Software error:Can't locate HTML/Template.pm in @INC (you may need to install the HTML::Template module)

[sraj214]

Hi @brianjohnhaas

I am trying to run TrinotateWeb but I get this error that HTML/Template.pm is not found.

I installed HTML::Template perl module and it is installed at /usr/local/Cellar/perl/5.30.2_1/lib/perl5/site_perl/5.30.2/HTML/Template.pm

However, when I try to run 'http://localhost:8080/cgi-bin/index.cgi' I still get the error

(@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4/darwin-thread-multi-2level /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Trinity/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/index.cgi line 15. BEGIN failed--compilation aborted at Trinity/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/index.cgi line 15.

Is there a way to link @INC path?

[brianjohnhaas]

Hi,

It looks like webserver is running a different version of perl (5.18) as compared to the one you're using in your environment (5.30).

I'm not sure how the environments are mixed here, but it's at least a clue to help you push forward.

best,

~b

On Tue, May 26, 2020 at 12:48 PM sraj214 notifications@github.com wrote:

Hi @brianjohnhaas https://github.com/brianjohnhaas

I am trying to run TrinotateWeb but I get this error that HTML/Template.pm is not found.

I installed HTML::Template perl module and it is installed at /usr/local/Cellar/perl/5.30.2_1/lib/perl5/site_perl/5.30.2/HTML/Template.pm

However, when I try to run 'http://localhost:8080/cgi-bin/index.cgi' I still get the error

(@inc https://github.com/inc contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4/darwin-thread-multi-2level /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Trinity/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/index.cgi line 15. BEGIN failed--compilation aborted at Trinity/Trinotate-Trinotate-v3.2.1/TrinotateWeb/cgi-bin/index.cgi line 15.

Is there a way to link @inc https://github.com/inc path?

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[sraj214]

Hi, It looks like webserver is running a different version of perl (5.18) as compared to the one you're using in your environment (5.30). I'm not sure how the environments are mixed here, but it's at least a clue to help you push forward. best, ~b …

Thank you Brian,

I installed the 5.18 version of perl but the problem persists. The issue I see here is that perl is unable to find the path to my HTML::Template module I installed. I looked for solutions online but could not figure out the solution. Do you have any suggestion if I could add path anywhere in the script

[brianjohnhaas]

Hi,

When you run the run_TrinotateWebserver.pl port_no, it creates a lighttpd config file under the TrinotateWeb.conf/ directory called 'lighttpd.conf.port${port_no}'. This file has all the configuration info including the version of perl that's supposed to be run under the section:

CGI module

cgi.assign = ( ".pl" => "/usr/local/bin/perl", ".cgi" => "/usr/local/bin/perl" ) #

Let's see what yours is configured to. You can run that version of perl with option '-V' on the command line and it should report the @INC settings at the bottom. When you install the HTML::Template module, it should be showing up as installed in one of those directories.

As a last resort, you can add your library installation directory as an environmental variable in this config file under: setenv.add-environment = ( "LOCAL_JS" => "1" )

by setting: setenv.add-environment = ( "LOCAL_JS" => "1" , "PERL5LIB" => "/path/to/your/perl/lib/installation/dir")

and that should in theory allow it to find the module.

best,

~brian

On Thu, May 28, 2020 at 10:19 AM sraj214 notifications@github.com wrote:

Hi, It looks like webserver is running a different version of perl (5.18) as compared to the one you're using in your environment (5.30). I'm not sure how the environments are mixed here, but it's at least a clue to help you push forward. best, ~b … <#m8607294276105574203>

Thank you Brian,

I installed the 5.18 version of perl but the problem persists. The issue I see here is that perl is unable to find the path to my HTML::Template module I installed. I looked for solutions online but could not figure out the solution. Do you have any suggestion if I could add path anywhere in the script

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/39#issuecomment-635379001, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXY7UDRBBRJQNP3TGRDRTZXFXANCNFSM4NKUYZVQ .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

[sraj214]

Hi Brian,

Adding the installed module path on setenv.add-environment worked. Thank you for the continuous help.

Raj