Good Afternoon Diego: This is the contents of your $HOME/.hg.conf file:
db.host=genome-mysql.cse.ucsc.edu db.user=genomep db.password=password Three lines exactly as listed above. That can be used for commands that require database access. See also: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 Most of the big* utility commands do not require database access. For the big* utility commands either supply a file name of a big* file you may have locally, or a URL to a remote big* file. The commands work the same way with either a local file or a URL. You do not need to fetch the files to use them. Just use the URL. All of the kent commands contain built-in usage messages. Simply run the command without arguments to see how to use them. Possible bigWig commands: bigWigInfo bigWigSummary bigWigToBedGraph bigWigToWig Use bigWigToWig to extract the values from the file. --Hiram Diego Pereira wrote: > Sorry for this question but, where can I find the $HOME/.hg.conf file to > set MySQL connection to the UCSC databases? > > How should I use the Kent source tree to query bigWig files (particularly > Orchid v1 and v2 tables) by position? > > Regards, > > Diego > > El 1 de diciembre de 2011 16:36, Diego Pereira > <[email protected]>escribió: > >> The 'make utils' command worked Hiram. >> >> Thanks! >> >> Now let's see if I can make the souce code work for me... >> >> Cheers >> >> Diego >> >> El 1 de diciembre de 2011 16:24, Hiram Clawson <[email protected]>escribió: >> >> If you want to install the CGI binaries in an Apache server, find out where >>> the html hierarchy for the Apache is and direct the build to place >>> everything >>> in that location. You can use the build scrips in src/product/scripts/ >>> after you set the variables in browserEnvironment.txt >>> View the README file there. >>> >>> However, you do not need the CGI binaries installed to build the command >>> line utilities. Try a 'make utils' from the src/ directory. >>> >>> --Hiram >>> >>> Diego Pereira wrote: >>> >>>> Thank you Hiram. >>>> >>>> Yeah you're right, but I would like to finish this installation first >>>> since >>>> I'll probably try several different tools in the near future. >>>> >>>> So, by reading the Readme.builing.source file, and found a work-around >>>> info >>>> about the apache folder. >>>> >>>> mkdir /usr/local/apache >>>> ln -s /var/www/cgi-bin-${LOGNAME} /usr/local/apache/cgi-bin >>>> >>>> It says the file exists and that the link was created. >>>> >>>> However, I'm still getting the same error as before. >>>> >>>> Many thanks again. >>>> >>>> Diego >>>> >>>> >>>> El 1 de diciembre de 2011 14:32, Hiram Clawson <[email protected] >>>>> escribió: >>>> Now that you have the libraries built, you can go to the directory of >>>>> the specific command you want to build and construct just that command. >>>>> You are attempting to construct the entire genome browser CGI binaries. >>>>> I believe you just want a couple of the big* commands. Note the >>>>> instructions in Step 3a of src/product/README.building.****source >>>>> >>>>> --Hiram >>>>> >>>>> Diego Pereira wrote: >>>>> >>>>> Thank you Hiram. >>>>>> Now I get this error: >>>>>> >>>>>> mv: cannot move `cartReset' to `/usr/local/apache/cgi-bin-** >>>>>> >>>>>> root/cartReset': >>>>>> No such file or directory >>>>>> make[2]: *** [my] Error 1 >>>>>> make[2]: Leaving directory `/usr/local/kent/src/hg/****cartReset' >>>>>> >>>>>> make[1]: *** [cartReset.bins] Error 2 >>>>>> make[1]: Leaving directory `/usr/local/kent/src/hg' >>>>>> make: *** [cgi] Error 2 >>>>>> >>>>>> As the error says I don't have an apache folder under my /usr/local >>>>>> folder. >>>>>> >>>>>> Thanks again. >>>>>> >>>>>> Diego >>>>>> >>>>>> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
