41
42 Perl modules:
43 - Bioperl
44 - DBI
45 - CGI
46 - Config::Simple
47 - File::Copy
48 - File::Basename
49 - Getopt::Std
50 - Term::ReadLine
51 - Term::ANSIColor
52 - Mail::Send
53
54 Software:
55 EMBOSS (eprimer3)
56 Mview
57 Primer3_core
58 NCBI blast (blastall, bl2seq)
59 Clustalw
60 phylip
61
62 Database system: Either postgres or mysql.
63 We have tested on the following version numbers:
64 Postgresql: 7.3.6 and 7.4.2.
65 Mysql: 3.23.58 and 4.0.17.
66
67 BASIC CONFIGURATION AND USAGE
68
69 To check that your package and all dependencies are installed and
70 configured correctly, test data is supplied (two baculovirus genomes in
71 Genbank format).
72
73 1. To search the test data for microsatellites, first move into the
74 "Microsatellites" directory and edit the configuration file
75 "msatminer.rc". Most values will work using the default settings, but
76 you will need to change the values of the variables in the [ VIEWER ]
77 section at the end of the file, and some in the [ COMMON ] section
78 at the beginning of the file.
79
80 To use the on-line database you will need a working cgi-bin and a mysql or
81 postgres database with two users. The first (priveleged) user must
82 have permission to create tables and is used by the scripts which
83 load your results into the database.
84 For security, you should also have a second unpriveleged user that should
85 only have read access to the database and is used by the CGI interface
86 to display the results in your database (you can use just one user, but
87 this is far less secure).
88
89 2. To run the search, type:
90
91 <Microsatellites> msatfinder -a -c -l example.list
92
93 Output from this search will be found in the directories /Fasta,
94 /Repeats, /Artemis, and /Primers. A database of these results will be
95 created that can be accessed from your cgi interface.
96
97 You can omit the "-c" flag if you don't want to load the database, and omit
98 the "-a" flag if you don't require an alignment to be generated. For further
99 details on how to set up searches of your own data, please see the Msatminer
100 user manual.
101
102 If you experience any problems running this software, please write to
103 the authors.