Hg.conf: Difference between revisions

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The hg.conf file goes in the CGI dir e.g. /usr/local/apache/cgi-bin. There are several settings in the hg.conf file to note:
'''NOTE''': This page is not necessarily maintained with the most up-to-date information.  The information in the README files in the source tree is guaranteed to be current: [http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/product src/product]
 
Please note the example template hg.conf file in the source tree:
[http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/ex.hg.conf src/product/ex.hg.conf]
and related discussions in the [http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.mysql.setup 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:
 
<pre>
db.host=localhost
db.user=readonly
db.password=access
</pre>
 
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.
* '''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're mirror, you better comment out the "bottleneck" statements. Otherwise your alignment tracks won't work.
* If you are running a mirror website, you better comment out the "bottleneck" statements. Otherwise your alignment tracks won't work.


[[Category:Mirror Site FAQ]]
[[Category:Mirror Site FAQ]]
[[Category:Browser Development]]
[[Category:Browser Development]]
[[category:installation]]

Latest revision as of 16:49, 16 May 2012

NOTE: This page is not necessarily maintained with the most up-to-date information. The information in the README files in the source tree is guaranteed to be current: src/product

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.