b70c24dfd5fa26cf2eded5becef8abd7ae5f2990 hiram Tue Aug 6 11:24:49 2013 -0700 add note about MySQL access refs #9149 diff --git src/userApps/README src/userApps/README index b49bb60..2e7a46a 100644 --- src/userApps/README +++ src/userApps/README @@ -1,170 +1,187 @@ ======================================================================== UCSC genome browser 'kent' 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: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/product ======================================================================== Pre-compiled binaries available: These binaries built at UCSC may already work in your linux/Mac environment. Please access via: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/ Or via FTP: ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/ ======================================================================== 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/ Optional: 'git' source code management: http://git-scm.com/downloads It is best to install these packages with your standard operating system package management tools. (see notes below about installing packages) ======================================================================== 1. Fetch the userApps directory: Alternative to 'git' command, a gzipped tar file is available with all the source, via FTP or HTTP: ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/userApps.src.tgz http://hgdownload.cse.ucsc.edu/admin/exe/userApps.src.tgz Unpacking that file (tar xvzf userApps.src.tgz) creates a directory: ./userApps/ with all the source. Proceed to step 2 to build this directory. Using 'git' to fetch the source, creates a directory ./userApps/ git archive --format=zip -9 \ --remote=git://genome-source.cse.ucsc.edu/kent.git \ beta src/userApps > userApps.zip unzip -d userApps -j userApps.zip cd userApps make fetchSource 2. Build the utilities: cd userApps make This build fetches (with git) approximately 200 Mb/7,800 files of kent source code, and constructs about 223 command binaries of approximate size near 600 Mb. The resulting binaries are in ./userApps/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. 3. Install utilities The binaries are built into ./userApps/bin/ To install them in a global bin/ directory, copy them to a desired location, e.g.: sudo rsync -a -P ./userApps/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. 4. Update utilities This procedure expects the 'git' command to be available. Without the 'git' command, run a 'make clean' to clean up the existing source tree, then repeat the fetch and unpack of the userApps.src.tgz file as mentioned in step 1. With the 'git' command available, the 'make update' will refresh the source tree and rebuild: cd userApps make update This runs a 'make clean' in the source tree, fetches all the source again, unpacks it to overlay the existing source tree, then runs a 'make utils' to rebuild everything. 5. There are 'parasol' binaries built into ./userApps/kent/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: 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 system installed: https://developer.apple.com/xcode/ And the Mac Ports install system: http://www.macports.org/ 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: https://help.ubuntu.com/8.04/serverguide/apt-get.html 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. ========================================================================