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If you need help at any time, you can read the CPANshell's manual page by typingperldoc CPAN or by starting upthe CPAN shell (with perl-MCPAN -eshell at a systemshell prompt) and entering h at thecpan> prompt:
After much activity, you should then have a fresh copy of LWP on yoursystem, with far less work than installing it manually onedistribution at a time. At the time of this writing, installBundle::LWP installs not just the libwww-perl distribution,but also URI and HTML-Parser. It does not install the HTML-Treedistribution that we'll use in Chapter 9, "HTML Processing with Trees" and Chapter 10, "Modifying HTML with Trees". To do that,enter:
The libwww-perl collection is a set of Perl modules which provides a simple and consistent application programming interface (API) to the World-Wide Web. The main focus of the library is to provide classes and functions that allow you to write WWW clients. The library also contain modules that are of more general use and even classes that help you implement simple HTTP servers.
What this means to libwww-perl is that communication always take place through these steps: First a request object is created and configured. This object is then passed to a server and we get a response object in return that we can examine. A request is always independent of any previous requests, i.e. the service is stateless. The same simple model is used for any kind of service we want to access.
The libwww-perl request object has the class name HTTP::Request. The fact that the class name uses HTTP:: as a prefix only implies that we use the HTTP model of communication. It does not limit the kind of services we can try to pass this request to. For instance, we will send HTTP::Requests both to ftp and gopher servers, as well as to the local file system.
Since we don't want to handle all possible code values directly in our programs, a libwww-perl response object has methods that can be used to query what kind of response this is. The most commonly used response classification methods are:
The class name for the user agent is LWP::UserAgent. Every libwww-perl application that wants to communicate should create at least one object of this class. The main method provided by this object is request(). This method takes an HTTP::Request object as argument and (eventually) returns a HTTP::Response object.
All modules contain detailed information on the interfaces they provide. The lwpcook manpage is the libwww-perl cookbook that contain examples of typical usage of the library. You might want to take a look at how the scripts lwp-request, lwp-download, lwp-dump and lwp-mirror are implemented.
LWP owes a lot in motivation, design, and code, to the libwww-perl library for Perl4 by Roy Fielding, which included work from Alberto Accomazzi, James Casey, Brooks Cutter, Martijn Koster, Oscar Nierstrasz, Mel Melchner, Gertjan van Oosten, Jared Rhine, Jack Shirazi, Gene Spafford, Marc VanHeyningen, Steven E. Brenner, Marion Hakanson, Waldemar Kebsch, Tony Sanders, and Larry Wall; see the libwww-perl-0.40 library for details.
We specialize in stable, secure, and easy-to-deploy Perl environments. Unlike other Perl distributions such as Strawberry Perl or perlbrew, our universal package manager, the State Tool, replaces CPAN and PPM and allows you to build runtimes with CPAN modules from source code (including linked C libraries), reducing your exposure to vulnerabilities and eliminate the need for a local compiler/build environment.
Recent versions of ActiveState Perl for Windows, Mac and Linux can be downloaded from the ActiveState Platform. Just copy the install script and paste it at a CMD command prompt to complete your installation of Perl. No prerequisite.
These are on one of your install discs, or available as a huge but free download from the Apple Developer Connection [free registration required] or the Mac App Store. I thought I had them, but apparently when we upgraded that computer to Tiger, they went missing.
Older versions of XCode installed the command line tools (which are required to properly install CPAN modules) by default, but apparently newer ones do not. To check whether you have the command line tools already installed, run the following from the Terminal:
Can't locate LWP/Simple.pm in @INC (@INC contains: /opt/local/lib/perl5/site_perl/5.12.3/darwin-multi-2level /opt/local/lib/perl5/site_perl/5.12.3 /opt/local/lib/perl5/vendor_perl/5.12.3/darwin-multi-2level /opt/local/lib/perl5/vendor_perl/5.12.3 /opt/local/lib/perl5/5.12.3/darwin-multi-2level /opt/local/lib/perl5/5.12.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at ./scmxml2dot.pl line 14. BEGIN failed--compilation aborted at ./scmxml2dot.pl line 14.
When perl encounters use My::Module it goes over the elements of the built-in @INC module that contains directory names. In each directory it check if there is a subdirectory called "My" and if in that subdirectory there is a file called "Module.pm".
local::lib enables you to install modules into a specified directory, without requiring root or administrator access. See the bootstrapping technique for how to get started. You can create a directory per user/project/company and deploy to other servers, by copying the directory (as long as you are on the same operating system and perl version).
cpanm from App::cpanminus is a script to get, unpack, build and install modules from CPAN. It's dependency free (can bootstrap itself) and requires zero configuration (install instructions). It automates the entire build process for the majority of modules on CPAN and works well with local::lib and perlbrew. Many experienced Perl developers use this as their tool of choice. Related tools: cpan-outdated, pm-uninstall, cpan-listchanges.
perlbrew from App::perlbrew is useful if your system perl is too old to support modern CPAN modules, or if it's troublesome in other capacities (RedHat/CentOS are included in this list). perlbrew makes the process of installing a Perl in any directory much easier, so that you can work completely independently of any system Perl without needing root or administrator privileges. You can use multiple versions of Perl (maybe as you upgrade) across different projects. The separation from your system Perl makes server maintenance much easier and you more confident about how your project is setup. Currently Windows is not supported.
ActiveState provide a binary distribution of Perl (for many platforms), as well as their own perl package manager (ppm). Some modules are not available as ppm's or have reported errors on the ppm build system, this does not mean they do not work. You can use the cpan script to build modules from CPAN against ActiveState Perl.
Can't locate LWP/Protocol/https.pm in @INC (@INC contains: /etc/cxs /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at (eval 5) line 2.
VEP's INSTALL.pl makes it easy to set up your environment for using the VEP. It will download and configure a minimal set of the Ensembl API for use by the VEP, and can also download cache files, FASTA files and plugins.
If you already have the latest version of the API installed you do not need to run the installer, although it can be used to simply update your API version (with post-release patches applied), and retrieve cache and FASTA files. The installer downloads the API within the VEP directory and will not affect any other Ensembl API installations.
By default the script will install the API modules in a subdirectory of the current directory named "Bio". Using this option you can configure where the Bio directory is created. If something other than the default is used, this directory must either be added to your PERL5LIB environment variable when running the VEP, or included using perl's -I flag:
INSTALL.pl will set up the minimum requirements for VEP. Some features and enhancements, however, require the installation of additional components. Most are perl modules that are easily installed using cpanm; see this guide for more information on how to install perl modules.
In order for VEP to be able to access bigWig format custom annotation files, the Bio::DB::BigFile perl module is required. Installation involves downloading and compiling the kent source tree. The current version of the kent source tree does not work correctly with Bio::DB::BigFile, so it is necessary to install an archive version known to work (v335).
We'll now use cpanm to install the perl module for Bio::DB::BigFile itself. See above for guidance on this. In this example we're going to install the module to a path within your home directory. In order to do this we must modify the paths that perl looks in to find modules by adding to the PERL5LIB environment module. To make this change permanent you must add the export line to your $HOME/.bashrc or $HOME/.profile.
I'm trying to use fetch to download a sequence. However, I keep on getting 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed) even though I have ran sudo cpan install LWP::Protocol::https
The icoutils use some features specific to gcc 2.95 and later (such as macros with variable number of arguments). The GNU C Compiler is part of the GNU Compiler Collection which can be downloaded from In Debian and many other distributions the package is called gcc.
The make program is required to build icoutils. icoutils uses Makefiles generated by GNU Automake. The recommended make is GNU Make which can be downloaded from In Debian and many other distributions the package is called make.
The icotool program uses libpng to read and write PNG images. Libpng can be downloaded from In Debian, the libpng package is called libpng12-0 (libpng3 in stable). The libpng12-dev (libpng-dev in stable) package is required when building the icoutils.
The extresso perl script uses libwww-perl for fetching files. Libwww-perl can be downloaded from Libwww-perl is licensed under the same terms as Perl itself. This also applies to all modules which libwww-perl depends on. 2b1af7f3a8