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INSTALL
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INSTALL
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Genome Annotation Library (GAL)
To install a basic functioning GAL you'll need a few Perl modules
installed via CPAN (http://www.cpan.org/). An installation script has
been provided which will automatically install all the dependencies
for you. There are some accessory scripts within the GAL package that
require additional dependencies, and the install script will ask you
if you want to install these. You can answer either yes or no and
it won't affect the basic functionality of the GAL library.
1) GAL Quick Install:
---------------------------------------- COMMAND LINE ----------------------------------------
perl Build.PL
sudo ./Build installdeps
./Build test
./Build install
----------------------------------------------------------------------------------------------
If you have trouble, try the complete installation instructions below
first and then contact the mailing list if you still need help.
See details at the bottom of this document for docs, examples and the
mailing list.
2) GAL complete install instructions:
If your computer has a minimal OS installation, as is often the case
for new compluters, you'll need to set up your computer to prepare it
for building software packages. Follow the instructions below for
your operating system and then return to step 1 above.
For all systems:
Some installations of perl are a a bit out of date and you may need to
update a few modules to install GAL. It won't hurt to update the
following two core modules just in case. Type the following and follow the prompts.
---------------------------------------- COMMAND LINE ----------------------------------------
sudo cpan TAP::Harness
sudo cpan Module::Build
----------------------------------------------------------------------------------------------
a) Linux
i) Red Hat, Fedora, CentOS and other Linux systems that use a
yum package manager:
Install a set of developer tools (All we really need is the
gcc compiler but it doesn't hurt to round out your
installation). Type and answer Yes to the prompts:
---------------------------------------- COMMAND LINE ----------------------------------------
sudo yum update # If you linux installation is out of date.
sudo yum groupinstall "Development Tools"
----------------------------------------------------------------------------------------------
ii) Debian, Ubuntu and other Linux systems that use the Advance
Packaging Tool (i.e. apt-get):
Install a set of developer tools (All we really need is the gcc compiler
but it doesn't hurt to round out your installation).
---------------------------------------- COMMAND LINE ----------------------------------------
sudo apt-get update # If your linux installation is out of date.
sudo apt-get install build-essential
----------------------------------------------------------------------------------------------
b) Mac OSX:
Install XCode from the App Store. Point your browser here
https://developer.apple.com/xcode/ and follow the link to the
App Store.
Have a look at the examples in GAL/bin/examples and look at the
documentation in GAL/docs/html.
Please contact the mailing list for help or to report any bugs.
http://sourceforge.net/p/song/mailman/