A question from our Systems administrator.. Gbrowse installations and Upgrades..

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A question from our Systems administrator.. Gbrowse installations and Upgrades..

Jayaraman, Pushkala

Hello,

I am forwarding a question from our Systems Administrator..

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Brodie, Kent [mailto:[hidden email]]
Sent: Thursday, November 18, 2010 9:28 AM
To: Jayaraman, Pushkala
Subject: gbrowse mailing list

 

 

Hi—can you send an email to your gbrowse-2 mailing list, and include the following? 

 

 

========================================================================================================================

Systems Administrator question:  As requested from our developer, I installed gbrowse-2 (2.16) .   While most of it worked OK, she uncovered a bug that apparently was NOT there in version 2.10.   So, I then downgraded to 2.10, running the reconfig and install as is normally done.

 

But--  the ‘broken behavior’ presumably introduced after 2.10 was still there.

 

My question:  I am not 100% positive that the install script(s) are always updating destination files (and/or perl libraries) when I do a “./Build install”.  As such, is there a way to UN-install gbrowse-2 and start with a clean slate?       

 

The other possibility of course, is that the ‘bug’ mentioned above may be caused by something totally separate – but a “clean uninstall” would let me verify that yes, I am indeed running vanilla 2.10 and don’t have 2.16 “leftovers” hanging around.

 

Any help on how to UN-install gbrowse2 would be quite helpful.   Thank you

 

 

 

---------------------------------------------------------------------

Kent C. Brodie             

Department of Physiology  

(and) Human and Molecular Genetics Center

Medical College of Wisconsin

[hidden email]                           +1 414 955 8590

 


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Spend less time writing and  rewriting code and more time creating great
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Re: A question from our Systems administrator.. Gbrowse installations and Upgrades..

Lincoln Stein
Unfortunately Perl modules do not have an "uninstall" method. However, installing will overwrite existing files and should work properly.

Lincoln

On Thu, Nov 18, 2010 at 10:30 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I am forwarding a question from our Systems Administrator..

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Brodie, Kent [mailto:[hidden email]]
Sent: Thursday, November 18, 2010 9:28 AM
To: Jayaraman, Pushkala
Subject: gbrowse mailing list

 

 

Hi—can you send an email to your gbrowse-2 mailing list, and include the following? 

 

 

========================================================================================================================

Systems Administrator question:  As requested from our developer, I installed gbrowse-2 (2.16) .   While most of it worked OK, she uncovered a bug that apparently was NOT there in version 2.10.   So, I then downgraded to 2.10, running the reconfig and install as is normally done.

 

But--  the ‘broken behavior’ presumably introduced after 2.10 was still there.

 

My question:  I am not 100% positive that the install script(s) are always updating destination files (and/or perl libraries) when I do a “./Build install”.  As such, is there a way to UN-install gbrowse-2 and start with a clean slate?       

 

The other possibility of course, is that the ‘bug’ mentioned above may be caused by something totally separate – but a “clean uninstall” would let me verify that yes, I am indeed running vanilla 2.10 and don’t have 2.16 “leftovers” hanging around.

 

Any help on how to UN-install gbrowse2 would be quite helpful.   Thank you

 

 

 

---------------------------------------------------------------------

Kent C. Brodie             

Department of Physiology  

(and) Human and Molecular Genetics Center

Medical College of Wisconsin

[hidden email]                           +1 414 955 8590

 




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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Re: A question from our Systems administrator.. Gbrowse installations and Upgrades..

Karthik-7

Hello Lincoln
I think the admin is right. Even my installation problem was because, the
build script did not update the perl libraries. But, the installation worked
fine after I cleared everything under Bio::Graphics::Browser2 and then did
the installation.
I'd recommend the admin to try that too.

Karthik
--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/A-question-from-our-Systems-administrator-Gbrowse-installations-and-Upgrades-tp3270906p3271166.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
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Gmod-gbrowse mailing list
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Re: A question from our Systems administrator.. Gbrowse installations and Upgrades..

Jayaraman, Pushkala
Yes,
We tried just that and it worked..
Thanks Karthik :)

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Karthik [mailto:[hidden email]]
Sent: Thursday, November 18, 2010 11:57 AM
To: [hidden email]
Subject: Re: [Gmod-gbrowse] A question from our Systems administrator..
Gbrowse installations and Upgrades..


Hello Lincoln
I think the admin is right. Even my installation problem was because,
the
build script did not update the perl libraries. But, the installation
worked
fine after I cleared everything under Bio::Graphics::Browser2 and then
did
the installation.
I'd recommend the admin to try that too.

Karthik
--
View this message in context:
http://generic-model-organism-system-database.450254.n5.nabble.com/A-que
stion-from-our-Systems-administrator-Gbrowse-installations-and-Upgrades-
tp3270906p3271166.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------
------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: A question from our Systems administrator.. Gbrowse installations and Upgrades..

Keiran Raine
Hi Pushkala,

I just thought I'd raise a way to prevent you from having this problem  
again.

If you have the GBrowse dependencies and libraries installed using the  
'--prefix' option you can make your life much easier.

Download the relevant archives from CPAN (web based not the 'perl -
MCPAN' tool).
unpack and enter package

perl Build.PL --prefix /gbrowse
./Build
./Build test
./Build install

repeat for each dependency.

If you need to roll back you can safely delete /gbrowse and re-install  
the dependencies without affecting the core perl libraries installed  
on your company network.

There is some apache config required to have the libraries in the '--
prefix' location used but hopefully your sysadmin can help with that  
(mine certainly did).

The other advantage of this is you can have multiple prefix areas and  
switch your server between each just by updating the apache config and  
restarting your server (makes it nice and quick to revert if you find  
a problem).

Hope this is useful,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703
[hidden email]





On 18 Nov 2010, at 18:41, Jayaraman, Pushkala wrote:

> Yes,
> We tried just that and it worked..
> Thanks Karthik :)
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Karthik [mailto:[hidden email]]
> Sent: Thursday, November 18, 2010 11:57 AM
> To: [hidden email]
> Subject: Re: [Gmod-gbrowse] A question from our Systems  
> administrator..
> Gbrowse installations and Upgrades..
>
>
> Hello Lincoln
> I think the admin is right. Even my installation problem was because,
> the
> build script did not update the perl libraries. But, the installation
> worked
> fine after I cleared everything under Bio::Graphics::Browser2 and then
> did
> the installation.
> I'd recommend the admin to try that too.
>
> Karthik
> --
> View this message in context:
> http://generic-model-organism-system-database.450254.n5.nabble.com/A-que
> stion-from-our-Systems-administrator-Gbrowse-installations-and-
> Upgrades-
> tp3270906p3271166.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------
> ------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating  
> great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating  
> great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: A question from our Systems administrator.. Gbrowse installations and Upgrades..

Lincoln Stein
This sounds like a great strategy.

I'm also going to check how difficult it would be to write an "uninstall" target for the Build script.

Lincoln

On Thu, Nov 18, 2010 at 6:11 PM, Keiran Raine <[hidden email]> wrote:
Hi Pushkala,

I just thought I'd raise a way to prevent you from having this problem
again.

If you have the GBrowse dependencies and libraries installed using the
'--prefix' option you can make your life much easier.

Download the relevant archives from CPAN (web based not the 'perl -
MCPAN' tool).
unpack and enter package

perl Build.PL --prefix /gbrowse
./Build
./Build test
./Build install

repeat for each dependency.

If you need to roll back you can safely delete /gbrowse and re-install
the dependencies without affecting the core perl libraries installed
on your company network.

There is some apache config required to have the libraries in the '--
prefix' location used but hopefully your sysadmin can help with that
(mine certainly did).

The other advantage of this is you can have multiple prefix areas and
switch your server between each just by updating the apache config and
restarting your server (makes it nice and quick to revert if you find
a problem).

Hope this is useful,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703
[hidden email]





On 18 Nov 2010, at 18:41, Jayaraman, Pushkala wrote:

> Yes,
> We tried just that and it worked..
> Thanks Karthik :)
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Karthik [mailto:[hidden email]]
> Sent: Thursday, November 18, 2010 11:57 AM
> To: [hidden email]
> Subject: Re: [Gmod-gbrowse] A question from our Systems
> administrator..
> Gbrowse installations and Upgrades..
>
>
> Hello Lincoln
> I think the admin is right. Even my installation problem was because,
> the
> build script did not update the perl libraries. But, the installation
> worked
> fine after I cleared everything under Bio::Graphics::Browser2 and then
> did
> the installation.
> I'd recommend the admin to try that too.
>
> Karthik
> --
> View this message in context:
> http://generic-model-organism-system-database.450254.n5.nabble.com/A-que
> stion-from-our-Systems-administrator-Gbrowse-installations-and-
> Upgrades-
> tp3270906p3271166.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------
> ------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating
> great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating
> great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: A question from our Systems administrator.. Gbrowse installations and Upgrades..

Fields, Christopher J
I recall this also being a strategy used if one wanted to (for instance) use the developer versions of some perl distributions *cough*bioperl*cough*.

chris

On Nov 19, 2010, at 8:36 AM, Lincoln Stein wrote:

> This sounds like a great strategy.
>
> I'm also going to check how difficult it would be to write an "uninstall" target for the Build script.
>
> Lincoln
>
> On Thu, Nov 18, 2010 at 6:11 PM, Keiran Raine <[hidden email]> wrote:
> Hi Pushkala,
>
> I just thought I'd raise a way to prevent you from having this problem
> again.
>
> If you have the GBrowse dependencies and libraries installed using the
> '--prefix' option you can make your life much easier.
>
> Download the relevant archives from CPAN (web based not the 'perl -
> MCPAN' tool).
> unpack and enter package
>
> perl Build.PL --prefix /gbrowse
> ./Build
> ./Build test
> ./Build install
>
> repeat for each dependency.
>
> If you need to roll back you can safely delete /gbrowse and re-install
> the dependencies without affecting the core perl libraries installed
> on your company network.
>
> There is some apache config required to have the libraries in the '--
> prefix' location used but hopefully your sysadmin can help with that
> (mine certainly did).
>
> The other advantage of this is you can have multiple prefix areas and
> switch your server between each just by updating the apache config and
> restarting your server (makes it nice and quick to revert if you find
> a problem).
>
> Hope this is useful,
>
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> [hidden email]
>
>
>
>
>
> On 18 Nov 2010, at 18:41, Jayaraman, Pushkala wrote:
>
> > Yes,
> > We tried just that and it worked..
> > Thanks Karthik :)
> >
> > Pushkala Jayaraman
> > Programmer/Analyst
> > Rat Genome Database
> > Human and Molecular Genetics Center
> > Medical College of Wisconsin
> > Email: [hidden email]
> > Work: 414-955-2229
> > www.rgd.mcw.edu
> >
> >
> > -----Original Message-----
> > From: Karthik [mailto:[hidden email]]
> > Sent: Thursday, November 18, 2010 11:57 AM
> > To: [hidden email]
> > Subject: Re: [Gmod-gbrowse] A question from our Systems
> > administrator..
> > Gbrowse installations and Upgrades..
> >
> >
> > Hello Lincoln
> > I think the admin is right. Even my installation problem was because,
> > the
> > build script did not update the perl libraries. But, the installation
> > worked
> > fine after I cleared everything under Bio::Graphics::Browser2 and then
> > did
> > the installation.
> > I'd recommend the admin to try that too.
> >
> > Karthik
> > --
> > View this message in context:
> > http://generic-model-organism-system-database.450254.n5.nabble.com/A-que
> > stion-from-our-Systems-administrator-Gbrowse-installations-and-
> > Upgrades-
> > tp3270906p3271166.html
> > Sent from the gmod-gbrowse mailing list archive at Nabble.com.
> >
> > ------------------------------------------------------------------------
> > ------
> > Beautiful is writing same markup. Internet Explorer 9 supports
> > standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> > Spend less time writing and  rewriting code and more time creating
> > great
> > experiences on the web. Be a part of the beta today
> > http://p.sf.net/sfu/msIE9-sfdev2dev
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> > ------------------------------------------------------------------------------
> > Beautiful is writing same markup. Internet Explorer 9 supports
> > standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> > Spend less time writing and  rewriting code and more time creating
> > great
> > experiences on the web. Be a part of the beta today
> > http://p.sf.net/sfu/msIE9-sfdev2dev
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: A question from our Systems administrator.. Gbrowse installations and Upgrades..

Keiran Raine
In reply to this post by Lincoln Stein
Hi Lincoln,

My sites-enabled/000-default looks like this.

Regards,
Keiran


FastCgiConfig  -initial-env GBROWSE_CONF=/gbrowse/etc/gbrowse2 -
initial-env PERL5LIB=/gbrowse/share/perl:/gbrowse/lib/perl/5.10.0

<VirtualHost *:80>
         ServerAdmin [hidden email]
         SetEnv PERL5LIB /gbrowse/share/perl:/gbrowse/lib/perl/5.10.0

         DocumentRoot /gbrowse/var/www/
         <Directory />
                 Options FollowSymLinks
                 AllowOverride None
         </Directory>
         <Directory /gbrowse/var/www/>
                 Options Indexes FollowSymLinks MultiViews
                 AllowOverride None
                 Order allow,deny
                 allow from all
         </Directory>

         ScriptAlias /cgi-bin/ /gbrowse/usr/lib/cgi-bin/
         <Directory "/gbrowse/usr/lib/cgi-bin">
                 AllowOverride None
                 Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
                 Order allow,deny
                 Allow from all
         </Directory>

         ErrorLog /var/log/apache2/error.log

         # Possible values include: debug, info, notice, warn, error,  
crit,
         # alert, emerg.
         LogLevel warn

         CustomLog /var/log/apache2/access.log combined

     Alias /doc/ "/usr/share/doc/"
     <Directory "/usr/share/doc/">
         Options Indexes MultiViews FollowSymLinks
         AllowOverride None
         Order deny,allow
         Deny from all
         Allow from 127.0.0.0/255.0.0.0 ::1/128
     </Directory>

     Alias        "/gbrowse2/i/" "/gbrowse/var/tmp/gbrowse2/images/"
     Alias        "/gbrowse2"    "/gbrowse/var/www/gbrowse2"
     ScriptAlias  "/gb2"      "/gbrowse/usr/lib/cgi-bin/gb2"

     <Directory "/gbrowse/var/www/gbrowse2">
        Options -Indexes -MultiViews +FollowSymLinks
     </Directory>

     <Directory "/gbrowse/usr/lib/cgi-bin/gb2">
        SetEnv GBROWSE_CONF   "/gbrowse/etc/gbrowse2"
     </Directory>

     <IfModule mod_fcgid.c>
         Alias /fgb2/ "/gbrowse/usr/lib/cgi-bin/gb2/"
         PerlRequire /gbrowse/lib/apache_startup.pl
         <Location /fgb2>
           SetHandler   fcgid-script
           Options      ExecCGI
         </Location>
     </IfModule>

</VirtualHost>



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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