SOBA/INSTALL at master · The-Sequence-Ontology/SOBA · GitHub

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Quick install docs for those comfortable with things like svn, installing C
libraries from source and CPAN.
--------------------------------------------------------------------------------

Check out the SOBAcl code from SVN

svn co svn://topaz.genetics.utah.edu/SOBA/trunk SOBA

Put the SOBAcl file in your path by softlinking it to somewhere in
your path or adding it's location to your path.  SOBAcl uses it's
location to find it's templates, so don't move the script to another
location or you'll lose those templates.

--------------------------------------------------------------------------------

Non-perl prerequisites:

SOBAcl requires several libraries to be installed for graphical
support.  Try to use a package manager like apt-get (Debian, Ubuntu)
or yum (RedHat, Fedora, CentOS) whenever possible to install the
following.

libgd # The GD library http://www.libgd.org/Main_Page
    libgd optionally requires (but you really need at least png or jpeg support).
    1. zlib, available from http://www.gzip.org/zlib/
       Data compression library.  You probably already have it.

    2. libpng, available from http://www.libpng.org/pub/png/
       Portable Network Graphics library; requires zlib.

    3. FreeType 2.x, available from http://www.freetype.org/
       Free, high-quality, and portable font engine

    4. JPEG library, available from http://www.ijg.org/
       Portable JPEG compression/decompression library

    5. XPM, available from http://koala.ilog.fr/lehors/xpm.html
       X Pixmap library
       This library is optional and is only used to import XPM
       graphics files.  Unless you know you need it, don't worry
       about it.

Graphviz: Graphviz is open source graph visualization software.  Here
we are talking about graphs as diagrams of abstract graphs and
networks not line graphs and pie charts like we were above.  The well
supported graphviz library provides binaries, installers, and source
code for installation.  See their website for details.  Again, see

http://www.graphviz.org/

System specific instructions for intalling compiled prerequisites with
package managers.  While we have made an effort to provide the correct
package names, these OS distributions are constantly being updated, so
you may have to search for the correct package name.  For libraries
not installed below, you'll have to find the package name yourself or
install from source.  If you find any corrections or updates to this
list please let me know so I can update these docs.

    RHEL (Should be similar for Fedora and CentOS):
      # Search with
      # yum list | grep zlib | less
      yum install zlib
      yum install libpng
      yum install freetype
      yum install libjpeg
      yum install gd
      # The gd-devel packages requires activation of the optional
      # rhel-x86_64-server-optional-6 channel
      yum install gd-devel

    Debian/Ubuntu
      # Search with
      # apt-cache search zlib | less
      apt-get install zlib1g
      apt-get install libpng3
      apt-get install libfreetype6
      apt-get install libjpeg62
      apt-get install libgd2-xpm-dev
      apt-get install graphviz

    MacOS X:
      zlib is already included
      fink install libpng3

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CPAN Prequisites:

Once the underlying libraries are installed as described above the
following Perl prerequisites can be install from the SOBA directory
with:

sudo perl -I'lib/' -MCPAN -e 'install Bundle::SOBA'

Getopt::Long
DBI
DBD::SQLite
Number::Format
Template
Template::Plugin::Number::Format
Statistics::Descriptive
Set::IntSpan::Fast
Text::Table
SQL::Abstract
GD::Graph
GraphViz