Hg.conf: Difference between revisions
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Please note the example template hg.conf file in the source tree | Please note the example template hg.conf file in the source tree | ||
[http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/ex.hg.conf src/product/ex.hg.conf] | [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/ex.hg.conf src/product/ex.hg.conf] | ||
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. | 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 | * 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]] | ||
Revision as of 10:07, 28 January 2011
Please note the example template hg.conf file in the source tree src/product/ex.hg.conf
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.
