Installation of Generic Genome Browser version 1.61
===================================================

tested the installation on Fan's desktop
Fan's note on 3/31/2004

Summary:
=========

1. installation procedure
-------------------------

perl Makefile.PL
make
make install

2. installation location:
---------------------------

2.1 default: /usr/local/apache

2.2 use option PREFIX to define a specific location.
make sure to have the following directories ready.
PREFIX
PREFIX/conf
PREFIX/cgi-bin
PREFIX/htdocs

for the installation on Fan's desktop, PREFIX=/usr/local/gmod.

2.3 use other options (see INSTALL for Generic-Genome-Browser 1.61) 


detailed notes for installation:
================================

1. The location for installing G-Browser software
--------------------------------------------------
/usr/local/gmod

postgres@gen-mac-fan:/usr/local$ sudo mkdir gmod 

postgres@gen-mac-fan:/usr/local$ ls -l
total 0
drwxr-xr-x   7 root  wheel  238 23 Mar 17:37 apache/
drwxr-xr-x  12 root  wheel  408 31 Mar 10:04 bin/
drwxr-xr-x   3 root  wheel  102 29 Mar 15:17 etc/
drwxr-xr-x   2 root  wheel   68 31 Mar 14:18 gmod/
drwxrwxr-x  19 root  wheel  646 23 Mar 10:03 include/
drwxrwxr-x  24 root  wheel  816 23 Mar 10:03 lib/
drwxr-xr-x   4 root  wheel  136 27 Mar 04:32 man/
drwxr-xr-x   3 root  wheel  102 18 Dec 23:29 perl/
drwxr-xr-x   4 root  wheel  136 29 Mar 15:17 sbin/


2. generate Makefile
---------------------
fkang@gen-mac-fan:~/Desktop/gmod-0.002/Generic-Genome-Browser-1.61$ perl Makefile.PL PREFIX=/usr/local/gmod

----------------------------------------------
                File Paths

 PREFIX /usr/local/gmod
   CONF /usr/local/gmod/conf
 HTDOCS /usr/local/gmod/htdocs
 CGIBIN /usr/local/gmod/cgi-bin
  DO_XS 1

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Checking if your kit is complete...
Warning: the following files are missing in your kit:
        Changes
Please inform the author.
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing Makefile for Generic-Genome-Browser


(Fan's note: the file "Changes" exists!!! a bug?)

3. make
--------

fkang@gen-mac-fan:~/Desktop/gmod-0.002/Generic-Genome-Browser-1.61$ make

a long list!
no errors.

4. make install
-----------------

fkang@gen-mac-fan:~/Desktop/gmod-0.002/Generic-Genome-Browser-1.61$ sudo make install
password:

/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Installing /usr/local/perl/5.80/Library/darwin/auto/Bio/Graphics/Browser/CAlign/CAlign.bs
Installing /usr/local/perl/5.80/Library/darwin/auto/Bio/Graphics/Browser/CAlign/CAlign.bundle
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Glyph/allele_tower.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Glyph/connector.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Glyph/drosophila_arrow.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Glyph/ideogram.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Glyph/insertion_chromosome.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Glyph/phased_exons.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Glyph/wormbase_transcript.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/CAlign.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/GFFhelper.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/I18n.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/Markup.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/PadAlignment.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/Plugin.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/Realign.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser/Util.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/GFF/Aggregator/orf.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/GFF/Aggregator/reftranscript.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/GFF/Aggregator/waba_alignment.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/GFF/Aggregator/wormbase_gene.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/BioSQL.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/Chado.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/Chado/Segment.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/Chado/Segment/Feature.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/BioSQL/DBAdaptor.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/BioSQL/Iterator.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm
Installing /usr/local/perl/5.80/Library/darwin/Bio/DB/Das/BioSQL/Segment.pm
Installing /usr/local/perl/5.80/man/man1/load_genbank.pl.1
Installing /usr/local/perl/5.80/man/man1/make_das_conf.pl.1
Installing /usr/local/perl/5.80/man/man1/process_gadfly.pl.1
Installing /usr/local/perl/5.80/man/man1/process_ncbi_human.pl.1
Installing /usr/local/perl/5.80/man/man1/process_sgd.pl.1
Installing /usr/local/perl/5.80/man/man1/process_wormbase.pl.1
Installing /usr/local/perl/5.80/man/man1/register_moby_services.pl.1
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::BioSQL.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::BioSQL::BioDatabaseAdaptor.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::BioSQL::DBAdaptor.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::BioSQL::PartialSeqAdaptor.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::BioSQL::Segment.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::Chado.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::Chado::Segment.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::Das::Chado::Segment::Feature.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::GFF::Aggregator::orf.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3
Installing /usr/local/perl/5.80/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser::CAlign.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser::GFFhelper.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser::Markup.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser::PadAlignment.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser::Plugin.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser::Realign.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Browser::Util.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Glyph::allele_tower.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Glyph::ideogram.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Glyph::insertion_chromosome.3
Installing /usr/local/perl/5.80/man/man3/Bio::Graphics::Glyph::wormbase_transcript.3
Installing /usr/local/perl/5.80/bin/load_genbank.pl
Installing /usr/local/perl/5.80/bin/make_das_conf.pl
Installing /usr/local/perl/5.80/bin/process_gadfly.pl
Installing /usr/local/perl/5.80/bin/process_ncbi_human.pl
Installing /usr/local/perl/5.80/bin/process_sgd.pl
Installing /usr/local/perl/5.80/bin/process_wormbase.pl
Installing /usr/local/perl/5.80/bin/register_moby_services.pl
Writing /usr/local/perl/5.80/Library/darwin/auto/Generic-Genome-Browser/.packlist
Appending installation info to /usr/local/perl/5.80/Library/darwin/perllocal.pod
/usr/local/bin/perl "/Users/fkang/Desktop/gmod-0.002/Generic-Genome-Browser-1.61/install_util/conf_install.pl" 'CGIBIN=/usr/local/gmod/cgi-bin' 'DO_XS=1' 'CONF=/usr/local/gmod/conf' 'PREFIX=/usr/local/gmod' 'HTDOCS=/usr/local/gmod/htdocs' 
Installing sample configuration files...
unable to make /usr/local/gmod/conf/gbrowse.conf directory
make: *** [conf_install] Error 2

troubleshooting:
-----------------
related codes in conf_install.pl

#!/usr/local/perl/5.80/bin/perl
use strict;
use File::Copy;
use Bio::Root::IO;
use Cwd;
use FindBin '$Bin';

my $origdir = cwd;
my $homedir = "$Bin/..";
                                                                                
chdir $homedir or die "couldn't cd to $homedir: $!\n";

foreach (@ARGV) {
  $_ =~ s/^\'(.*)\'$/$1/;
}

# get configuration stuff from command line
my %options = map {split /=/} @ARGV;
my $dir = "$options{CONF}/gbrowse.conf";

#start the installation...
print "Installing sample configuration files...\n";

if (! (-e $dir)) {
    mkdir($dir,0777) or die "unable to make $dir directory\n";
}

...
...

Fan's note: 
-----------
for /usr/localgmod/conf/gbrowse.conf, the parent directory 'conf" doesn't exist!

solution:
---------
create the parent directory and try again.


5. new installation (complete procedure)
-----------------------------------------

mv Generic-Genome-Browser-1.61  Generic-Genome-Browser-1.61-test1

restart!!!

make the sub-directories in /usr/lcoal/gmod

postgres@gen-mac-fan:/usr/local/gmod$ ls -l
total 0
drwxr-xr-x  2 root  wheel  68 31 Mar 15:22 cgi-bin/
drwxr-xr-x  2 root  wheel  68 31 Mar 15:22 conf/
drwxr-xr-x  2 root  wheel  68 31 Mar 15:22 htdocs/


fkang@gen-mac-fan:~/Desktop/gmod-0.002$ tar zxvf Generic-Genome-Browser-1.61.tar.gz

fkang@gen-mac-fan:~/Desktop/gmod-0.002$ cd Generic-Genome-Browser-1.61

fkang@gen-mac-fan:~/Desktop/gmod-0.002/Generic-Genome-Browser-1.61$ perl Makefile.PL PREFIX=/usr/local/gmod

fkang@gen-mac-fan:~/Desktop/gmod-0.002/Generic-Genome-Browser-1.61$ make
fkang@gen-mac-fan:~/Desktop/gmod-0.002/Generic-Genome-Browser-1.61$ sudo make install

Password:
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Writing /usr/local/perl/5.80/Library/darwin/auto/Generic-Genome-Browser/.packlist
Appending installation info to /usr/local/perl/5.80/Library/darwin/perllocal.pod
/usr/local/bin/perl "/Users/fkang/Desktop/gmod-0.002/Generic-Genome-Browser-1.61/install_util/conf_install.pl" 'CGIBIN=/usr/local/gmod/cgi-bin' 'DO_XS=1' 'CONF=/usr/local/gmod/conf' 'PREFIX=/usr/local/gmod' 'HTDOCS=/usr/local/gmod/htdocs' 
Installing sample configuration files...
/usr/local/bin/perl "/Users/fkang/Desktop/gmod-0.002/Generic-Genome-Browser-1.61/install_util/cgi_install.pl" 'CGIBIN=/usr/local/gmod/cgi-bin' 'DO_XS=1' 'CONF=/usr/local/gmod/conf' 'PREFIX=/usr/local/gmod' 'HTDOCS=/usr/local/gmod/htdocs' 
Installing gbrowse CGI scripts...
copying das to /usr/local/gmod/cgi-bin/das
copying gbrowse to /usr/local/gmod/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/gmod/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/gmod/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/gmod/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/gmod/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/gmod/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/gmod/cgi-bin/moby_server
/usr/local/bin/perl "/Users/fkang/Desktop/gmod-0.002/Generic-Genome-Browser-1.61/install_util/htdocs_install.pl" 'CGIBIN=/usr/local/gmod/cgi-bin' 'DO_XS=1' 'CONF=/usr/local/gmod/conf' 'PREFIX=/usr/local/gmod' 'HTDOCS=/usr/local/gmod/htdocs' 
Installing stylesheet and images...
Making /usr/local/gmod/htdocs/gbrowse/images...
Making /usr/local/gmod/htdocs/gbrowse/images/buttons...
Making /usr/local/gmod/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/gmod/htdocs/gbrowse/tmp...
Installing documentation...
Installing tutorial...
Installing sample_data...
Installing contrib...
Installing sample data files...

#############################################################################
GBrowse is now installed.  Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse/ for the online tutorial and reference manual.
#############################################################################

6. try the browser
------------------

fkang@gen-mac-fan:/Library/WebServer/CGI-Executables$ sudo cp -p /usr/local/gmod/cgi-bin/gbrowse .


http://localhost/cgi-bin/gbrowse/yeast_chr1

The page is displayed !