This repository consists a portfolio for the master's project course "Applied Bioinformatics" taken during period 1 of fall semester 2015 at Uppsala University.

Our contribution concerning the addition of KEGG metabolic pathways on tracks details can be found under kent/cgi-bin/listPathways.py and kent/cgi-bin/Path.py.

More details are included in the report "Project_Report.pdf".

This directory contains the entire source tree for the UCSC Genome Bioinformatics Group's suite of biological analysis and web display programs as well as some of Jim Kent's own tools.
All files are copyrighted, but license is hereby granted for personal, academic, and non-profit use. A license is also granted for the contents of the src/lib, src/inc and src/utils and python directories for commercial users. Commercial users should contact kent@soe.ucsc.edu for access to other modules. Commercial users interested in the UCSC Genome Browser in particular please see http://genome.ucsc.edu/license/.

Most source code users will only be interested in the src/inc and src/lib directories, which contain the interfaces and implementations to the library routines, and in a few specific applications. The applications are scattered in other directories. Many of them are web based.
The UCSC Genome Browser in particular is mostly found in src/hg/hgTracks.

GENERAL INSTALL INSTRUCTIONS

1. Get the code. The best way to do this now for Unix users is via Git following the instructions at: http://genome.ucsc.edu/admin/git.html Or, fetch the entire source in a single file: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip Note further documentation for the build process in your unpacked source tree in src/product/README.* Especially note README.building.source and the "Known problems" for typical situations you may encounter.
2. Check that the environment variable MACHTYPE exists on your system. It should exist on Unix/Linux.
   (And making this on non-Unix systems is beyond the scope of this README). The default MACHTYPE is often a long string: "i386-redhat-linux-gnu" which will not function correctly in this build environment. It needs to be something simple such as one of: i386 i686 sparc alpha x86_64 ppc etc ... with no other alpha characters such as: - To determine what your system reports itself as, try the uname options: 'uname -m' or 'uname -p' or 'uname -a' on your command line. If necessary set this environment variable. Do this under the bash shell as so: MACHTYPE=something export MACHTYPE or under tcsh as so: setenv MACHTYPE something and place this setting in your home directory .bashrc or .tcshrc environment files so it will be set properly the next time you login. Remember to "export" it as show here for the bash shell.
3. Make the directory ~/bin/$MACHTYPE which is where the (non-web) executables will go. Add this directory to your path.
4. Go to the src/lib directory. If it doesn't already exist do a mkdir $MACHTYPE.
5. Type make. On Alphas there will be some warning messages about "crudeAli.c" otherwise it should compile cleanly. It's using gcc.
6. Go to src/jkOwnLib and type make.
7. Go to the application you want to make and type make. (If you're not sure, as a simple test go to src/utils/fixcr and type make, then 'rehash' if necessary so your shell can find the fixcr program in ~/bin/$(MACHTYPE). The fixcr program changes Microsoft style line terminations to Unix style terminations. Look at the "gotCr.c" file in the fixCr directory, and then do a "fixcr gotCr.c" on it.

INSTALL INSTRUCTIONS FOR BLAT

1. Follow the general install instructions above.
2. If you're on an alpha system do a: setenv SOCKETLIB -lxnet on Solaris do setenv SOCKETLIB "-lsocket -lnsl" on SunOS do setenv SOCKETLIB "-lsocket -lnsl -lresolv" on Linux you can skip this step.
3. Execute make in each of the following directories: src/gfServer src/gfClient src/blat src/utils/faToNib

INSTALL INSTRUCTIONS FOR CODE USING THE BROWSER DATABASE (and other code in the src/hg subdirectory)

1. Follow the general install instructions above.
2. Make the environment variable MYSQLINC point to where MySQL's include files are. (On my system they are at /usr/include/mysql.) While you're at it set the MYSQLLIBS variable to point to something like /usr/lib/mysql/libmysqlclient.a -lz When available, the commands: mysql_config --include and mysql_config --libs will display the required arguments for these environment settings.
3. Execute make in src/hg/lib
4. Execute make in the directory containing the application you wish to build.
5. See also: http://genome.ucsc.edu/admin/jk-install.html and more documentation in this source tree about setting up a working browser in README files: src/product/README.building.source src/product/README.local.git.source src/product/README.mysql.setup src/product/README.install src/product/README.trackDb src/hg/makeDb/trackDb/README There are numerous README files in the source tree describing functions or modules in that area of the source tree. The src/README in particular should be read by anyone modifying the C source code, and python/README by anyone modifying the Python.