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Scott Cain committed Dec 1, 2003
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117 changes: 70 additions & 47 deletions docs/pod/INSTALL.MacOSX.pod
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# ===============================================
# Author: Todd Harris (harris@cshl.org)
# gbrowse_on_osx.pod
# Revision $Id: INSTALL.MacOSX.pod,v 1.2 2003-11-24 14:06:39 tharris Exp $
# Revision $Id: INSTALL.MacOSX.pod,v 1.3 2003-12-01 18:15:08 scottcain Exp $
# Copyright @ 2003 Cold Spring Harbor Laboratory
# ===============================================

Expand All @@ -16,7 +16,7 @@ the Generic Genome Browser (GBrowse) on a stock Mac OS X system.

=head2 1. Hardware requirements

The minimum suggested hardware is:
The minimum suggested hardware is:

Mac OS X.2 (Jaguar or above)
500 Mhz G4 or higher
Expand Down Expand Up @@ -44,7 +44,8 @@ To install the Package, simply double click on it and follow the
included documentation. The package also includes an installer for
the MySQL database.

The package installer will:
The package installer will:

1. Install all required libraries
2. (Optionally) install the MySQL database
3. Install GBrowse
Expand All @@ -60,7 +61,8 @@ GBrowse is distributed with scripts that automate the fetching and
building of GBrowse and all of its software dependencies. These
scripts are locate in contrib/install_macosx.

For example, to build GBrowse on Mac OS X,
For example, to build GBrowse on Mac OS X,

% cd contrib/install_macosx
% make libraries (wait and wait and wait)
% make gbrowse
Expand Down Expand Up @@ -124,7 +126,8 @@ widely used for web applications.

=item 4. Perl, version 5.005 or higher

Preinstalled on MacOS X.
Preinstalled on MacOS X.

http://www.perl.org

=item 5. Perl modules
Expand All @@ -137,17 +140,18 @@ widely used for web applications.
6. Text::Shellwords
7. IO::String

The following are optional
The following are optional

1. XML::Twig 3.04 or higher
2. XML::Dom 1.34 or higher
3. XML::Writer 0.4 or higher
4. XML::Parser 2.30 or higher
5. LWP 5.53 or higher

If these modules are present, the "Sequence Dumper" plugin will be
able to produce GAME and BSML output. They can be downloaded from
CPAN. The LWP module enables loading of remote 3rd party
annotations.
If these modules are present, the "Sequence Dumper" plugin will be
able to produce GAME and BSML output. They can be downloaded from
CPAN. The LWP module enables loading of remote 3rd party
annotations.

=item 6. Libraries

Expand Down Expand Up @@ -200,7 +204,7 @@ fastest and easiest way to install X.

NOTE: X11 will come preinstalled with OS X.3 and greater.

1. Fetch the Apple X11 and X11 SDK installer packages.
Fetch the Apple X11 and X11 SDK installer packages.

http://www.apple.com/macosx/x11/download

Expand All @@ -211,7 +215,7 @@ instructions.

=item 2. Creating users for MySQL

Since we are going to be installing, MySQL, it's appropriate to create
Since we are going to be installing MySQL, it's appropriate to create
specific users and groups for the database.

User and group management under Mac OS X is handled by the NetInfo
Expand All @@ -227,7 +231,8 @@ accordingly if they are.
uid gid
mysql 2001 2001

The mysql user:
The mysql user:

$ niutil -create / /users/mysql
$ niutil -createprop / /users/mysql uid 2001
$ niutil -createprop / /users/mysql gid 2001
Expand All @@ -239,31 +244,36 @@ accordingly if they are.
$ niutil -createprop / /users/mysql home /usr/local/mysql
$ niutil -createprop / /users/mysql shell /dev/null

The mysql group:
The mysql group:

$ niutil -create / /groups/mysql
$ niutil -createprop / /groups/mysql gid 2001
$ niutil -createprop / /groups/mysql passwd *

Note that the mysql user's home directory was set to
/usr/local/mysql, a directory that will be created during the
installation of MySQL.
Note that the mysql user's home directory was set to
/usr/local/mysql, a directory that will be created during the
installation of MySQL.

=item 3. MySQL

MySQL can be installed on Mac OS X as a precompiled package,
compiled directly from source, or through the fink package manager
as either source or binary. Installation from a precompiled binary
is the fastest and most sure-fire way to get a working installation.
However, I've found that a source install, although a little slower,
more closely mirrors mysql installations on unix systems.
MySQL can be installed on Mac OS X as a precompiled package,
compiled directly from source, or through the fink package manager
as either source or binary. Installation from a precompiled binary
is the fastest and most sure-fire way to get a working installation.
However, I've found that a source install, although a little slower,
more closely mirrors mysql installations on unix systems.

=over 4

=item Installing MySQL from source

=item 3a. Installing MySQL from source
=over 4

1. Download the source tarball from mysql.com
=item 1. Download the source tarball from mysql.com

% curl -O ftp://ftp.orst.edu/pub/mysql/Downloads/MySQL-4.0/mysql-4.0.13.tar.gz

2. Unpack and install the distribution
=item 2. Unpack and install the distribution

% gnutar -zxf mysql-4.0.12.tar.gz
% cd mysql-4.0.12
Expand All @@ -275,46 +285,59 @@ accordingly if they are.
% sudo make install
% sudo mkdir /usr/local/mysql/run

1. Configure the installation
=item 3. Configure the installation

% sudo /usr/local/mysql/bin/mysql_install_db --force # create var/ for DBs
% sudo chown -R mysql /usr/local/mysql/var /usr/local/mysql/run
% sudo chgrp -R mysql /usr/local/mysql

=item 3b. Installing MySQL from a precompiled package
=back

=item Installing MySQL from a precompiled package

=over 4

1. Download the package from mysql.com
=item 1. Download the package from mysql.com

http://www.mysql.com/downloads/

Find the "standard" release in pkg/dmg form and download it from a
nearby mirror. Double click the .dmg file and follow the typical
installer instructions. The package places everything in standard
paths (ie the mysql.sock is found in /etc/).
Find the "standard" release in pkg/dmg form and download it from a
nearby mirror. Double click the .dmg file and follow the typical
installer instructions. The package places everything in standard
paths (ie the mysql.sock is found in /etc/).

2. Configure the installation
=item 2. Configure the installation

% sudo chown -R mysql /usr/local/mysql/data
% sudo chgrp -R mysql /usr/local/mysql
% cd /usr/local/mysql
% sudo ./configure # installs the appropriate databases

=back

=back

=item 4. Starting MySQL

1. Start the mysql database daemon
=over 4

=item 1. Start the mysql database daemon

% sudo /usr/local/mysql/bin/mysqld_safe --user=mysql &
OR (for Fink installs):
% sudo /sw/bin/mysqld_safe &

2. Set a root user for the MySQL installation
=item 2. Set a root user for the MySQL installation

% mysqladmin -u root password 'new_password'

3. Finally, be sure to add the mysql/bin directory to your path.
=item 3. Finally, be sure to add the mysql/bin directory to your path.

4. You will also probably want to create a mysql user and group.
See the MySQL documentation for more information.
=item 4. You will also probably want to create a mysql user and group.

See the MySQL documentation for more information.

=back

=item 5. Installing libjpeg, libpng, gd, and GD

Expand All @@ -324,7 +347,7 @@ fink, there are path and versioning difficulties that have yet to be
worked out. In addition to <little> gd, there is <big> GD, a perl
library for interacting with little gd.

Install jpegsrc and libpng
Install jpegsrc and libpng

% curl -O ftp://ftp.uu.net/graphics/jpeg/jpegsrc.v6b.tar.gz
% gnutar -xzf jpegsrc.v6b.tar.gz
Expand All @@ -336,8 +359,8 @@ library for interacting with little gd.
% sudo ranlib /usr/local/lib/libjpeg.a
% popd

Now you need to compile the libpng code. This allows you to
manipulate PNG files.
Now you need to compile the libpng code. This allows you to
manipulate PNG files.

% curl -O http://www.libpng.org/pub/png/src/libpng-1.2.5.tar.gz
% gnutar -xzf libpng-1.2.5.tar.gz
Expand Down Expand Up @@ -417,7 +440,7 @@ files.
DBD::mysql looks for libmysqlclient.dylib in /usr/local/mysql/lib dyld
looks for it in /usr/local/mysql/lib/mysql/.

We remedy this conflict in the Makefile
We remedy this conflict in the Makefile

# Fetch DBD-mysql-2.9002 from CPAN
% gnutar xvfz DBD-mysql-2.9002
Expand Down Expand Up @@ -491,8 +514,8 @@ install it in the default locations for Apache.
% make
% sudo make install

Here I am using the default Sites folder to store the
gbrowse-specific files.
Here I am using the default Sites folder to store the
gbrowse-specific files.

=head2 --- Populating the database

Expand All @@ -506,7 +529,7 @@ need to let Apache know where they are. Specifically, this may
required modifying the DocumentRoot, adding a ScriptAlias, or creating
a VirtualHost. See the Apache documentation for more information.

You can start Apache by:
You can start Apache by:

% sudo /usr/sbin/apachectl start

Expand Down Expand Up @@ -547,7 +570,7 @@ Material in this document is copyright 2001-2003 by the Cold Spring
Harbor Laboratory. This information is provided "AS-IS" without any
warranty, expressed or implied.

$Id: INSTALL.MacOSX.pod,v 1.2 2003-11-24 14:06:39 tharris Exp $
$Id: INSTALL.MacOSX.pod,v 1.3 2003-12-01 18:15:08 scottcain Exp $

=cut

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