File: INSTALL

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INSTALL
=======

If you have never installed a perl module before, you may want to seek
help from a friendly nearby perl programmer or sys admin. The
instructions below aren't guaranteed to work on all systems. These
instructions are for Linux/Unix and Mac OS X. Other users have
installed successfully on PCs before; we are unable to provide
installation instruction, but the protocols below may work.

You will of course need perl in order to run this; perl5.8 is required
(version 5.6.x should also work, but go-perl is no longer tested with
this setup)

There's a lot of instructions here. There are a number of different
ways to set up go-perl; the best way for you depends on your
experience of perl and how your system is set up. These ways are
described as different protocols below. Hopefully you should only need
to follow one protocol to get going!

Protocol I - set up via CPAN installer
--------------------------------------

If you are already familiar with installing CPAN modules, go-perl is
no different from any other. If you aren't, you may wish to experiment
now.

Try typing the following:

----------
perl -MCPAN -e shell
install GO::Parser
----------

The following may also work:

----------
cpan GO::Parser
----------

If this is the first time using the CPAN installer, you will be asked
a barrage of questions. You are best to answer with the defaults - you
can always change this later.

If you do NOT have access to the system-wide perl directories on your
system (these will typically be in /Library or /usr/local), then you
should either get some help setting up CPAN for use with your system,
OR you should follow an alternate protocol below. (You may wish to
modify the value of PREFIX to ~ in the CPAN setup, as detailed in
protocol III)

If you are on OS X you may need to do this:

----------
sudo cpan GO::Parser
----------

Providing you do have write-access to these directories, the above
commands should hopefully go smoothly. When installing go-perl, you
may be asked if you wish to also install Data::Stag and IO::String -
you should answer 'yes'

After this, you should be ready to use go-perl! The scripts should be
in your path and the libraries should be in the standard place. You
may wish to start by trying "map2slim" or "go2obo_xml"

There are certain applications that require additional third-party
modules. All these are available from CPAN, and can be installed in
the above manner. For example, if you try and use the
go-filter-subset.pl script to generate a PNG image of an ontology
subgraph, the system will complain you do not have the module
"GraphViz" installed. To install this, simply type:

----------
perl -MCPAN -e shell
install GraphViz
----------

Depending on what you use go-perl for, you may not ever need to
install other CPAN modules

Protocol II - Manual installation
---------------------------------

these are step-by-step manual installation instructions. These should
be followed if protocol I does not work for you

Installing required modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~

go-perl requires the Data::Stag module in order to run. You can
download this module from here:

http://search.cpan.org/~cmungall/Data-Stag/

(version 0.07 or higher is required; these docs assume you have
downloaded 0.08)

Data::Stag in turn requires the following module:

http://search.cpan.org/~gaas/IO-String/

After downloading, type the following instructions to install IO-String:

----------
cd ~
tar -zxvf IO-String-1.06
cd IO-String-1.06
perl Makefile.PL
make test
----------

If you have permission to install system-wide, you should then type:

----------
make install
----------

On Mac OS X, you may need to type

----------
sudo make install
----------

If you do not have permission to install perl modules in the default
directory on your system, you need to follow protocol III

Once you have installed IO::String, you can install Data::Stag - the
directions are the same:

----------
cd ~
tar -zxvf Data-Stag-0.08.tar.gz
cd Data-Stag-0.08
perl Makefile.PL
make test
make install
----------

Once you have installed Data::Stag, you are now ready to install
go-perl

NOTE: There are certain applications that require additional
third-party modules (all available from CPAN); if you run into
problems running any of these applications, see the section
"Additional Modules" below

Installing go-perl
~~~~~~~~~~~~~~~~~~

If you are reading this, then presumably you have unpacked the
distribution - either the go-perl distribution, or the go-dev
distribution that contains go-perl.

To install the modules system wide, type this:

----------------
cd go-perl-0.02
perl Makefile.PL
make test
make install
----------------

The first command may tell you that you have certain optional modules
missing - these may not be required. If you do require them, see
"Additional Modules" below

If the system complains when you type "make install" you may not have
sufficient permissions. In this case you need to use the modules from
your home directory


Additional Modules
~~~~~~~~~~~~~~~~~~

You may need additional modules for running certain scripts in certain
modes. You can obtain all these from this website:

http://www.cpan.org/

Protocol III - installing modules in your home directory
-------------------------------------------------------

If you do not have sufficient permission to install system-wide, there
is a third method you can try, which is to install IO::String,
Data::Stag and go-perl in your home directory. To do this, you need to
set the PREFIX variable when installing.

First download Data::Stag and IO::String from CPAN, as detailed in
protocol II.

Then try this:

----------
setenv PERL5LIB "${PERL5LIB}:$HOME/lib/perl5/site_perl/5.8.0/
cd ~
tar -zxvf IO-String-1.06
cd IO-String-1.06
perl Makefile.PL PREFIX=~
make test
make install
cd ~
tar -zxvf Data-Stag-0.08.tar.gz
cd Data-Stag-0.08
perl Makefile.PL PREFIX=~
make test
make install
make install
cd
cd go-perl-0.02
perl Makefile.PL PREFIX=~
make test
make install
----------

If this works, then place this in your startup file:

----------
setenv PERL5LIB "${PERL5LIB}:$HOME/lib/perl5/site_perl/5.8.0/
setenv PATH "${PATH}:$HOME/bin"
----------

You may need to modify the above, depending on your
setup. Instructions for this are outwith the scope of this
document. Try consulting online sources, such as:

http://www.perl.com/pub/a/2002/04/10/mod_perl.html


Additional Modules
------------------

Certain applications (for example, those involving XML parsing) will
require additional modules from CPAN. If you are going on to install
go-db-perl and/or AmiGO you will probably need a few extra modules.

If this is the case, you are strongly advised to use the CPAN
auto-installer. Once you have set this up, installing perl modules
will be *much* easier.

To use this, type:
--------------------
perl -MCPAN -e shell
--------------------

Then follow the setup instructions

Then type:
--------------------
install <<Module name here>>
quit
--------------------

You can use the CPAN installer to install go-perl itself; just type
--------------------
perl -MCPAN -e shell
install go-perl
--------------------

This is the easiest way of keeping up to date with go-perl releases


Using go-perl as part of go-dev
-------------------------------

go-perl is part of the wider go-dev distribution, although it can be
used independently. go-dev also includes go-db-perl (for GO MySQL DB
access) and an xml library (for converting to other XML based formats
such as OWL), the AmiGO web application and the schema for the GO
MySQL db

If you are using all of go-dev, you may need to alter the instructions
above (for example, your go-perl library may be unpacked in
~/go-dev/go-perl). You may also need to set GO_ROOT:

The GO_ROOT environment variable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If you are using go-perl as part of the wider go-dev distribution,
there are some applications that require you to specify the location
of go-dev using the GO_ROOT env var

bash shells:

----------
export GO_ROOT=$HOME/go-dev
----------

other shells:

----------
setenv GO_ROOT $HOME/go-dev
----------

It is a good idea to put this in your startup file

Installing from CVS
-------------------

You can get the latest bleeding-edge version of go-perl from the
go-dev cvs tree. See http://www.godatabase.org/dev for details

Once you have checked out go-dev/go-perl, do the usual thing (if
you're installing from cvs it's assumed you're a bleeding edge user
and know how to do this):

cd ~/cvs/go-dev/go-perl
perl Makefile.PL
make test
setenv GO_ROOT ~/cvs/go-dev
setenv PERL5LIB "$PERL5LIB:~/cvs/go-dev/go-perl"

The assumption is that if you are using cvs you want to use the
working copy; if you want to install from cvs, instead do the
following steps:

cd go-dev/go-perl
perl Makefile.PL
make GO/xsl
make test
make install

The "make GO/xsl" stage is not strictly necessary; if you omit it you
will get warnings. You can ignore these, but if you ever want to use
the XSL you will need to check out go-dev/xml and set the GO_ROOT
environment variaable as above.

Note that none of this is necessary if you install from CPAN - the
installation of the XSL is taken care of automatically

Documentation
-------------

For full documentation, see the doc/ directory, or look online

http://www.godatabase.org/dev

Mailing List
------------

http://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev


Installing Documentation Locally
--------------------------------

it's unlikely you'll need to do this: you can always browse the pod
documentation online at:

http://www.godatabase.org/dev/pod

The documentation can be installed in a web-viewable directory; this
is best done in a directory that is visible as $BASE_URL/dev/pod

Just type

----------
cd go-perl
perl Makefile.PL
make pod
cp -pR pod/* $HTTP_DOCUMENT_ROOT/dev/pod
----------

substituting HTTP_DOCUMENT_ROOT with the root path of the WWW
documents on your webserver

You can now browse the documentation:
http://www.yourhost.com/dev/pod

(You may also wish to copy the whole go-dev distribution under the
/dev/ directory)