[Gmod-gbrowse] Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?

Discussion:

Allen Qiu

2014-10-13 08:46:49 UTC

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

Scott Cain

2014-10-13 13:28:12 UTC

Permalink

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

Post by 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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Samy Jeevan Karloss Antony

2014-10-13 14:05:39 UTC

Permalink

Hello,

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

http://gmod.org/wiki/GBrowse_syn_AGS_Tutorial

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

Scott Cain

2014-10-13 14:13:00 UTC

Permalink

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 <

Post by 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.
http://gmod.org/wiki/GBrowse_syn_AGS_Tutorial
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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Sheldon McKay

2014-10-13 14:14:26 UTC

Permalink

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 <

Josh Goodman

2014-10-13 16:54:35 UTC

Permalink

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

Post by Scott Cain
Hi Allen,
Using a custom perl shouldn't be a problem. There are only two things I can
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
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

Post by 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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--
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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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Allen Qiu

2014-10-15 16:05:24 UTC

Permalink

Hi Scott,
Thank you very much! I'll check it out.
Regards,
Allen

2014-10-16

Allen Qiu

åä»¶äººïŒScott Cain <***@scottcain.net>
åéæ¶éŽïŒ2014-10-13 21:28
äž»é¢ïŒRe: [Gmod-gbrowse] Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?
æ¶ä»¶äººïŒ"Allen Qiu"<***@163.com>
æéïŒ"gmod-gbrowse"<gmod-***@lists.sourceforge.net>

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 <***@163.com> 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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Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://p.sf.net/sfu/Zoho
_______________________________________________
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Gmod-***@lists.sourceforge.net
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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