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root/Genquire/genquire.conf_example
Revision: 1.8
Committed: Tue Apr 22 17:17:07 2003 UTC (13 years, 5 months ago) by markw
Branch: MAIN
CVS Tags: Release4, HEAD
Changes since 1.7: +1 -1 lines
Log Message:
missing quote in example

Line File contents
1 {
2
3 # ATTENTION MICROSOFT WINDOWES USERS!!!
4 # when you edit the settings below, be sure to use a
5 # **SINGLE** quote (') character in place of a
6 # double (") quote chacter, or genquire will not run!
7
8 # eg. your paths will look like:
9 #
10 # use lib 'C:\BioPerl\bioperl-live';
11 #
12
13
14
15 use lib "/home/markw/BIOPERL/bioperl/bioperl-gui";
16 use lib "/home/markw/BIOPERL/bioperl/bioperl-live";
17 use lib "/home/markw/BIOPERL/go-dev/perl-api";
18 use lib "/home/markw/OPEN_Genquire/Genquire";
19 use lib "/home/markw/OPEN_Genquire/Genquire/PLUGINS";
20
21
22 # Windows users probably wont have SIm4 - just leave it blank (" ")
23 $SIM4_DIR = "/home/markw/SIM4";
24
25 # usually 'C:\temp' for Windows users
26 $TEMP_DIR = "/tmp";
27
28 # Blast is available from NCBI for Windows, and runs nicely!
29 $blast_BINARIES = "/home/markw/BLAST";
30
31 # Windows users must enter the FULL PATH AND FILENAME to their browser
32 $BROWSER = "netscape";
33
34 # it is difficult to find a public CGI Blast program that still
35 # outputs a Blast report instead of a "please wait and click after 17 seconds"
36 # report. The latter WILL NOT WORK with Genquire!!
37 $BLAST_URL = "http://fingal/PANDA/pandablast.cgi";
38
39
40 $WORKING_DIR = "/home/markw/OPEN_Genquire/Genquire/";
41 $PLUGINS_DIR = "/home/markw/OPEN_Genquire/Genquire/PLUGINS/";
42 $DATA_SOURCES = [
43 ["GENQUIRE_LOCAL", "gq_local.cfg"],
44 ["BioSQL (bioperl-db)", "BioSQL.cfg"],
45 ["DAS_elegans", "das_elegans.cfg"], # doesn't exist yet...
46 ["GENBANK_FLAT", "gb_flat.cfg"],
47 ["GENBANK_NET", "gb_net.cfg"], # doesn't exist yet, but will one day!
48 ];
49
50 $BLAST_CONFIG = {
51 # below is a list of all *acceptable* Blast parameters
52 # note that some are removed because the GUI must be able
53 # to receive and interpret the results.
54 # when CGI_param is not avalable for your particular CGI,
55 # leave it undef. Pay attention to the -i parameter, as it is not
56 # identical to the meaning in blastall...
57 #
58 # blastall_param #[CGI_param, default]
59 '-i' => ['seq', undef], # NOTA BENE!! This parameter holds the input sequence Fasta *string* (NOT filename!!)
60 '-p' => ['blastprogram', 'blastn'], # NB Genquire is only set up to handle nucleotide query inputs to Blast!
61 '-e' => [undef, '10.0'],
62 '-d' => ['database', 'nt'], # NB Genquire is only set up to handle nucleotide query inputs to Blast!
63 '-F' => [undef, 'T'],
64 '-G' => [undef, '0'],
65 '-E' => [undef, '0'],
66 '-X' => [undef, '0'],
67 '-I' => [undef, 'F'],
68 '-q' => [undef, '-3'],
69 '-r' => [undef, '1'],
70 '-v' => [undef, '500'],
71 '-b' => [undef, '250'],
72 '-f' => [undef, '0'],
73 '-g' => [undef, 'T'],
74 '-Q' => [undef, '1'],
75 '-D' => [undef, '1'],
76 '-a' => [undef, '1'],
77 '-J' => [undef, 'F'],
78 '-M' => [undef, 'BLOSUM62'],
79 '-W' => [undef, '0'],
80 '-z' => [undef, '0'],
81 '-K' => [undef, '100'],
82 '-L' => [undef, '20'],
83 '-Y' => [undef, '0'],
84 '-S' => [undef, '3'],
85 '-T' => [undef, 'F'],
86 '-U' => [undef, 'F'],
87 '-y' => [undef, '0.0'],
88 '-Z' => [undef, '0'],
89 };
90
91 }