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)