Jim Kent command line bioinformatic utilities
These are only the command line bioinformatic utilities from the kent source tree. This is not the genome browser install. For the genome browser install, use the instructions from the source tree:
- Linux/Ubuntu/CentOS/Unix/MacOSX operating system
- gnu gcc - C code development system - http://www.gnu.org/software/gcc/
- gnu make - http://www.gnu.org/software/make/
- MySQL development system and libraries - http://dev.mysql.com/
- libpng runtime and development packages - http://www.libpng.org/
- libssl runtime and development packages - http://www.openssl.org/
- 'git' source code management: http://git-scm.com/downloads
These procedures expect the 'git' command to be available.
It is best to install these packages with your standard operating system package management tools. See also: notes below about installing packages.
Obtain a read-only copy of the source:
git clone git://github.com/ENCODE-DCC/kentUtils.git
Creates the directory: ./kentUtils/
In the directory kentUtils/ run a 'make' command:
cd kentUtils
make
The resulting binaries are placed in the directory: ./bin/
Note: there are no required shell environment settings as discussed
in the genome browser build instructions. In fact, this build
system will ignore and override any shell environment settings
you may have for the genome browser build environment.
The binaries are built into ./bin/
To install them in a global bin/ directory, copy them to a desired location, for example:
sudo rsync -a -P ./bin/ /usr/local/bin/kentUtils/
The destination bin/kentUtils/ should be its own unique directory to avoid overwriting same-named binaries in a standard bin/ directory.
Users add '/usr/local/bin/kentUtils' to their shell PATH to access the commands.
This procedure expects the 'git' command to be available.
With the 'git' command available, the 'make update' will refresh the source tree and rebuild. In this directory:
make update
This runs a 'make clean' in the source tree, runs a 'git pull' update for the source, then runs a 'make utils' to rebuild everything.
There are 'parasol' binaries built into ./src/parasol/bin/ Use these binaries to set up a job control system on a compute cluster or large machine with many CPU cores. See also: parasol README for more information. The usage messages from each command will help with the setup.
Each 'kent' command contains its own documentation. Simply run the commands without any arguments to see the usage message for operating instructions.
When the utilities are built here, their usage messages have been collected together in one file:
kentUtils.Documentation.txt
Many of the commands can use the UCSC public MySQL server, or your own local MySQL server with UCSC data formats. Add these three lines to a file in your HOME directory called '.hg.conf' and set its permissions to: 'chmod 600 .hg.conf'
db.host=genome-mysql.cse.ucsc.edu
db.user=genomep
db.password=password
This '.hg.conf' file is used by the kent commands to determine the MySQL host and user/password to the database. For your local MySQL installation, use your host name and your read-only user/password names.
On a MacOS system, you will need the XCode system installed.
And the Mac Ports install system.
With the Mac ports and XCode systems installed, you can install the additional packages required (and helpful):
sudo port install git-core gnutls rsync libpng mysql55 openssl curl wget
On a typical Linux system, for example Ubuntu, use the apt-get command to install additional packages:
sudo apt-get install git libssl-dev openssl mysql-client-5.1 mysql-client-core-5.1
Depending upon the version of your Linux/Ubuntu/CentOS operating system, the specific version of packages you need may be different than this example.
Please use your standard operating system package management install system (e.g. 'yum' on CentOS) to obtain correct versions of these packages for your specific operating system version.
See also:
Please advise UCSC if you have the recommended installed libraries and development system and this build will not function. email to: [email protected]. edu
- These procedures will not work as-is on sparc or alpha machines or with the Sun Solaris operating system.
- 16 Jul 2014 - brought up to date to version 302 source
- 17 Dec 2013 - brought up to date from version version 286 to version 293 source
============================================================================