Difference between revisions of "Managing Perl Libraries"

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   /path/to/application/extlib
 
   /path/to/application/extlib
  
Installing modules in a local path is made significantly easier through the use of local::lib and Apache2/mod_perl2 "PerlSwitches" directive.
+
= Installing a local CPAN repository =
  
local::lib dispenses with the need to maintain multiple CPAN configurations or manual tweaks to your environment variables in order to recognize already installed modules.
+
''I maintain a local mirror of CPAN. This makes installing our web application significantly faster.''
  
= Installation Script =
+
$ sudo perl -MCPAN -e shell
 +
$ cpan> install CPAN::Mini
  
The steps described in this document are almost entirely scripted:
+
Create a ~/.minicpanrc file:
  
  wormbase-admin:maintenance/install_perl_modules.sh
+
<pre>
 +
# CPAN::Mini configuration file
 +
# to set up our local WormBase CPAN
  
  Usage:
+
local: /usr/local/wormbase/minicpan
  $ ./install_perl_modules.sh /path/to/private/libraries/extlib
+
remote: http://mirror.rit.edu/CPAN/
 +
exact_mirror: 1
 +
</pre>
  
  Usage (for installing Catalyst and its dependencies):
+
Set up your CPAN to use the local mirror:
  $ ./install_perl_modules.sh /path/to/private/libraries/extlib CATALYST
+
<pre>
 +
$ cpan
 +
cpan> o conf urllist file:///usr/local/wormbase/minicpan/
 +
cpan> o conf commit
 +
</pre>
  
Read on for additional (important) details that include appropriate settings for interactive steps in the script.
+
Don't forget cpanplus:
 +
<pre>
 +
$ cpanp
 +
$ CPAN Terminal> s reconfigure
 +
$ select the System configuration, then the mirror option, custom, and as above. Save and quit.
 +
</pre>
  
= Private library locations =
+
Set up the minicpan to run once a day:
 +
* 3 * * * minicpan
  
By convention, 3rd party Perl modules are maintained in an "extlib" directory within each project directory:
+
= Required Perl modules =
  
  website-classic/extlib - ''The "Classic" WormBase website
+
''See the [https://bitbucket.org/tharris/wormbase/src/d91a1c3571d4/Makefile.PL Makefile.PL] for a complete list of required Perl modules.''
  website/extlib - 'The rearchitecture
 
  website-2.01/extlib - Version 2.01 of the rearchitecture
 
  
And so on...
+
= Installation Paths =
  
 +
By convention, 3rd party Perl modules are maintained in an "extlib" directory within each version of the site. This enables us to keep unique sets of libraries for each website.
  
 +
website/production/extlib - ''The current production version of the website''
 +
website/tharris/extlib - ''My private development space''
  
= Required Perl modules =
+
To set up your environment, copy the wormbase.env.template file to ''wormbase.env''.  Change the $APP variable to match your directory (ie ''tharris'). Then:
 +
 +
$ source wormbase.env
  
== WormBase "Classic" ==
+
== local::lib ==
  
Install the following Perl modules via CPAN. Note that you DO NOT AND SHOULD NOT be sudo.
+
The ''wormbase.env'' file uses local::lib to easily set up a local library path. local::lib is already installed into the system Perl path:
  
cd /usr/local/wormbase/extlib/classic
+
  sudo perl -MCPAN -e install 'local::lib'
perl -Mlocal::lib=./
 
eval $(perl -Mlocal::lib=--self-contained,./)
 
perl -MCPAN -e 'CPAN::install(MODULE)'
 
  
// Some basics...
+
local::lib dispenses with the need to maintain multiple CPAN configurations or manual tweaks to your environment variables in order to recognize already installed modules.
YAML
 
LWP
 
ExtUtils::MakeMaker
 
Bundle::CPAN
 
 
// The rest...
 
Bio::Graphics
 
BioPerl 
 
    // When prompted, choose to download all optional modules. This will also install Ace:
 
Ace
 
    // During configuration, choose option (3), then set the remaining variables as follows:
 
    Site-specific configuration files:  /usr/local/wormbase/website-classic/conf
 
    CGI path:  /usr/local/wormbase/website-classic/cgi-bin
 
    HTML path:  /usr/local/wormbase/website-classic/html
 
  
    // For Catalyst-based apps:
+
'''To set a local installation environment, you would:'''
    Site-specific configuration files:  /usr/local/wormbase/website/conf
 
    CGI path: /usr/local/wormbase/website/root/cgi
 
    HTML path:  /usr/local/wormbase/website/root/static
 
  
  Cache::Cache
+
  $ cd /usr/local/wormbase/website/tharris/extlib
  Cache::FileCache
+
  $ perl -Mlocal::lib=./
  CGI
+
  export MODULEBUILDRC="/usr/local/wormbase/website/tharris/extlib/.modulebuildrc"
CGI::Session 
+
export PERL_MM_OPT="INSTALL_BASE=/usr/local/wormbase/website/tharris/extlib"
CGI::Cache
+
  export PERL5LIB="/usr/local/wormbase/website/tharris/extlib/lib/perl5:/usr/local/wormbase/website/tharris/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:$PERL5LIB"
CGI::Toggle
+
  export PATH="/usr/local/wormbase/website/tharris/extlib/bin:$PATH"
Class::Base
 
Data::Stag
 
Date::Calc
 
Date::Manip
 
DB_File
 
DBI
 
DBD::mysql  (mysql devel package must be installed first)
 
    // To build by hand:
 
    perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/extlib/classic --testuser=USER --testpassword=PASS
 
    make ; make test ; make install
 
  Digest::MD5
 
Flickr::API
 
Flickr::API::Simple
 
    // This is a private library
 
    cd /usr/local/wormbase/build
 
    perl ./Build.PL --install_base /usr/local/wormbase/extlib/classic
 
    ./Build install
 
GD
 
GD::SVG
 
  GD::Graph
 
GD::Graph::pie
 
HTML::TokeParser
 
IO::Scalar
 
IO::String
 
Image::GD::Thumbnail
 
Log::Log4perl
 
MIME::Lite
 
mod_perl2  // Requires that apache2 already be installed; apxs is at /usr/local/apache2/bin/apxs
 
Net::FTP
 
Proc::Simple
 
Search::Indexer
 
SOAP::Lite
 
Statistics::OLS
 
Storable
 
SVG
 
SVG::Graph
 
Term::ReadKey
 
Test::Pod
 
Text::Shellwords
 
Time::Format
 
WeakRef
 
XML::SAX
 
XML::Parser
 
XML::DOM
 
XML::Writer
 
XML::Twig
 
XML::Simple
 
  
== WormBase > 2.0 ==
+
$ eval $(perl -Mlocal::lib=--self-contained,./)
  
WormBase2.0 and above uses the Catalyst web framework.  In addition to the modules described above we also need to install Catalyst.
+
'''To install a module'''
  
These first two bundles will install the majority of the Catalyst web framework:
+
$ perl -MCPAN -Mlocal::lib=--self-contained -e 'CPAN::install(MODULE)'
  
Task::Catalyst
+
'''Installing a module without using local::lib'''
Catalyst::Devel
 
  
  We also need:
+
You may on occasion need to install something without using local::lib.  For EUMM modules, use
  
Catalyst::Model::DBI
+
  perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL INSTALL_BASE=/usr/local/wormbase/[PROECT]/extlib
Catalyst::Model::Adaptor
 
Catalyst::Plugin::ConfigLoader
 
Catalyst::Plugin::Session
 
Catalyst::Plugin::Session::State
 
Catalyst::Plugin::Session::State::Cookie
 
Catalyst::Plugin::Session::Store::FastMMap
 
Catalyst::Action::RenderView
 
Catalyst::Action::Rest
 
Catalyst::Log::Log4perl
 
Test::YAML::Valid
 
  
= local::lib =
+
And for Module::Build
 +
 
 +
  perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL --install_base /usr/local/wormbase/[PROJECT]/extlib
  
== Installation ==
+
Alternatively, you can manually edit ~/.cpan/CPAN/MyConfig.pm
  
local::lib is installed into the system Perl path:
+
= Installing WebApp Dependencies =
  
  sudo perl -MCPAN -e install 'local::lib'
+
Build all requirements is as easy as:
  
== Setting a library path ==
+
$ cd /usr/local/wormbase/website/$APP
 +
$ source wormbase.env
 +
$ perl Makefile.PL
 +
$ make installdeps
  
$ cd /usr/local/wormbase/extlib/classic
+
Note: the wormbase.env should ensure local::lib use /usr/local/wormbase/extlib/ as installation path for packages.
$ perl -Mlocal::lib=./
 
export MODULEBUILDRC="/usr/local/wormbase/extlib/classic/.modulebuildrc"
 
export PERL_MM_OPT="INSTALL_BASE=/usr/local/wormbase/extlib/classic"
 
export PERL5LIB="/usr/local/wormbase/extlib/classic/lib/perl5:/usr/local/wormbase/extlib/classic/lib/perl5/x86_64-linux-gnu-thread-multi:$PERL5LIB"
 
export PATH="/usr/local/wormbase/extlib/classic/bin:$PATH"
 
  
Take note: we will use some of these variables for, say, setting up apache.
+
= Tips and Tricks =
  
$ eval $(perl -Mlocal::lib=--self-contained,./)
+
== ACePerl ==
  
== Installing a module ==
+
Adjust the values below as necessary for your
  
$ perl -MCPAN -Mlocal::lib=--self-contained -e 'CPAN::install(MODULE)'
+
[tharris@wb-dev: AcePerl-1.92-BlHove]> sudo perl Makefile.PL
  
== Installing a module without using local::lib ==
+
What do you want to build?
  
You may on occasion need to install something without using local::lib.  For EUMM modules, use
+
  1) Interface to Ace socket server and local databases (pure Perl)
 +
  2) The above plus XS optimizations (requires C compiler)
 +
  3) The above plus RPC server interface (requires C compiler)
  
  perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL INSTALL_BASE=/usr/local/wormbase/[PROECT]/extlib
+
Enter your choice:  [1] 3
  
And for Module::Build
+
Do you want to install Ace::Browser?  [n] y
  
  perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL --install_base /usr/local/wormbase/[PROJECT]/extlib
+
You have installed Ace::Browser before, using old settings for defaults.
 +
Directory for the site-specific configuration files (~username ok): [/usr/local/wormbase/website/tharris/conf/ace]
 +
Directory for the acebrowser CGI scripts (~username ok): [/usr/local/wormbase/website/tharris/root/cgi-bin/ace]
 +
Directory for the acebrowser HTML files and images (~username ok): [/usr/local/wormbase/website/tharris/root/static/ace]  
  
Alternatively, you can manually edit ~/.cpan/CPAN/MyConfig.pm
 
  
= Tips and Tricks =
 
  
 
''Some modules may require a little TLC.  After running the script you can find source at ~/.cpan/build/module-*''
 
''Some modules may require a little TLC.  After running the script you can find source at ~/.cpan/build/module-*''
Line 202: Line 145:
  
 
You will need to specify a test user and test password for tests to pass.
 
You will need to specify a test user and test password for tests to pass.
 
== ModPerl2 ==
 
 
You will need to be sudo in order to install the dso.
 
  
 
= Updating Modules =
 
= Updating Modules =
Line 235: Line 174:
 
(Or just use the install script).
 
(Or just use the install script).
  
 
+
[[Category:Maintenance (Web Dev)]]
 
[[Category:Developer documentation]]
 
[[Category:Developer documentation]]

Latest revision as of 18:47, 13 April 2015

Overview

Maintaining Perl modules across our server farm can be a time consuming and tedious task because of the heterogeneity of our setup. Further, we often need to maintain unique sets of libraries for different applications with collisions.

To solve these problems, I maintain local copies of libraries for each application. Typically, these are found at

 /path/to/application/extlib

Installing a local CPAN repository

I maintain a local mirror of CPAN. This makes installing our web application significantly faster.

$ sudo perl -MCPAN -e shell
$ cpan> install CPAN::Mini

Create a ~/.minicpanrc file:

# CPAN::Mini configuration file
# to set up our local WormBase CPAN

local: /usr/local/wormbase/minicpan
remote: http://mirror.rit.edu/CPAN/
exact_mirror: 1

Set up your CPAN to use the local mirror:

$ cpan
cpan> o conf urllist file:///usr/local/wormbase/minicpan/
cpan> o conf commit

Don't forget cpanplus:

$ cpanp
$ CPAN Terminal> s reconfigure
$ select the System configuration, then the mirror option, custom, and as above. Save and quit.

Set up the minicpan to run once a day:

  • 3 * * * minicpan

Required Perl modules

See the Makefile.PL for a complete list of required Perl modules.

Installation Paths

By convention, 3rd party Perl modules are maintained in an "extlib" directory within each version of the site. This enables us to keep unique sets of libraries for each website.

website/production/extlib - The current production version of the website
website/tharris/extlib - My private development space

To set up your environment, copy the wormbase.env.template file to wormbase.env. Change the $APP variable to match your directory (ie tharris'). Then:

$ source wormbase.env

local::lib

The wormbase.env file uses local::lib to easily set up a local library path. local::lib is already installed into the system Perl path:

 sudo perl -MCPAN -e install 'local::lib'

local::lib dispenses with the need to maintain multiple CPAN configurations or manual tweaks to your environment variables in order to recognize already installed modules.

To set a local installation environment, you would:

$ cd /usr/local/wormbase/website/tharris/extlib
$ perl -Mlocal::lib=./
export MODULEBUILDRC="/usr/local/wormbase/website/tharris/extlib/.modulebuildrc"
export PERL_MM_OPT="INSTALL_BASE=/usr/local/wormbase/website/tharris/extlib"
export PERL5LIB="/usr/local/wormbase/website/tharris/extlib/lib/perl5:/usr/local/wormbase/website/tharris/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:$PERL5LIB"
export PATH="/usr/local/wormbase/website/tharris/extlib/bin:$PATH"
$ eval $(perl -Mlocal::lib=--self-contained,./)

To install a module

$ perl -MCPAN -Mlocal::lib=--self-contained -e 'CPAN::install(MODULE)'

Installing a module without using local::lib

You may on occasion need to install something without using local::lib. For EUMM modules, use

 perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL INSTALL_BASE=/usr/local/wormbase/[PROECT]/extlib

And for Module::Build

 perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL --install_base /usr/local/wormbase/[PROJECT]/extlib 

Alternatively, you can manually edit ~/.cpan/CPAN/MyConfig.pm

Installing WebApp Dependencies

Build all requirements is as easy as:

$ cd /usr/local/wormbase/website/$APP
$ source wormbase.env
$ perl Makefile.PL
$ make installdeps

Note: the wormbase.env should ensure local::lib use /usr/local/wormbase/extlib/ as installation path for packages.

Tips and Tricks

ACePerl

Adjust the values below as necessary for your

[tharris@wb-dev: AcePerl-1.92-BlHove]> sudo perl Makefile.PL

What do you want to build?

 1) Interface to Ace socket server and local databases (pure Perl)
 2) The above plus XS optimizations (requires C compiler)
 3) The above plus RPC server interface (requires C compiler)

Enter your choice: [1] 3

Do you want to install Ace::Browser? [n] y

You have installed Ace::Browser before, using old settings for defaults. Directory for the site-specific configuration files (~username ok): [/usr/local/wormbase/website/tharris/conf/ace] Directory for the acebrowser CGI scripts (~username ok): [/usr/local/wormbase/website/tharris/root/cgi-bin/ace] Directory for the acebrowser HTML files and images (~username ok): [/usr/local/wormbase/website/tharris/root/static/ace]


Some modules may require a little TLC. After running the script you can find source at ~/.cpan/build/module-*

BioPerl

Instead of building BioPerl from CPAN, it might be necessary to build from SVN:

 $ cd /usr/local/wormbase/build
 $ svn co svn+ssh://USERNAME@dev.open-bio.org/home/svn-repositories/bioperl/bioperl-live/trunk bioperl-live
 $ mv bioperl-live bioperl-live-tharris
 $ cd bioperl-live-tharris
 $ perl ./Build.PL install_base /usr/local/wormbase/extlib
 $ ./Build test
 $ ./Build install

DBD::mysql

You will need to specify a test user and test password for tests to pass.

Updating Modules

To show all modules that are out-of-date with those on CPAN:

$ cd /path/to/extlib
$ perl -Mlocal::lib=./
$ eval $(perl -Mlocal::lib=--self-contained,./)
$ perl -MCPAN -e 'CPAN::Shell->r'

To update all of these modules at once:

$ perl -MCPAN -e 'CPAN::Shell->install(CPAN::Shell->r)'

Managing libraries across architectures

Via CPAN bundles

# Create a bundle
$ cd /path/to/extlib
$ perl -Mlocal::lib=./
$ eval $(perl -Mlocal::lib=--self-contained,./)
$ perl -MCPAN -e autobundle   # The bundle is (typically) in extlib
# To reinstall:
$ perl -MCPAN -e 'install Bundle::Snapshot_YYYY_MM_DD_00'

(Or just use the install script).