Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?

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Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?

Allen Qiu
Hi all,
Is it OK to use perlbrew to install another copy of perl&modules under my home directory, since I don't have root to install required perl modules? If so, how should I let the linux(RHEL)/Gbrowser/Apache? to use my local perl instead of the system's?
Regards,
Allen
 
 
2014-10-13

Allen Qiu

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Re: Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?

Scott Cain
Hi Allen,

Using a custom perl shouldn't be a problem.  There are only two things I can think of that you'll have to do:

1. Use your perlbrew when executing things like the cpan shell and "perl Build.PL" on the command line.  That will ensure that installed modules will go where they need to go.  You probably already have your environment set up to do that automatically.

2. Add a PERL5LIB entry to your apache config.  First you need to enable the mod_env module (on RH systems, I think all you need to do is uncomment the "LoadModule" line for it if it isn't already), and then add a line like this to the bottom of the httpd.conf file:

  SetEnv PERL5LIB /path/to/your/perl

and restart apache.

If I've missed anything, you'll probably get an error message in your apache log when you try to access GBrowse; if you can't sort out what they mean, please send them back to the list and we'll help.

Scott


On Mon, Oct 13, 2014 at 4:46 AM, Allen Qiu <[hidden email]> wrote:
Hi all,
Is it OK to use perlbrew to install another copy of perl&modules under my home directory, since I don't have root to install required perl modules? If so, how should I let the linux(RHEL)/Gbrowser/Apache? to use my local perl instead of the system's?
Regards,
Allen
 
 
2014-10-13

Allen Qiu

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GBrowse_synteny error

Samy Jeevan Karloss Antony
Hello, 

I am following the instructions in the page below to see GBrwose_Synteny up and running with the given test data. 


I am getting this error below. Could someone tell me What exactly its trying to do and how to fix this? 

gbrowse_syn: mkdir /var/www/html//var: Permission denied at /usr/local/lib64/perl5/Legacy/Graphics/Browser.pm line 1662

Thanks,
Jeevan

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Re: GBrowse_synteny error

Scott Cain
Hi Jeevan,

That looks like a configuration error; can you send you configuration file to the list?

Scott


On Mon, Oct 13, 2014 at 10:05 AM, Samy Jeevan Karloss Antony <[hidden email]> wrote:
Hello, 

I am following the instructions in the page below to see GBrwose_Synteny up and running with the given test data. 


I am getting this error below. Could someone tell me What exactly its trying to do and how to fix this? 

gbrowse_syn: mkdir /var/www/html//var: Permission denied at /usr/local/lib64/perl5/Legacy/Graphics/Browser.pm line 1662

Thanks,
Jeevan

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Re: GBrowse_synteny error

Sheldon McKay
In reply to this post by Samy Jeevan Karloss Antony
Hi Jeevan,

I believe this error has been resolved in the most recent version of GBrowse on github.  https://github.com/GMOD/GBrowse

Sheldon


On Mon, Oct 13, 2014 at 10:05 AM, Samy Jeevan Karloss Antony <[hidden email]> wrote:
Hello, 

I am following the instructions in the page below to see GBrwose_Synteny up and running with the given test data. 


I am getting this error below. Could someone tell me What exactly its trying to do and how to fix this? 

gbrowse_syn: mkdir /var/www/html//var: Permission denied at /usr/local/lib64/perl5/Legacy/Graphics/Browser.pm line 1662

Thanks,
Jeevan

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Re: Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?

Josh Goodman
In reply to this post by Scott Cain
Allen,

FlyBase runs GBrowse 2.x under perlbrew with no issues.

I would add one more item to Scott's list.  After the install, you
will want to double check that the hash bang perl location at the top
of all the GBrowse cgi-bin scripts points to the correct location.

Regards,
Josh


On Mon, Oct 13, 2014 at 9:28 AM, Scott Cain <[hidden email]> wrote:

> Hi Allen,
>
> Using a custom perl shouldn't be a problem.  There are only two things I can
> think of that you'll have to do:
>
> 1. Use your perlbrew when executing things like the cpan shell and "perl
> Build.PL" on the command line.  That will ensure that installed modules will
> go where they need to go.  You probably already have your environment set up
> to do that automatically.
>
> 2. Add a PERL5LIB entry to your apache config.  First you need to enable the
> mod_env module (on RH systems, I think all you need to do is uncomment the
> "LoadModule" line for it if it isn't already), and then add a line like this
> to the bottom of the httpd.conf file:
>
>   SetEnv PERL5LIB /path/to/your/perl
>
> and restart apache.
>
> If I've missed anything, you'll probably get an error message in your apache
> log when you try to access GBrowse; if you can't sort out what they mean,
> please send them back to the list and we'll help.
>
> Scott
>
>
> On Mon, Oct 13, 2014 at 4:46 AM, Allen Qiu <[hidden email]> wrote:
>>
>> Hi all,
>> Is it OK to use perlbrew to install another copy of perl&modules under my
>> home directory, since I don't have root to install required perl modules? If
>> so, how should I let the linux(RHEL)/Gbrowser/Apache? to use my local perl
>> instead of the system's?
>> Regards,
>> Allen
>>
>>
>> 2014-10-13
>> ________________________________
>> Allen Qiu
>>
>>
>> ------------------------------------------------------------------------------
>> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
>> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
>> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
>> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
>> http://p.sf.net/sfu/Zoho
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
> http://p.sf.net/sfu/Zoho
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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Re: Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?

Allen Qiu
In reply to this post by Scott Cain
Hi Scott,
Thank you very much! I'll check it out.
Regards,
Allen
 
2014-10-16

Allen Qiu

发件人:Scott Cain <[hidden email]>
发送时间:2014-10-13 21:28
主题:Re: [Gmod-gbrowse] Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?
收件人:"Allen Qiu"<[hidden email]>
抄送:"gmod-gbrowse"<[hidden email]>
 
Hi Allen,

Using a custom perl shouldn't be a problem.  There are only two things I can think of that you'll have to do:

1. Use your perlbrew when executing things like the cpan shell and "perl Build.PL" on the command line.  That will ensure that installed modules will go where they need to go.  You probably already have your environment set up to do that automatically.

2. Add a PERL5LIB entry to your apache config.  First you need to enable the mod_env module (on RH systems, I think all you need to do is uncomment the "LoadModule" line for it if it isn't already), and then add a line like this to the bottom of the httpd.conf file:

  SetEnv PERL5LIB /path/to/your/perl

and restart apache.

If I've missed anything, you'll probably get an error message in your apache log when you try to access GBrowse; if you can't sort out what they mean, please send them back to the list and we'll help.

Scott


On Mon, Oct 13, 2014 at 4:46 AM, Allen Qiu <[hidden email]> wrote:
Hi all,
Is it OK to use perlbrew to install another copy of perl&modules under my home directory, since I don't have root to install required perl modules? If so, how should I let the linux(RHEL)/Gbrowser/Apache? to use my local perl instead of the system's?
Regards,
Allen
 
 
2014-10-13

Allen Qiu

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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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