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Revision: 1.9
Committed: Wed Aug 25 20:44:19 2004 UTC (11 years, 11 months ago) by skchan
Branch: MAIN
CVS Tags: HEAD
Changes since 1.8: +40 -25 lines
Log Message:
updated the docs

Line File contents
1 Simon Chan
2 skchan@cs.usask.ca
3
4 ### Instructions ###
5 Lines that contain '***' are lines that specify which files to change the use libs.
6
7
8 ### General Instructions: ###
9 1. Obtain the tar ball for GenQuire: Go to http://www.bioinformatics.org.
10 2. Run the Installer script, install.pl. Follow the instructions.
11 3. Run GenQuire: Genquire.pl
12 4. Choose your options.
13 5. The main loading scripts are located in the ./Admin directory.
14
15 ### Specific Instructions: ###
16 I installed genquire in a directory called 'gq' in my home directory. So, my '.' directory is /home/skchan/gq
17
18 1. Download GenQuire from its home page, which is located here: http://bioinformatics.org/ (In the 'Hosted Projects' column on the right
19 side of the screen).
20 2. Unpack your file: your_prompt> gunzip -dc Genquire.3.4.1.tar.gz | tar -xvf -
21 3. Within ./Genquire/Installer is the installation script, called install.pl, written by Matt Links. Run the install script
22 and follow the instructions. This is pretty simple and will not take that long at all.
23 When presented with the option of where to install Genquire, click on the 'gq' folder.
24 4. After the installation is complete, a good place to start would be modify the genquire.conf, which should be located here:
25 /home/skchan/gq/BIO_SUPPORT/Genquire.
26 Modify $WORKING_DIR within genquire.conf to specify the location of the script Genquire.pl
27 5. Modify the use lib in load_tigr.cfg to specify the location of HelperMethods.pm, which should be located here:
28 /home/skchan/gq/BIO_SUPPORT/Genquire/Admin
29
30 this copy of genquire will contain the 'good copy'
31 will include the various scripts I want to be included in the tar ball.
32
33 Changes from the original:
34 in /home/skchan/gq/BIO_SUPPORT/Genquire (this dir)
35 1. added this file simons_docs
36 2. renamed 'gq_local.cfg_example' to 'gq_local.cfg'
37 3. change the genquire.conf file to include gq_local.cfg
38 4. *** the user needs to specify the use libs within genquire.conf
39 5. change the database connection parameters in BioSQL.cfg
40 For example:
41 my $host = "some_host";
42 my $db_name = "database_name";
43 my $db_user = "user_name";
44 my $driver = 'mysql';
45 my $db_pass = 'password_for_user_name';
46 6. added load_tigr.cfg that allows the user to run ./Admin/Data_Dump.pl within GenQuire.
47
48
49 in /home/skchan/gq/BIO_SUPPORT/Genquire/Admin
50 1. replaced the version of schema_v3.4.sql with the updated version (includes IGNORE tables)
51 2. replaced the version of org.data with my modified version.
52 3. Added Data_Dump.pl and Data_Output.pl
53 4. modified create_tilingpath.pl. Made it more user-friendly as well as added more input-checking code.
54 5. Added Make_Tiling_Path.pl, Data_Tiling_Path.pl, HelperMethods.pm to allow the GenQuire user to run Data_Dump.pl via the interface.
55 6. User needs to specify the use within Make_Tiling_Path.pl to point to the directory HelperMethods.pm is in.
56
57 in /home/skchan/gq/BIO_SUPPORT/Genquire/Admin/Obtain_Microarray_Data
58 1. Added MicroarrayAccess.pm, microarray_fetch.pl, parse_tair_microarray.pl to this directory.
59 MicroarrayAccess.pm is a package of methods that parse_tair_microarray.pl uses.
60 microarray_fetch.pl is a program that fetches the microarray data from TAIR's FTP site and unzips them on the local machine.
61 parse_tair_microarray.pl program that parses the microarray data and adds them to the proper tables in the database schema.
62
63
64 in /home/skchan/gq/BIO_SUPPORT/Genquire/PLUGINS
65 1. Added zinc_plugin.pl, genquire_response.xml, ExProfile.pm, plugins.conf
66 2. Be sure to modify plugins.conf to point to the correct location of genquire_response.xml
67 3. ***User needs to modify the use libs within ExProfile.pm to point to the correct location of the Tk::Zinc module.
68
69
70 in /home/skchan/gq/BIO_SUPPORT/bioperl-gui/Bio/Tk
71 1. Added my versions of SeqCanvas.pm, SeqCanvasFeatures.pm, AnnotMap.pm, bioTk_Map.pm
72 2. Added zinc_seqcanvas_plugin.pm, which is what makes the actual calls to Tk::Zinc.
73 3. Added the directory ./TkZinc_Example (/home/skchan/gq/BIO_SUPPORT/bioperl-gui/Bio/Tk/TkZinc_Example)
74 Within this directory, there will some genbank files (testseq.gb*) and the SeqCanvas test script (s.pl)
75 4. Added drawing_test.pl, which is a script I coded up to compare the different canvases (Tk::Zinc vs Tk::Canvas)
76 Most of this work (1-3) was done at the ICAPTURE Centre with Mark Wilkinson.
77 5. ***User needs to specify the use lib in zinc_seqcanvas_plugin.pm to point to Zinc.pm, Zinc.so, Zinc.bs
78 6. ***User needs to specify the use lib in bioTk_Map.pm to point to the PLUGINS directory (within the Genquire directory) to point to the
79 ExProfile.pm package.
80 7. ***User needs to specify the use lib in SeqCanvas.pm to point to the directory zinc_seqcanvas_plugin.pm is located in.
81
82 in /home/skchan/gq/BIO_SUPPORT/Genquire/GQ/Client
83 1. Added my verisons of PlugInHandler.pm and QueryScreen.pm
84
85 in /home/skchan/gq/BIO_SUPPORT/TkZinc
86 1. I downloaded the latest version of TkZinc (3.298). We should modify Matt's Installer script to automatically download TkZinc as well.
87
88 in /home/skchan/gq/BIO_SUPPORT/bioperl-live/Bio/SeqIO
89 1. I renamed tigr.pm (the orignal) to lauricha_tigr.pm
90 2. I copyed into this directory a copy of tigr.pm that Guo and I worked on (independently).
91 3. Added seqio_test.pl, which was an important tester script for my version of tigr.pm
92
93 in /home/skchan/gq/BIO_SUPPORT/Genquire/GQ/Server/
94 The following error messages occur when I use some of the modules in this directory:
95 1. Useless use of push with no values at /home/skchan/gq/BIO_SUPPORT/Genquire/GQ/Server/GenericFeature.pm line 98.
96 2. Useless use of unshift with no values at /home/skchan/gq/BIO_SUPPORT/Genquire/GQ/Server/GenericFeature.pm line 152.
97 3. Useless use of string in void context at /home/skchan/gq/BIO_SUPPORT/Genquire/GQ/Server/GenericFeature.pm line 600.
98 4. Useless use of string in void context at /home/skchan/gq/BIO_SUPPORT/Genquire/GQ/Server/Feature.pm line 152.
99
100 So I've gone into those modules and fix the problems.
101 1. comment out the 'push'
102 2. Change the 'unshift' to 'shift'
103 3. Change ' eval {"require Bio::SeqFeature::Gene::$type;"}; ' to ' eval {require "Bio::SeqFeature::Gene::$type;"}; '
104 4. Change ' eval {"require Bio::SeqFeature::Gene::$type;"}; ' to ' eval {require "Bio::SeqFeature::Gene::$type;"}; '
105
106 in /home/skchan/gq/BIO_SUPPORT/Genquire/GQ/Server/DB/Context.pm
107 1. in the subroutine "contig", I added an if conditional. I noticed that the script create_tilingpath.pl attempts to get the contigs that
108 are to the left/right of the current contig. The names of those contigs are stored in the database (Table Tiling_Path), however, that's all we know about them (data regarding these contigs are not stored in the xml). Thus, $contigobj->id is undefined. To prevent error messages, I added the conditional.
109
110 Added use libs '/path/to/module' in the following files:
111 1. ***Within GQ::Client::Utilities.pm, added " use lib '/home/skchan/gq/BIO_SUPPORT/bioperl-live'; " to point to Bio::Tools::Blast.pm
112 2. ***Within GQ::Client::txtHandAnnotate.pm, added " use lib '/home/skchan/gq/BIO_SUPPORT/bioperl-gui'; " to point to Bio::Tk::GO_Browser.pm
113 3. ***Within Bio::Tk::GO_Browser, added " use lib '/home/skchan/gq/BIO_SUPPORT/go-dev/perl-api'; " to point to GO::AppHandle.pm
114
115 Added /genbank_files within the /Genquire directory. This is where one can store genbank files.
116
117 Change version of Tk::Zinc:
118 An older version of Tk::Zinc, 3.296, allows us to render the images. However, it does not have the ability to allow the user to specify
119 where the zooming point should be located. All subsequent versions, however, do allow this zooming option.
120 BUT, there is a bug in the newer versions that prevents it from allowing us to render the images. It seems that we can't get the best
121 of both worlds! :-(
122 So, what I do is switch between the two versions when I want to test things.
123 To do so, all you need to do is change the 'use lib' in 'ExProfile.pm' and 'zinc_seqcanvas_plugin.pm' to point to the version of Tk::Zinc
124 you want. Also, be sure to change the value of $render_switch in zinc_seqcanvas_plugin.pm to a true value.
125 I have spoken to the main developer of Tk::Zinc and the latest version of Tk::Zinc to be released will fix this problem. However, when
126 exactly the next version will come out remains to be seen....