Good afternoon Hiram, I tried the following and some variations but I couldn't make it work.
bigWigToWig http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig-chrom=chr1 -start=1000 -end=1010 May I ask you to write it down correctly? Many thanks, Diego El 1 de diciembre de 2011 18:47, Hiram Clawson <[email protected]>escribió: > Good Afternoon Diego: > > This is the contents of your $HOME/.hg.conf file: > > db.host=genome-mysql.cse.ucsc.**edu <http://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<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
