Mojolicious aims to provide a complete web development experience. It thus has no hard dependencies, comes with a built-in development and production server and many other features one needs to build a web application. It's easy to install, has an applciation generator script and many plugins and extensions.

Libraries for developing Web applications

• Amon2
• Catalyst - Overflowing with features. Very popular.
• Dancer (Official site)
• Dancer2
• Gantry - Web application framework for mod_perl, cgi, etc.
• Kossy - A Web framework with simple interface.
• Mojolicious - An all in one framework.
• Poet - a modern Perl web framework for Mason developers

Address of the bookmark: https://www.ynonperek.com/2017/09/28/perl-mojolicious-web-development/

Features

• An amazing real-time web framework, allowing you to easily grow single file prototypes into well-structured MVC web applications.
  • Powerful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session management, form validation, testing framework, static file server, CGI/PSGI detection, first class Unicode support and much more for you to discover.
• A powerful web development toolkit, that you can use for all kinds of applications, independently of the web framework.
  • Full stack HTTP and WebSocket client/server implementation with IPv6, TLS, SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support.
  • Built-in non-blocking I/O web server, supporting multiple event loops as well as optional pre-forking and hot deployment, perfect for building highly scalable web services.
  • JSON and HTML/XML parser with CSS selector support.
• Very clean, portable and object-oriented pure-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed)
• Fresh code based upon years of experience developing Catalyst, free and open source.
• Hundreds of 3rd party extensions and high quality spin-off projects like the Minion job queue.

http://mojolicious.org/

Address of the bookmark: http://mojolicious.org/

More at https://www.raku.org/

Address of the bookmark: https://www.raku.org/

More at https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module

2. exec””

 syntax: exec "command";

3. Backticks “ or qx//

syntax: `command`;

syntax: qx/command/;

4. IPC::Open3

syntax: $output = open3(\*CHLD_IN, \*CHLD_OUT, \*CHLD_ERR, 'command arg1 arg2', 'optarg',...);

It is very similar to IPC::Open2 with the capability to capture all three file handles of the process, i.e., STDIN, STDOUT, and STDERR. It can also be used with or without the shell. You can read about it more in the documentation: IPC::Open3.

$output = open3(my $o ut, my $in, 'command arg1 arg2');

OR without using the shell

$output = open3(my $out, my $in, 'command', 'arg1', 'arg2');

5.a2p

syntax: a2p [options] [awkscript]

There is a Perl utility known as a2p which translates awk command to Perl. It takes awk script as input and generates a comparable Perl script as the output. Suppose, you want to execute the following awk statement

awk '{$1 = ""; $2 = ""; print}' f1.txt

This statement gives error sometimes even after escaping the variables (\$1, \$2) but by using a2p it can be easily converted to Perl script:

For further information, you can read it’s documentation: a2p

More help at https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl

6. system()

syntax: system( "command" );

It is also a Perl function (perlfunc) that executes a command and waits for it to get finished first and then resume the Perl script. The return value is the exit status of the command. It can be called in two ways:

system( "command arg1 arg2" );

OR

system( "command", "arg1", "arg2" );

HELP

Here are some useful Perl cheat sheets that can be used as a quick reference guide.-- https://www.pcwdld.com/perl-cheat-sheet

In comparative genome analysis work, we usually compare more than two genomes and looks for syntenic regions amongst them. In my research I used Evolution Highway (RH) http://eh-demo.ncsa.uiuc.edu/, which is a collaborative project designed to provide a visual means for simultaneously comparing genomes of multiple amniote species. The tool removes the burden of manually aligning these maps and allows cognitive skills to be used toward something more valuable than preparation and transformation of data. In addition to EH, attractive Circos (http://circos.ca/) is also very popular for this kind of analysis.

The EH is available online, and can be easily access and use, whereas Circos installation is not entirely straightforward. One of the most difficult parts of the installation involves installing the GD library. Since there weren't good instructions for installing this library on the internet I decided to post instructions here in case they are useful to anyone else.

Following are the steps to install GD modules in Mac OS

1. Setup

Create a folder for the files:

$ mkdir -p /SourceCache
$ cd /SourceCache

Get and unpack the required Jpeg-6b and GD libraries:
Download Jpeg-6b (http://code.google.com/p/google-desktop-for-linux-mirror/downloads/detail?name=jpeg-6b.tar.gz&can=2&q)
Download GD (http://search.cpan.org/~lds/GD-2.46/)

Place the "tar.gz" files in "/SourceCache" and double click to unpack.

2. Install libjpeg

Copy the "config.sub" and "config.guess" files to "/SourceCache". Note that your "config.sub" and ""config.guess" files may be in a slightly different location. The commands below show where they were on my machine:

$ cd /SourceCache/jpeg-6b/src
$ cp /usr/share/libtool/config/config.sub .
$ cp /usr/share/libtool/config/config.guess .

Configure libjpeg as follows. Note that this was installed on a 64 bit machine. However, this method may configure it in a 32 bit format. This may not be the best way to configure the installation but it works.

$ .configure --enable-shared
$ make

Check to see if the following directories exist on your machine. Create the missing directories in the following manner:

$ mkdir -p /usr/local/include
$ mkdir -p /usr/local/bin
$ mkdir -p /usr/local/lib
$ mkdir -p /usr/local/man/man1

Finish making and installing libjpeg:

$ make install

3. Install GD

$ cd /SourceCache/GD-2.46/GD/
$ perl Makefile.PL
$ make
$ make test (optional)
$ make html (optional)
$ make install

Other way for Mac OS
The easiest way to get a lot of these is with a program called Fink, which is similar in nature to the CPAN installer, but installs common GNU utilities. Fink is available from <http://sourceforge.net/projects/fink/>.

Follow the instructions for setting up Fink. Once it's installed, you'll want to run the following as root: fink install gd

It will prompt you for a number of dependencies, type 'y' and hit enter to install all of the dependencies. Then watch it work.

To prevent creating conflicts with the software that Apple installs by default, Fink creates its own directory tree at /sw where it installs most of the software that it installs. This means your libraries and headers for libgd will be at /sw/lib and /sw/include instead of /usr/lib and /usr/local/include. Because of these changed locations for the libraries, the Perl GD module will not install directly via CPAN, because it looks for the specific paths instead of getting them from your environment. But there's a way around that :-)

Instead of typing "install GD" at the cpan> prompt, type look GD. This should go through the motions of downloading the latest version of the GD module, then it will open a shell and drop you into the build directory. Apply below patch to the Makefile.PL file (save the patch into a file and use the command patch < patchfile.)

Then, run these commands to finish the installation of the GD module:

perl Makefile.PL
make
make test
make install
And don't forget to run exit to get back to CPAN.

Install on MS Window, using PPM

C:\Documents and Settings\Owner>ppm
PPM interactive shell (2.2.0) - type 'help' for available commands.
PPM> install GD
Install package 'GD?' (y/N): y
Installing package 'GD'...
Downloading http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW. ...
Installing C:\Perl\site\lib\auto\GD\GD.bs
Installing C:\Perl\site\lib\auto\GD\GD.dll
Installing C:\Perl\site\lib\auto\GD\GD.exp
Installing C:\Perl\site\lib\auto\GD\GD.lib
Installing C:\Perl\html\site\lib\GD.html
Installing C:\Perl\site\lib\GD.pm
Installing C:\Perl\site\lib\qd.pl
Installing C:\Perl\site\lib\auto\GD\autosplit.ix
PPM>


If you can't install it from ppm. You can download it:
http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW.


BTW,All Perl 5.6.1 Modules are located at:

http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW.

Install the Perl GD Module on Linux

$ sudo perl -MCPAN -e shell

Since it was the first time I had run this command on this particular machine I had to answer a lot of questions but simply selected the defaults for everything as this usually works for me. Once in the CPAN shell I entered

$ install Bundle::CPAN

and selected all of the defaults again. Once the CPAN bundle had finished installing I tried to install GD::Graph by typing

$ install GD::Graph

but it failed with hundreds of errors – the first of which was

GD.xs:7:16: error: gd.h: No such file or directory

This was fixed with the following apt-get command (in the bash shell)

$ sudo apt-get install libgd2-xpm-dev

back in the CPAN shell I still couldn’t get GD::Graph to build and I guessed this was because of some left over files from the failed build. I don’t know the command to clean things up inside the CPAN shell and am too lazy to read the docs so I simply went into the .cpan/build directory in my home directory and deleted anything that started with GD – eg

$ rm -rf GD-2.35-HC_vkB

$ rm -rf GDGraph-1.44-Evfibe

and so on. Those strings at the end (VkB and so on) look random so they might be different on your machine. Then I went back into the CPAN shell and ran

$ install GD::Graph

There were a few dependencies which the script fetched and installed for me but everything worked smoothly.

Manual and other Perl Module instalation are mentioned in my previous blog @ http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

Address of the bookmark: http://www.citrusperl.com/

Address of the bookmark: http://cbb.sjtu.edu.cn/course/database/beginning.pdf