Hi,
I run BioMart 0.6 on my laptop under Windows XP.
I agree that there is an issue with paths in the configureBioMart.pl
script. I had to hack it so to disable some of the checks for files and
versions, and hardcode some Windows style paths (see attached diff file,
which might not make it onto the list). Sounds like this is what you
tried too, Roger, and although you say it repeatedly fails for you, I am
fortunate that this patched script works for me. I'm not much of a Perl
programmer, and agree that a better fix is desirable.
Once started, martservice runs as expected except that there is a small
problem with session information occasionally not being cleared properly
(I am using the MySQL session storage option). I haven't solved this
problem, I just clear when necessary all session information from the
MySQL session table with an SQL statement in a mysql client. This is not
too inconvenient since the number of queries I do per development round
is small.
Hope this helps.
Matthew Hobbs
Roger Hull wrote:
I tried this in BioMart 6. I found that the Java programs run fine, but
not the biomart-perl, even with all the pre-requisites installed. The
biomart-perl installation script seems to use Unix conventions and
utilities for files and directories, which failed to run under Windows
XP (even with some Unix-alike utilities installed, and with Windows
support for forward-slash path separators). I found that the script
repeatedly failed even when I tried to patch it each time, and I gave
up. (The script appears to have some support for Windows conventions,
but it didn't look as if this had actually been tested.)
It would be useful for demo though, if someone could fix the script.
Regards,
Roger.
Richard Holland wrote:
MartView/MartService are designed to be served from within an Apache
instance, which in turn must have mod_perl enabled, and the system
must have a number of Perl modules installed as prerequisites for
MartView to work.
As long as you can install Apache+mod_perl+the Perl modules on your XP
machine, I can't see any reason why MartView wouldn't work. But, I've
never actually tried it on a Windows machine. Perhaps someone else on
this list has?
2008/6/20 <[EMAIL PROTECTED]>:
Hi mart-dev,
I'm looking to give a demo of Biomart on a Windows laptop? Can BioMart
successfully be run on Windows? is so, are there any troubleshooting
tips
for install?
Thanks
Robert
145,153c145,155
< my $apxs = dirname($OPTIONS{httpd}).'/apxs';
< -f $apxs or $apxs .= 2;
< my $httpd_libdir = `$apxs -q LIBEXECDIR`;
< chomp($httpd_libdir);
< #warn "httpd_libdir = '$httpd_libdir',
version='$httpd_version'";
< $httpd_modperl_dsopath = $httpd_version eq '1.3' ?
$httpd_libdir.'/libperl.so'
< : $httpd_version eq '2.0' ?
$httpd_libdir.'/mod_perl.so'
< : $httpd_version eq '2.1+' ?
$httpd_libdir.'/mod_perl.so'
< : undef
---
> # my $apxs = dirname($OPTIONS{httpd}).'/apxs';
> # -f $apxs or $apxs .= 2;
> # my $httpd_libdir = `$apxs -q LIBEXECDIR`;
> my $httpd_libdir =
> 'C:\cygwin\usr\local\BioMart\Apache\modules';
> # chomp($httpd_libdir);
> # #warn "httpd_libdir = '$httpd_libdir',
> version='$httpd_version'";
> # $httpd_modperl_dsopath = $httpd_version eq '1.3' ?
> $httpd_libdir.'/libperl.so'
> # : $httpd_version eq '2.0' ?
> $httpd_libdir.'/mod_perl.so'
> # : $httpd_version eq '2.1+' ?
> $httpd_libdir.'/mod_perl.so'
> # : undef
> my $httpd_modperl_dsopath =
> 'C:\cygwin\usr\local\BioMart\Apache\modules\mod_perl.so';
155c157
< #warn "httpd_modperl_dsopath =
'$httpd_modperl_dsopath'";
---
> warn "httpd_modperl_dsopath = '$httpd_modperl_dsopath'";
188,190c190,193
< my $apxs = dirname($OPTIONS{httpd}).'/apxs';
< -f $apxs or $apxs .= 2;
< my $httpd_libdir = `$apxs -q LIBEXECDIR`;
---
> # my $apxs = dirname($OPTIONS{httpd}).'/apxs';
> # -f $apxs or $apxs .= 2;
> # my $httpd_libdir = `$apxs -q LIBEXECDIR`;
> my $httpd_libdir =
> 'C:\cygwin\usr\local\BioMart\Apache\modules';
192,193c195,197
< my $gzipModule = $httpd_libdir.'/mod_gzip.so';
< #print "\n===== $gzipModule \n";
---
> # my $gzipModule = $httpd_libdir.'/mod_gzip.so';
> my $gzipModule = $httpd_libdir.'\ApacheModuleGzip.dll';
> print "\n===== $gzipModule \n";
195,197c199,202
< { #warn "httpd_libdir = '$httpd_libdir',
version='$httpd_version'";
< $httpd_modperl_dsopath = $httpd_libdir ;
< push
@{$OPTIONS{httpd_modperl_dsopath_modules}}, "gzip_module
".$httpd_libdir."/mod_gzip.so";
---
> { warn "httpd_libdir = '$httpd_libdir',
> version='$httpd_version'";
> # $httpd_modperl_dsopath = $httpd_libdir ;
> # push
> @{$OPTIONS{httpd_modperl_dsopath_modules}}, "gzip_module
> ".$httpd_libdir."/mod_gzip.so";
> push
> @{$OPTIONS{httpd_modperl_dsopath_modules}}, "gzip_module ".$gzipModule;
202a208,210
> my $httpd_modperl_dsopath =
> 'C:\cygwin\usr\local\BioMart\Apache\modules\mod_perl.so';
> warn "httpd_modperl = '$httpd_modperl'";
> warn "httpd_modperl_dsopath = '$httpd_modperl_dsopath'";
