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Makefile.PL
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Makefile.PL
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#!/usr/bin/perl
use lib './install_util';
use ExtUtils::MakeMaker;
use GuessDirectories;
use FindBin '$Bin';
use IO::File;
use Cwd;
require 5.005003;
my $VERSION = '1.71b';
my $working_dir = cwd;
my @OPTIONS = qw(APACHE CONF HTDOCS CGIBIN GBROWSE_ROOT INSTALL_BASE
LIB BIN YES PREFIX PACKAGE_DIR
DO_XS NONROOT SELINUX COURSE);
my $OPTIONS = join ('|',@OPTIONS);
my %OPTIONS;
my $OPTIONS_TO_ARGV = "LIB|PREFIX";
my @argv = @ARGV;
@ARGV = ();
foreach (@argv) {
if (/^--?h/i) {
die <<END;
To customize install locations, provide one or more of the options
CONF, HTDOCS, or CGIBIN as in CONF=/usr/local/apache/conf. To accept
the default values without being prompted for them, provide YES=1 as
an argument.
CONF is the directory in which you will place the gbrowse configuration
files. Usually this is the same as the Apache configuration directory, but
it doesn't have to be.
CGIBIN is the directory in which to place the GBrowse CGI scripts. This must
be the same as, or a subdirectory of, your Apache server's CGI executable
directory.
HTDOCS is the document root in which the HTML files for your web server reside.
If you are using a virtual server, use the appropriate HTDOCS directory
for the virtual server's document root.
GBROWSE_ROOT (optional) is the location under HTDOCS in which you would like
GBrowse's static files (stylesheets, images, documentation) to be stored. For
example, if you specify
HTDOCS=/var/www/html
and
GBROWSE_ROOT=genomes/gbrowse
then the static files will be stored at /var/www/html/genomes/gbrowse. The
default location is "gbrowse".
Finally, PACKAGE_DIR is for creating packages for various distributions like
deb or rpm packagers. The argument provided here will be removed from other
paths before in place subsitutions are done. For example, if you want the
final cgi directory to be /usr/lib/cgi-bin and you are building a package
in /tmp, you would provide PACKAGE_DIR=/tmp and CGIBIN=/tmp/usr/lib/cgi-bin.
Examples:
For RedHat Linux:
perl Makefile.PL CONF=/etc/httpd/conf \\
HTDOCS=/var/www/html \\
CGIBIN=/var/www/cgi-bin \\
DO_XS=1
For Ubuntu Linux (running Apache version 2):
perl Makefile.PL CONF=/etc/apache2 \\
HTDOCS=/var/www \\
CGIBIN=/usr/lib/cgi-bin \\
DO_XS=1
For Macintosh OS X:
perl Makefile.PL CONF=/etc/httpd \\
HTDOCS=/Library/WebServer/Documents \\
CGIBIN=/Library/WebServer/CGI-Executables \\
DO_XS=1
For Slackware Linux systems:
perl Makefile.PL CONF=/etc/apache \\
HTDOCS=/var/www/htdocs \\
CGIBIN=/var/www/cgi-bin \\
DO_XS=1
You can also supply the argument APACHE to specify the prefix of the
Apache installation tree, for systems in which you installed Apache
from scratch. For example:
perl Makefile.PL APACHE=/usr/local/apache DO_XS=1
This will set CONF to /usr/local/apache/conf, HTDOCS to
/usr/local/apache/htdocs, and CGIBIN to /usr/local/apache/cgi-bin.
To install as a user without root privileges, in addition to
the arguments above, provide the arguments NONROOT=1,
LIB=/path/to/perl/libs and BIN=/path/to/scripts
For example:
perl Makefile.PL APACHE=~/gbrowse/www \\
LIB=~/gbrowse/lib \\
BIN=~/gbrowse/bin \\
PREFIX=~/gbrowse \\
NONROOT=1
will perform a non-privileged installation that places all gbrowse
components (including perl libraries) in the path ~/gbrowse.
To make the CGI scipts aware of the custom library location, you can
either ask someone with root privileges to edit the apache
configuration file or define the environmental variable $PERL5LIB for
the owner of the httpd processes serving gbrowse. Failing that, you
will want to add the line
use lib "$ENV{HOME}/gbrowse/lib";
to each of the CGI scripts.
If you have a C compiler and wish to compile the XS extensions, set
DO_XS=1. Currently all this does is to speed up the multiple
alignment plugin.
END
;
}
elsif (/($OPTIONS)=(.+)/og) {
$OPTIONS{$1} = interpolate($2);
}
else {
push @ARGV,$_;
}
}
if (-e 'GGB.def' && !%OPTIONS) {
print STDERR "\nShould I use your previous settings to set the file paths and options (y/n) [y]? ";
chomp (my $line = <>);
if (!$line || $line =~ /^[yY]/) {
print STDERR "Using previous settings for file paths and options.\n";
open F,'GGB.def' or die "GGB.def: $!";
while (<F>) {
chomp;
next if /^\#/;
next unless /^($OPTIONS)=(.*)/o;
my $key = $1;
$OPTIONS{$1} = interpolate($2);
if ($key =~ /$OPTIONS_TO_ARGV/) {
push @ARGV, "$key=$OPTIONS{$key}";
}
}
close F;
}
}
if (-e 'GGB.def' && !$OPTIONS{GBROWSE_ROOT} && $OPTIONS{HTDOCS} ) {
print STDERR <<END;
--------------WARNING--------------------
You may have already installed GBrowse in this directory because you have
the HTDOCS variable set but not the GBROWSE_ROOT variable. Please see
the help document for how these variables have changed. You probably
want to have GBROWSE_ROOT equal to 'gbrowse' and remove 'gbrowse' from
the end of your HTDOCS.
Please check the file paths that are printed out at the end of this
output for sanity.
END
}
if(-e '/proc/filesystems'
&& `grep selinux /proc/filesystems`
&& !$OPTIONS{SELINUX} ) {
die <<"END"
------------------------------------------------------------------
WARNING:
You appear to have SELinux installed on this computer.
GBrowse can have problems working on SELinux systems.
Before you complete this installation please read 'README.fedora'
Then you can avoid this message by adding the flag --SELINUX=1 when
you execute perl Makefile.PL.
------------------------------------------------------------------
perl Makefile.PL aborted.
END
;
}
$OPTIONS{APACHE} ||= $OPTIONS{PREFIX} if exists $OPTIONS{PREFIX};
$OPTIONS{BIN} ||= $OPTIONS{INSTALLSCRIPT} if exists $OPTIONS{INSTALLSCRIPT};
if ($OPTIONS{APACHE} && !(defined $OPTIONS{CONF})) {
$OPTIONS{CONF} = "$OPTIONS{APACHE}/conf";
}
if ($OPTIONS{APACHE} && !(defined $OPTIONS{HTDOCS})) {
$OPTIONS{HTDOCS} = "$OPTIONS{APACHE}/htdocs";
}
if ($OPTIONS{APACHE} && !(defined $OPTIONS{CGIBIN})) {
$OPTIONS{CGIBIN} = "$OPTIONS{APACHE}/cgi-bin";
}
# set hard-coded values
if ($OPTIONS{YES}) {
print "Accepting default install locations.\n";
$OPTIONS{APACHE} ||= GuessDirectories->root;
$OPTIONS{CONF} ||= GuessDirectories->conf($OPTIONS{APACHE});
$OPTIONS{HTDOCS} ||= GuessDirectories->htdocs($OPTIONS{APACHE});
$OPTIONS{CGIBIN} ||= GuessDirectories->cgibin($OPTIONS{APACHE});
$OPTIONS{GBROWSE_ROOT} ||= 'gbrowse';
}
else {
$OPTIONS{APACHE} ||= prompt('Apache root directory (enter \'\' for none)?',
GuessDirectories->root) unless exists $OPTIONS{APACHE};
$OPTIONS{CONF} ||= prompt('Apache conf directory?',
GuessDirectories->conf($OPTIONS{APACHE}));
$OPTIONS{HTDOCS} ||= prompt('Apache htdocs directory?',
GuessDirectories->htdocs($OPTIONS{APACHE}));
$OPTIONS{CGIBIN} ||= prompt('Apache cgibin directory?',
GuessDirectories->cgibin($OPTIONS{APACHE}));
$OPTIONS{GBROWSE_ROOT} ||= prompt('GBrowse root for static files?',
'gbrowse');
}
unless (defined $OPTIONS{DO_XS}) {
$OPTIONS{DO_XS} = $^O =~ /^(MSWin|dos)/i ? 0 : 1;
}
$OPTIONS{APACHE} ||= '/';
# look for non-root installation
if (defined $OPTIONS{NONROOT}) {
$OPTIONS{INSTALLSITEMAN3DIR} = 'none';
$OPTIONS{INSTALLSITEMAN1DIR} = 'none';
}
# workaround for known bug in FindBin library
$Bin = "." if -f './Makefile.PL' && -T './Makefile.PL';
my $biographics_version = biographics_version();
my $patch_version = biographics_patch_version();
my $bioperl_needs_patching = $biographics_version < $patch_version;
open F,">$Bin/GGB.def" or die "Can't open $Bin/GGB.def for writing: $!";
print F "# This hints file contains configuration information used by the generic browser\n\n";
print F "# To reconfigure, run perl Makefile.PL `cat GGB.def`\n\n";
foreach (keys %OPTIONS) {
print F "$_=$OPTIONS{$_}\n";
}
print F "VERSION=$VERSION\n";
print F "BIOGRAPHICS_VERSION=$biographics_version\n";
close F;
print STDERR <<END;
----------------------------------------------
File Paths
END
;
foreach (@OPTIONS) {
printf STDERR "%13s %s\n",$_,$OPTIONS{$_} unless $_ eq 'APACHE'; #this confuses people
}
print STDERR <<END;
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
END
;
if ($bioperl_needs_patching) {
print STDERR "\nInstalled Bio::Graphics version $biographics_version is less than desired version $patch_version.\nYou probably need to update your BioPerl to version 1.6 or better and\ninstall Bio::Graphics separately from CPAN.\n\n";
die;
}
my @dir = ();
push @dir,'libalign' if $OPTIONS{DO_XS};
unless (IO::File->can('binmode')) {
warn "\n\nYour installed version of IO::File is too old; please update it.\n\n";
}
#push @dir,'extras/BioPerl' if $bioperl_needs_patching;
# See lib/ExtUtils/MakeMaker.pm for details of how to influence
# the contents of the Makefile that is written.
WriteMakefile(
'NAME' => 'Generic-Genome-Browser',
'VERSION' => $VERSION,
'PREREQ_PM' => {
Bio::Perl => 1.006,
GD => 2.07,
IO::String => 0,
IO::File => 1.0,
Text::ParseWords => 1,
CGI::Session => 4.02,
File::Temp => 0,
Digest::MD5 => 0,
Statistics::Descriptive => 0,
Bio::Graphics => 1.97,
},
PL_FILES => {
'install_util/htdocs_install.PLS' => 'install_util/htdocs_install.pl',
'install_util/cgi_install.PLS' => 'install_util/cgi_install.pl',
'install_util/conf_install.PLS' => 'install_util/conf_install.pl',
'bin/make_das_conf.PLS' => 'bin/make_das_conf.pl',
'bin/process_sgd.PLS' => 'bin/process_sgd.pl',
'bin/process_wormbase.PLS' => 'bin/process_wormbase.pl',
'bin/ucsc_genes2gff.PLS' => 'bin/ucsc_genes2gff.pl',
# 'bin/load_genbank.PLS' => 'bin/load_genbank.pl',
'bin/register_moby_services.PLS' => 'bin/register_moby_services.pl',
'bin/wiggle2gff3.PLS' => 'bin/wiggle2gff3.pl',
'install_util/gbrowse_ppm_install.PLS' => 'install_util/gbrowse_ppm_install.pl',
'cgi-bin/gbrowse.PLS' => 'cgi-bin/gbrowse',
'cgi-bin/gbrowse_img.PLS' => 'cgi-bin/gbrowse_img',
'cgi-bin/gbrowse_syn.PLS' => 'cgi-bin/gbrowse_syn',
'cgi-bin/gbrowse_details.PLS' => 'cgi-bin/gbrowse_details',
'cgi-bin/gbrowse_est.PLS' => 'cgi-bin/gbrowse_est',
'cgi-bin/gbrowse_moby.PLS' => 'cgi-bin/gbrowse_moby',
'cgi-bin/moby_server.PLS' => 'cgi-bin/moby_server',
'cgi-bin/das.PLS' => 'cgi-bin/das',
'cgi-bin/gbgff.PLS' => 'cgi-bin/gbgff',
'conf/MobyServices/GbrowseServices.PMS' => 'conf/MobyServices/GbrowseServices.pm',
},
EXE_FILES => [
'bin/register_moby_services.pl',
'bin/make_das_conf.pl',
'bin/process_wormbase.pl',
'bin/process_sgd.pl',
# 'bin/load_genbank.pl',
'bin/wiggle2gff3.pl',
],
'LIBS' => [''], # e.g., '-lm'
'LIB' => $OPTIONS{LIB}, # custom location for perl modules
'DIR' => \@dir,
'DEFINE' => '',
'INC' => '', # e.g., '-I/usr/include/other'
($] ge '5.005') ? (
'AUTHOR' => 'Lincoln Stein (lstein@cshl.org)',
'ABSTRACT' => 'A CGI-driven browser for genomic annotations.',
) : (),
'INSTALLSITEMAN1DIR' => $OPTIONS{INSTALLSITEMAN1DIR}, # don't install man pages for
'INSTALLSITEMAN3DIR' => $OPTIONS{INSTALLSITEMAN3DIR}, # non-root user
#'INSTALLSITESCRIPT' => $OPTIONS{BIN} || $OPTIONS{INSTALLSCRIPT},
'INSTALLSITEBIN' => $OPTIONS{BIN},
'PREFIX' => $OPTIONS{PREFIX} ? $OPTIONS{PREFIX} : undef,
);
sub biographics_version {
delete $INC{'Bio/Graphics/Panel.pm'};
eval <<'END' || 0;
require Bio::Graphics::Panel;
Bio::Graphics::Panel->api_version;
END
}
sub biographics_patch_version {
return 1.7; # what is in pre bioperl 1.6?
}
sub interpolate {
my $path = shift;
my ($to_expand,$homedir);
return $path unless $path =~ m!^~([^/]*)!;
eval {
if ($to_expand = $1) {
$homedir = (getpwnam($to_expand))[7];
} else {
$homedir = (getpwuid($<))[7];
}
return $path unless $homedir;
$path =~ s!^~[^/]*!$homedir!;
};
return $path;
}
sub MY::dist {
package MY;
my $inherited = shift->SUPER::dist(@_);
$inherited;
}
sub MY::clean {
package MY;
my $inherited = shift->SUPER::clean(@_);
$inherited .= "\t-\$(PERL) install_util/make_clean_add.pl\n";
$inherited;
}
sub MY::dist_dir {
package MY;
my $inherited = shift->SUPER::dist_dir(@_);
$inherited =~ s!^(\s+.+)!\tpod2text docs/pod/INSTALL.pod > INSTALL\n$1!m;
$inherited;
}
sub MY::processPL {
package MY;
my $inherited = shift->SUPER::processPL(@_);
$inherited =~ s/(cgi-bin\/gbrowse\w*)\s\:\:.+/$1 : FORCE/g;
$inherited;
}
sub MY::install {
package MY;
my $inherited = shift->SUPER::install(@_);
$inherited =~ s/doc_install/doc_install conf_install cgi_install htdocs_install/;
$inherited;
}
sub MY::postamble {
my $paths;
for my $key (keys %OPTIONS) {
$paths .= qq("$key=$OPTIONS{$key}" ) if defined $OPTIONS{$key};
}
qq{
conf_install ::
\$(PERL) \"$working_dir/install_util/conf_install.pl\" $paths
htdocs_install ::
\$(PERL) \"$working_dir/install_util/htdocs_install.pl\" $paths
cgi_install ::
\$(PERL) \"$working_dir/install_util/cgi_install.pl\" $paths
};
}
sub MY::libscan {
package MY;
my $self = shift;
my $from = shift;
my $to = $self->SUPER::libscan($from);
return undef if $to=~/README/;
return $to;
}
sub MY::ppd {
package MY;
my $repository = 'http://www.gmod.org/ggb/ppm';
my $arch = 'MSWin32-x86-multi-thread';
my $inherited = shift->SUPER::ppd(@_);
my $implementation;
my $newimp;
my $oldMM =0;
#VERY irritating--different versions of ExtUtils::MakeMaker has
#different ways of generating the ppd file.
if ($inherited =~ /qq\{(<S.*R>\\n)\}.*qq\{(\\t<I.*\/>\\n)\}.*qq\{(\\t\\t<O.*G>\\n)\}/sg){
$oldMM=1;
my $xml = $1.$2.$3;
#warn "$xml\n";
$inherited =~ s/qq\{.*>>/qq{$xml}" >/s;
} elsif ($inherited =~ /NOECHO/) {
my @la = split /\n/, $inherited;
my $grab = 0;
for (@la) {
$grab++ if (m!<IMPLEMENTATION>!);
if ($grab and $_ =~ /\'(.*)\'/) {
$implementation .= "$1\n";
}
$grab = 0 if (m!</IMPLEMENTATION>!);
}
}
my $impl58;
if ($oldMM and $inherited =~ /(\s*\<IMPLEMENTATION\>.*\<\/IMPLEMENTATION\>)/m) {
$implementation = $newimp = $1;
$newimp =~ s/ARCHITECTURE NAME=\\"\S+\\"/ARCHITECTURE NAME=\\"$arch\\"/;
$newimp =~ s/\$\(OSNAME\)/MSWin32/;
$impl58 = $newimp;
$impl58 =~ s/\Q$arch\E/$arch\-5\.8/;
$newimp .= "\\n\\t\\t$impl58";
$inherited =~ s/\Q$implementation\E/$newimp/;
} elsif (!$oldMM and $implementation) {
$newimp = $implementation;
$newimp =~ s/ARCHITECTURE NAME="\S+"/ARCHITECTURE NAME="$arch"/;
$newimp =~ s/\$\(OSNAME\)/MSWin32/;
$impl58 = $newimp;
$impl58 =~ s/\Q$arch\E/$arch\-5\.8/;
$newimp .= $impl58;
@la = split /\n/, $newimp;
for my $line (@la) {
$line = qq{\t\$(NOECHO) \$(ECHO) '$line' >> \$(DISTNAME).ppd};
}
my @inherit_array = split /\n/, $inherited;
my @newinherit;
$inherited = '';
for (@inherit_array) {
if (/<IMPLEMENTATION>/) {
push @newinherit, @la;
last;
} else {
push @newinherit, $_;
}
}
push @newinherit, qq{\t\$(NOECHO) \$(ECHO) '</SOFTPKG>' >> \$(DISTNAME).ppd\n};
$inherited = join "\n", @newinherit;
}
$inherited .= <<END;
\@echo "creating Generic-Genome-Browser.ppd"
\@echo "creating gbrowse_ppm_support_files-$VERSION.tar.gz"
\@\$(TAR) zcf gbrowse_ppm_support_files-$VERSION.tar.gz --exclude CVS --exclude '*~' --exclude '*.PLS' --exclude '.*' --exclude README --exclude '#*' DISCLAIMER INSTALL docs htdocs conf cgi-bin install_util sample_data contrib
\@echo "creating gbrowse_ppm-$VERSION.tar.gz"
\@\$(TAR) zcf gbrowse_ppm-$VERSION.tar.gz --exclude man1 --exclude man3 blib
\@perl -pi -e 's!HREF=""!HREF="$repository/gbrowse_ppm-$VERSION.tar.gz"!' Generic-Genome-Browser.ppd
\@perl -pi -e 's!(\\s*</IMPLEMENTATION>)!\\t\\t<INSTALL HREF="$repository/gbrowse_ppm_install.pl" EXEC="PPM_PERL" />\\n\\1!' Generic-Genome-Browser.ppd
\@perl -pi -e 's!Bio-Perl!bioperl!' Generic-Genome-Browser.ppd
\@cp install_util/gbrowse_ppm_install.pl .
END
;
}