1. assume the following modules are installed already
=====================================================
CGI
DBI
DBD-Oracle
GD

downloaded files for new module installations:
------------------------
~fkang/Desktop/downloads

2. Digest::MD5
==============
Perl Makefile.PL
make
make test
sudo make install

3. Text::Shellwords
===================
Perl Makefile.PL
make
make test
sudo make install

4. XML related modules
=======================
   Expat
   XML::Parser (for chado)
   XML::Simple  (for chado)
   HTML::Tagset 
   HTML::Parser
   URI   
   LWP (for chado)
   XML::Parser::PerlSAX (libxml-perl-007) (for chado)
   XML::RegExp
   XML::DOM (for chado)

4.1 XML::Parser
----------------

4.1.1 requires the installation of Expat.
download:

http://aleron.dl.sourceforge.net/sourceforge/expat/expat-1.95.7.tar.gz

Readme for expat:
       ./configure
There are many options which you may provide to configure (which you
can discover by running configure with the --help option).  But the
one of most interest is the one that sets the installation directory.
By default, the configure script will set things up to install
libexpat into /usr/local/lib, expat.h into /usr/local/include, and
xmlwf into /usr/local/bin.

installation:
./configure

make
lib/expat.h:985: warning: `cdecl' attribute directive ignored

sudo make install

4.1.2 install XML::Parser

worked with the following procedure:

perl Makefile.PL EXPATLIBPATH=/usr/local/lib \
  EXPATINCPATH=/usr/local/include
make
make test
make install

4.2 XML::Simple
----------------
Perl Makefile.PL
make
make test
sudo make install

4.3. XML::DOM
--------------
4.3.1 prerequisites:

a) XML::DOM prerequisites:
   LWP::UserAgent
   (as LMP: libwww-perl-5.76)
   XML::Parser::PerlSAX
   XML::RegExp
 
b) LMP prerequisites:
   HTML:Parser
   URI

c) HTML::Parser prerequisite:
   HTML::Tagset
 
4.3.2 install the dependencies

a) steps for each installation:
   Perl Makefile.PL
   make
   make test
   sudo make install

b) module installation in the following orders:
   HTML::Tagset
   HTML::Parser
   URI   
   LWP
   XML::Parser::PerlSAX (libxml-perl-007)
   XML::RegExp
   XML::DOM

4.4. XML::Parser::PerlSAX
-------------------------
installed above as the prerequisite for XML::DOM


5. DBD:Pg
==========

5.1 set the following environment variables before installing DBD::Pg

file:  ~fkang/.install_dbd_pg on fan's desktop

file content:
# add the environment variables required for insatlling DBD::Pg
POSTGRES_LIB="/Users/postgres/pgsql/lib -lssl -lcrypto"
#POSTGRES_LIB=/Users/postgres/pgsql/lib
POSTGRES_INCLUDE=/Users/postgres/pgsql/include
POSTGRES_HOME=/Users/postgres/pgsql

5.2. answer the questions during the first step "perl makefile/PL"

on Fan's desktop (for PostgreSQl version 7.4.2):

kang@gen-mac-fan:~/Desktop/downloads/DBD-Pg-1.32$ perl Makefile.PL
Configuring Pg
Remember to actually read the README file!
Path to pg_config? 
/Users/postgres/pgsql/bin/
Enter a valid PostgreSQL major version number  
7
Enter a valid PostgreSQL minor version number 
4
Enter a valid PostgreSQL patch version number 
2
Enter a valid PostgreSQL include directory 
/Users/postgres/pgsql/include
Enter a valid PostgreSQL library directory 
/Users/postgres/pgsql/lib

the following messages:
OS: darwin
PostgreSQL version: 7.4.2
Using DBI 1.38 installed in /usr/local/perl/5.80/Library/darwin/auto/DBI
Checking if your kit is complete...
Looks good
Using DBI 1.38 installed in /usr/local/perl/5.80/Library/darwin/auto/DBI
Writing Makefile for DBD::Pg

5.3. make

5.4 make test
need three environment variables

make test on fan's desktop:

fkang@gen-mac-fan:~/Desktop/downloads/DBD-Pg-1.32$ export DBI_DSN=dbi:Pg:dbname=chadotest
fkang@gen-mac-fan:~/Desktop/downloads/DBD-Pg-1.32$ export DBI_USER=postgres
fkang@gen-mac-fan:~/Desktop/downloads/DBD-Pg-1.32$ export DBI_PASS=???
(note: put postgres database password here)

fkang@gen-mac-fan:~/Desktop/downloads/DBD-Pg-1.32$ make test
PERL_DL_NONLAZY=1 /usr/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00basic...........ok                                                       
t/01connect.........ok 8/8#                                                  
# Program       Version
# DBD::Pg       1.32
# PostgreSQL    7.4.2
# DBI           1.38
t/01connect.........ok                                                       
t/01constants.......ok                                                       
t/01setup...........ok                                                       
t/02attribs.........ok                                                       
        4/92 skipped: Test::Simple version 0.47 or better required for testing of attribute "InactiveDestroy"
t/03dbmethod........ok                                                       
t/03smethod.........ok                                                       
t/04misc............ok                                                       
t/05arrays..........ok                                                       
        15/17 skipped: various reasons
t/12placeholders....ok                                                       
t/99_pod............skipped
        all skipped: Test::Pod 0.95 required for testing POD
t/99cleanup.........ok                                                       
All tests successful, 1 test and 19 subtests skipped.
Files=12, Tests=348,  4 wallclock secs ( 1.66 cusr +  0.35 csys =  2.01 CPU)


5.5 sudo make install
Password:
Installing /usr/local/perl/5.80/Library/darwin/auto/DBD/Pg/Pg.bs
Installing /usr/local/perl/5.80/Library/darwin/auto/DBD/Pg/Pg.bundle
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/perl/5.80/Library/darwin/DBD/Pg.pm
Installing /usr/local/perl/5.80/man/man3/DBD::Pg.3
Writing /usr/local/perl/5.80/Library/darwin/auto/DBD/Pg/.packlist
Appending installation info to /usr/local/perl/5.80/Library/darwin/perllocal.pod


6. Class::DBI 
=============
6.1 prerequisite 
for Class::DBI  
    Class::Accessor
    Class::Data::Inheritable
    Class::Trigger
    Ima::DBI
    Test::More (test-simple-0.47)
    UNIVERSAL::moniker

for Class::Trigger
    IO::Scalar (IO-stringy-2.109.tar.gz)

for Ima::DBI
    Class::WhiteHole
    DBIx::ContextualFetch

test installation for Class::DBI requires DBD::SQLite


6.2 Install all the modules listed above 
a) steps for each installation:
   Perl Makefile.PL
   make
   make test
   sudo make install

b) module installation in the following orders:
    Class::Accessor
    Class::Data::Inheritable
    IO::Scalar
    Class::Trigger
    Class::WhiteHole
    DBIx::ContextualFetch
    Ima::DBI
    Test::More (test-simple-0.47)
    UNIVERSAL::moniker
    DBD::SQLite
    Class::DBI 


7. Class::DBI::Pager
====================
7.1 prerequisites
    Class::DBI (installed as described above)
    Data::Page
    Exporter::Lite

7.2 Install all the modules listed above 

a) steps for each installation:
   Perl Makefile.PL
   make
   make test
   sudo make install

b) module installation in the following orders:
    Data::Page
    Exporter::Lite
    Class::DBI::Pager

8. Log::log4perl
=================
steps for each installation:
   Perl Makefile.PL
   make
   make test
   sudo make install


9. Term::ProgressBar
======================
9.1 prerequisites
    Class::MethodMaker
    Term::ReadKey 

9.2 install Class::MethodMaker
   ./configure
   make
   make test
   sudo make install

9.3 install Term::ReadKey
   Perl Makefile.PL
   make
   make test
   sudo make install

9.4 install Term::ProgressBar
   ./configure
   make
   make test
   sudo make install


10. Apache 1.3.29
=====================

    ./configure --prefix=/usr/local/apache
    make
    sudo make install

message:
| You now have successfully built and installed the      |
| Apache 1.3 HTTP server. To verify that Apache actually |
| works correctly you now should first check the         |
| (initially created or preserved) configuration files   |
|                                                        |
|   /etc/httpd/httpd.conf
|                                                        |
| and then you should be able to immediately fire up     |
| Apache the first time by running:                      |
|                                                        |
|   /usr/local/apache/sbin/apachectl start               |


11. Bioperl 1.4
=================

11.1 prerequisites
     HTML::Entities 
     IO::Scalar (IO-stringy-2.109, installation: in 6.2)
     IO::String

11.2 install HTML::Entities

the same as HTML::Parser (HTML-Parser-3.35, installation: in 4.3.2)

11.3 install IO::String
   Perl Makefile.PL
   make
   make test
   sudo make install

11.4 install Bioperl

11.4.1. identify optional modules for Bioperl 

fkang@gen-mac-fan:~/Desktop/downloads/bioperl-1.4$ perl Makefile.PL

Bioperl comes with a number of useful scripts which you may wish to install.
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] 

answer: a

messages for missing external Modules:

External Module GD::SVG, Generate optional SVG output,
 is not installed on this computer.
  The  in Bioperl needs it for Bio::Graphics

External Module Ace, Aceperl,
 is not installed on this computer.
  The Bio::DB::Ace in Bioperl needs it for access of ACeDB database

External Module SOAP::Lite, SOAP protocol,
 is not installed on this computer.
  The Bio::DB::XEMBLService in Bioperl needs it for XEMBL Services (also Bibliographic queries in Biblio::) 

External Module XML::Twig, Available on CPAN,
 is not installed on this computer.
  The Module Bio::Variation::IO::xml.pm in Bioperl needs it for parsing of XML documents

External Module SVG, Generate optional SVG output,
 is not installed on this computer.
  The  in Bioperl needs it for Bio::Graphics

External Module XML::Writer, Parsing + writing of XML documents,
 is not installed on this computer.
  The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation code, GAME parser

External Module DBD::mysql, Mysql driver,
 is not installed on this computer.
  The Bio::DB::GFF in Bioperl needs it for loading and querying of Mysql-based GFF feature databases

External Module Graph::Directed, Generic Graph data stucture and algorithms,
 is not installed on this computer.
  The Bio::Ontology::SimpleOntologyEngine in Bioperl needs it for Ontology Engine implementation for the GO parser


Information:

   There are some external packages and perl modules, listed above, which 
   bioperl uses. This only effects the functionality which is listed above:
   the rest of bioperl will work fine, which includes nearly all of the
   core packages.

   The installation of these external packages is very simple. You
   can read more about bioperl external dependencies in the INSTALL
   file or at:

   http://bioperl.org/Core/Latest/INSTALL

   Enjoy the rest of bioperl, which you can use after going 'make install'

Writing Makefile for Bio


11.4.2 install some of the external modules mentioned above
   GD::SVG
   SOAP::Lite
   XML::Twig
   SVG
   XML::Writer  
   Graph::Directed  (same as GRAPH, needs Heap)

leave out modules Ace and DBD:mysql

a) steps for each installation:
   Perl Makefile.PL
   make
   make test
   sudo make install

b) module installation in the following orders:
   SVG
   GD::SVG (prerequisites: GD and SVG)
   SOAP::Lite
   XML::Twig (needs XML::Parser and the expat library installed)
   XML::Writer 
   Heap
   Graph::Directed  (same as GRAPH)   

11.4.3 install Bioperl 1.4 again

fkang@gen-mac-fan:~/Desktop/downloads/Bioperl-1.4$ perl Makefile.PL
*** Script Install Section ****

Bioperl comes with a number of useful scripts which you may wish to install.
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] 

...

External Module Ace, Aceperl,
 is not installed on this computer.
  The Bio::DB::Ace in Bioperl needs it for access of ACeDB database

External Module DBD::mysql, Mysql driver,
 is not installed on this computer.
  The Bio::DB::GFF in Bioperl needs it for loading and querying of Mysql-based GFF feature databases


Information:

   There are some external packages and perl modules, listed above, which 
   bioperl uses. This only effects the functionality which is listed above:
   the rest of bioperl will work fine, which includes nearly all of the
   core packages.

   The installation of these external packages is very simple. You
   can read more about bioperl external dependencies in the INSTALL
   file or at:

   http://bioperl.org/Core/Latest/INSTALL

   Enjoy the rest of bioperl, which you can use after going 'make install'

Writing Makefile for Bio

fkang@gen-mac-fan:~/Desktop/downloads/Bioperl-1.4$ make 
fkang@gen-mac-fan:~/Desktop/downloads/Bioperl-1.4$ make test
Failed 2/179 test scripts, 98.88% okay

fkang@gen-mac-fan:~/Desktop/downloads/Bioperl-1.4$ sudo make install
 

12. SQL::Translator
====================
12.1
a) prerequisites for SQL::Translator:
    Class::Base
    GraphViz
    IO::Scalar (installed, section 11.3)
    Parse::RecDescent
    Spreadsheet::ParseExcel
    Template
    Test::Differences
    Test::Exception
    Text::RecordParser
    XML::Writer (installed, section 11.4)
    XML::XPath
    YAML 

b) prerequisites for GraphViz
    IPC::Run
    Math::Bezier

c)  prerequisites for Spreadsheet::ParseExcel
    OLE::Storage_Lite  

d)  prerequisites for Template  
    AppConfig 

e)  prerequisites for Test::Differences
    Text::Diff (prerequisite Algorithm::Diff)

f)  prerequisites for Test::Exception
    Sub::Uplevel
    Test::Builder::Tester  

12.2 installation of the above modules
    
a) steps for each installation:
   Perl Makefile.PL
   make
   make test
   sudo make install

b) module installation in the following orders:
    Class::Base
    IPC::Run
    Math::Bezier
    GraphViz
    Parse::RecDescent
    OLE::Storage_Lite
    Spreadsheet::ParseExcel
    Algorithm::Diff
    Text::Diff
    Test::Differences
    Sub::Uplevel
    Test::Builder::Tester
    Test::Exception
    Text::RecordParser
    XML::XPath
    YAML
    AppConfig
    Template
    SQL::Translator

c) SQL::Translator warning
fkang@gen-mac-fan:~/Desktop/downloads/SQL-Translator-0.05$ perl Makefile.PL
WARNING: SIGN is not a known parameter.
'SIGN' is not a known MakeMaker parameter name.
Writing Makefile for SQL::Translator

13. Module:Build
a) required for chado installation
   (not mentione din INSTALL or README)

b) prerequisite: 
ExtUtils::ParseXS (needs ExtUtils::CBuilder)
Archive::Tar

c) installation orders:
   ExtUtils::CBuilder
   ExtUtils::ParseXS
   Archive::Tar
   Module:Build

14. installed Perl modules

fkang@gen-mac-fan:~$ perl list_perl_modules.pl
(the notes are added for ???)
Algorithm::Diff -- 1.15
AppConfig -- 1.56
Archive::Tar -- 1.08
Bio -- ???  (bioperl 1.4)
Bundle::SQL::Translator -- 1.00  
Class-MethodMaker -- ??? (2.00)
Class::Accessor -- 0.19
Class::Base -- 0.03
Class::DBI -- 0.95
Class::DBI::Pager -- 0.05
Class::DBI::Pg -- 0.03
Class::Data::Inheritable -- 0.02
Class::Trigger -- 0.08
Class::WhiteHole -- 0.04
DBD::Oracle -- 1.14
DBD::Pg -- 1.32
DBD::SQLite -- 0.31
DBI -- 1.38
DBIx::ContextualFetch -- 1.01
Data-Page -- ??? (1.01)
Digest::MD5 -- 2.33
Exporter::Lite -- 0.01
Exporter::Lite -- 0.01
ExtUtils::CBuilder -- 0.02
GD -- 2.11
GD::SVG -- 0.25
Graph -- 0.20101
GraphViz -- 1.8
HTML::Parser -- 3.35
HTML::Tagset -- 3.03
Heap -- 0.70
IO-stringy -- ??? (IO::Scalar 2.109)
IO::String -- 1.04
IPC::Run -- 0.78
Ima::DBI -- 0.33
Log::Log4perl -- 0.42
Math::Bezier -- 0.01
OLE::Storage_Lite -- 0.11
Parse::RecDescent -- 1.94
Perl -- 5.8.0
SOAP::Lite -- 0.60
SQL::Translator -- 0.05
SVG -- 2.28
Spreadsheet::ParseExcel -- 0.2602
Sub::Uplevel -- 0.08
Template -- 2.13
Term-ProgressBar -- ??? (2.06)
Term::ReadKey -- 2.21
Test::Builder::Tester -- 0.09
Test::Differences -- 0.47
Test::Exception -- 0.15
Test::Simple -- 0.47
Text::Diff -- 0.35
Text::RecordParser -- 0.05
Text::Shellwords -- 1.03
UNIVERSAL::moniker -- 0.07
URI -- 1.30
XML-DOM -- ??? (1.43)
XML::Parser -- 2.34
XML::RegExp -- 0.02
XML::Simple -- 2.11
XML::Twig -- 3.14
XML::Writer -- 0.500
XML::XPath -- 1.13
YAML -- 0.35
libwww-perl -- ??? (LWP 5.76)
libxml-perl -- ??? (XML::Parser::PerlSAX 0.07)