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root/Genquire/genquire.conf
Revision: 1.9
Committed: Thu Nov 4 18:48:04 2004 UTC (11 years, 8 months ago) by mlinks
Branch: MAIN
CVS Tags: HEAD
Changes since 1.8: +78 -96 lines
Log Message:
*** empty log message ***

Line File contents
1
2 {
3
4 if (defined $ENV{GENQUIRE}){
5 # Use environment variables if they have been set
6 use lib "$ENV{GENQUIRE}";
7 use lib "$ENV{GENQUIRE}/PLUGINS";
8 $WORKING_DIR = $ENV{GENQUIRE};
9 $PLUGINS_DIR = "$ENV{GENQUIRE}/PLUGINS";
10 }else{
11 use lib "../Genquire";
12 use lib "../Genquire/PLUGINS";
13 $WORKING_DIR = "../Genquire";
14 $PLUGINS_DIR = "../Genquire/PLUGINS";
15 }
16 if (defined $ENV{GENQUIRE_LIBS}){
17 use lib "$ENV{GENQUIRE_LIBS}";
18 use lib "$ENV{GENQUIRE_LIBS}/bioperl-live";
19 use lib "$ENV{GENQUIRE_LIBS}/bioperl-gui";
20 use lib "$ENV{GENQUIRE_LIBS}/go-dev/go-db-perl";
21 use lib "$ENV{GENQUIRE_LIBS}/go-dev/go-perl";
22 }else{
23 use lib "../bioperl-gui";
24 use lib "../bioperl-live";
25 use lib "../go-dev/go-db-perl";
26 use lib "../go-dev/go-perl/";
27 }
28 if (defined $ENV{GENQUIRE_TMP}){
29 $TEMP_DIR = $ENV{GENQUIRE_TMP};
30 }else{
31 $TEMP_DIR = "../tmp";
32 }
33
34 $SIM4_DIR = ""; # Fine to leave blank
35 $BROWSER = "netscape";
36
37 $blast_BINARIES = "../BLAST";
38 $BLAST_URL = "";
39 $DATA_SOURCES = [
40 ["SARS-SAMPLE","gq_demo.cfg"], # Bioinfo public
41 ["BioSQL", "BioSQL.cfg"],
42 ["GENQUIRE_LOCAL", "gq_local.cfg"],
43 ["GENBANK_FLAT", "gb_flat.cfg"],
44 ];
45
46 $BLAST_CONFIG = {
47 # below is a list of all *acceptable* Blast parameters
48 # note that some are removed because the GUI must be able
49 # to receive and interpret the results.
50 # when CGI_param is not avalable for your particular CGI,
51 # leave it undef. Pay attention to the -i parameter, as it is not
52 # identical to the meaning in blastall...
53 #
54 # blastall_param #[CGI_param, default]
55 '-i' => ['seq', undef], # NOTA BENE!! This parameter holds the input sequence Fasta *string* (NOT filename!!)
56 '-p' => ['blastprogram', 'blastn'], # NB Genquire is only set up to handle nucleotide query inputs to Blast!
57 '-e' => [undef, '10.0'],
58 '-d' => ['database', 'nt'], # NB Genquire is only set up to handle nucleotide query inputs to Blast!
59 '-F' => [undef, 'T'],
60 '-G' => [undef, '0'],
61 '-E' => [undef, '0'],
62 '-X' => [undef, '0'],
63 '-I' => [undef, 'F'],
64 '-q' => [undef, '-3'],
65 '-r' => [undef, '1'],
66 '-v' => [undef, '500'],
67 '-b' => [undef, '250'],
68 '-f' => [undef, '0'],
69 '-g' => [undef, 'T'],
70 '-Q' => [undef, '1'],
71 '-D' => [undef, '1'],
72 '-a' => [undef, '1'],
73 '-J' => [undef, 'F'],
74 '-M' => [undef, 'BLOSUM62'],
75 '-W' => [undef, '0'],
76 '-z' => [undef, '0'],
77 '-K' => [undef, '100'],
78 '-L' => [undef, '20'],
79 '-Y' => [undef, '0'],
80 '-S' => [undef, '3'],
81 '-T' => [undef, 'F'],
82 '-U' => [undef, 'F'],
83 '-y' => [undef, '0.0'],
84 '-Z' => [undef, '0'],
85 };
86
87 }