Institute of Bioinformatics WWU Münster
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Install the UCSC Browser in FreeBSD

Remarks

  • This is a description about the scripts that will do a more-or-less automatic installation of the ucsc browser in FreeBSD 10.2. It should work in previous (10.*) and coming releases, too.
  • It is the best to install the browser in a jail (container / virtual environment). The describtion of setup a jail is not focus of this documentation. But it is easy to do and programs executed in a jail perform with the speed of the "native" host environment. The advantage of using a jail environment is that you can easily restart or delete the installed ucsc brwoser without affecting thehost system.
  • The installation of apache and mysql is done in the folder /ucsc.
  • The port used for the web browser is by default 50300. This can easily be adapted to needs.

How to

Preparation

This has only to be done once, as long as you don't want to take newer installation scripts - but changes to them will only happen very rarely.
Be user root (for all following actions!) and execute
cd /root
mkdir ucsc
cd ucsc
wget http://www.bioinformatics.uni-muenster.de/download/ucsc/install-ucsc.tgz
tar -xvzf install-ucsc.tgz
rm install-ucsc.tgz
The file ucsc.conf provides basic settings for installation and upgrade. Please change it if you would like to change the web user or mysql password.

Installation

The installation of the browser is done with the command
cd /root/ucsc
./install
The time taken for installation and upgrade can be about 1 hour, depending on used hardware and internet connection. (what means: take a coffee brake :-))

Upgrade

The upgrade of the browser is done with the command
cd /root/ucsc
./upgrade
It will upgrade binaries and the html files to the newest version.
The old directories will be renamed to *.old (in folder /ucsc/apache), so if something fails, the old state can easily be restored by renaming appl.old and htdocs.old back to appl and htdocs.