Hg.conf

Please note the example template hg.conf file in the source tree: src/product/ex.hg.conf and related discussions in the README.mysql.setup source tree file and other README.* information in that directory.

There are usually at least *two* hg.conf files:

• A file called .hg.conf in the home directory of each genome annotator / user. This file is used by the command line tools like overlapSelect, featureBits, hgLoadBed etc to find a copy of the UCSC genome browser database that they run on.
• A file called hg.conf in the CGI directory of the webserver, e.g. /usr/local/apache/cgi-bin. This file is used by the genome browser itself when run from a webbrowser / the webserver.

There should be discussion in there of the options and what you may need. A minimal .hg.conf could look this this:

db.host=localhost
db.user=readonly
db.password=access

There are several settings in the hg.conf file to note:

• db.trackDb can be set to one or multiple trackDb tables. The tables are listed in the order of priority. If the first and second trackDb table both have a row where the tableName is the same, the row from the first table is used. Otherwise the rows of the tables are all added together into one giant trackDb table.
• If you are running a mirror website, you better comment out the "bottleneck" statements. Otherwise your alignment tracks won't work.