diff --git a/README.md b/README.md index e811845..969ff38 100644 --- a/README.md +++ b/README.md @@ -1,179 +1,24 @@ -kentUtils -==================== - PLEASE NOTE: This repository is not the UCSC Genome Browser source code repo, but an outdated collection of some UCSC binary tools from -2014 used by the ENCODE DCC. For up to date source and binary images -please refer to: +2014 used by the ENCODE DCC. If you are looking for compiled +binary command line programs from the UCSC Genome Browser group, please +download them from our server: - http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads - http://hgdownload.soe.ucsc.edu/admin/exe/ + +More instructions about our source code: + + http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads +The UCSC Genome Browser source code Github repository: + https://github.com/ucscGenomeBrowser/kent 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, see instructions: +For a genome browser local installation, see these instructions: http://genome.ucsc.edu/goldenPath/help/mirror.html -System Requirements -------------------- - -* 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](https://github.com/ENCODE-DCC/kentUtils#installing-required-packages) about installing packages. - - -Download source ---------------- - -Obtain a read-only copy of the source: - - git clone git://github.com/ENCODE-DCC/kentUtils.git - -Creates the directory: ./kentUtils/ - -Build utilities ---------------- - -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. - -Install utilities ------------------ - -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. - -Update utilities ----------------- - -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. - -Parasol -------- - -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](http://genecats.cse.ucsc.edu/eng/parasol.htm) -for more information. The usage messages from each command will help -with the setup. - -Documentation -------------- - -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 - -MySQL database access ---------------------- - -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. - -Installing required packages ----------------------------- - -On a MacOS system, you will need the [XCode](https://developer.apple.com/xcode/) -system installed. - -And the [Mac Ports](http://www.macports.org/) 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: - -* [apt-get](https://help.ubuntu.com/8.04/serverguide/apt-get.html) -* [yum](http://www.centos.org/docs/5/html/yum/) - -Known Problems --------------- - -Please advise UCSC if you have the recommended installed libraries -and development system and this build will not function. -email to: -genome-www@soe.ucsc. -edu - -1. These procedures will not work as-is on sparc or alpha machines or - with the Sun Solaris operating system. - -Update history --------------- -* 14 Mar 2018 - add note about this being obsolete and point to current sources -* 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 -============================================================================