Thank you very much Vanessa for pointing me in the right direction!. I tried to install the source code as described in this page http://genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubuntubut I'm getting the following errors during the compilation:
cd kent/src/lib make bbiRead.c: In function ‘bbiTotalSummary’: bbiRead.c:703:34: error: variable ‘chromEnd’ set but not used [-Werror=unused-but-set-variable] bbiRead.c:703:22: error: variable ‘chromStart’ set but not used [-Werror=unused-but-set-variable] bbiRead.c:703:13: error: variable ‘chromId’ set but not used [-Werror=unused-but-set-variable] cc1: all warnings being treated as errors make: *** [bbiRead.o] Error 1 cd ../jkOwnLib make ffSeedExtend.c: In function ‘clumpToExactRange’: ffSeedExtend.c:218:57: error: variable ‘lastTe’ set but not used [-Werror=unused-but-set-variable] cc1: all warnings being treated as errors make: *** [ffSeedExtend.o] Error 1 I also tried to follow the instructions of the readme file included in the package but I got a little bit confused with the apache web server document root path, since I don't find a cgi-bin directory in it. (????) I finally set the environment variable MACHTYPE to i686 since I'm working on ubuntu x64, but I'm still getting the same error. My system settings are: Ubuntu 11.10 mysql-server 5.1.58 apache2.2.20 libmysqlclient16-dev libpng12-dev Finally I wonder if the utilities found in the source code will allow me to get the Orchid scores for selected intervals without having to download the entire bigWig files??? Many thanks for your help! Regards, Diego El 29 de noviembre de 2011 19:26, Vanessa Kirkup Swing <[email protected] > escribió: > Hi Diego, > > Most of our bigBed/bigWig/bam files used by our database entries are > available via URLs somewhere in the hierarchy: > http://hgdownload.cse.ucsc.edu/gbdb/and > in the readme file included in the package > <http://hgdownload.cse.ucsc.edu/gbdb/> > > The files that you see in the database schema, for example: > > /gbdb/some/path/name.bigFile > > can be found on our downloads site: > http://hgdownload.cse.ucsc.edu<http://hgdownload.cse.ucsc.edu/gbdb/some/path/name.bigFile>by > adding the file path found in the database schema to the URL like this: > > http://hgdownload.cse.ucsc.edu/gbdb/some/path/name.bigFile > > If you download the source code, there are utilities that can use the URL > path names. The utilities are listed here: > http://genomewiki.ucsc.edu/index.php/Kent_source_utilities and all the > ones that start with "big" you are able to utilize the URL path names. > > bigBedSummary:Extract summary information from a bigBed file. > bigBedToBed:Convert > from bigBed to ascii bed format. bigWigInfo:Print out information about > bigWig file. bigWigSummary:Extract summary information from a bigWig file. > bigWigToBedGraph:Convert from bigWig to bedGraph format. > > If using these utilities interest you, you can download the source code > from this page: > > http://genome.ucsc.edu/FAQ/FAQlicense.html#license3 > > > Our files are all for public use with the exception that there are some > restrictions regarding the publication of ENCODE data. Information > regarding the publication restrictions for ENCODE data can be found here: > http://genome.ucsc.edu/ENCODE/terms.html > > I hope this helps to clarify things for you. If you have further > questions, please contact the mailing list. > > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Diego F. Pereira <[email protected]> > Date: Tue, Nov 29, 2011 at 2:06 PM > Subject: RE: [Genome] Hg19 tables > To: Vanessa Kirkup Swing <[email protected]> > Cc: [email protected] > > > Few more questions about this topic... > The aforementioned files (bigBed, BigWig and bam) are intended to be used > just internally by the UCSC people or external users like me can do > something with them? > If the last is true, where can I find information about the usability? > Thanks, > Diego > > -----Original Message----- > From: Vanessa Kirkup Swing [mailto:[email protected]] > Sent: Thursday, September 15, 2011 2:02 PM > To: Diego F. Pereira > Cc: [email protected] > Subject: Re: [Genome] Hg19 tables > > Hi Diego, > > bigBed is also another file type that we store as a file in a table. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > On Thu, Sep 15, 2011 at 11:44 AM, Diego F. Pereira > <[email protected]> wrote: > > Thank you very much Vanessa. > > Best, > > Diego > > > > -----Original Message----- > > From: Vanessa Kirkup Swing [mailto:[email protected]] > > Sent: Thursday, September 15, 2011 1:28 PM > > To: Diego F. Pereira > > Cc: [email protected] > > Subject: Re: [Genome] Hg19 tables > > > > Hi Diego, > > > > The tables list a path to a file name. We have 2 different types of > > files types that we store as files in tables which are bigWig and bam. > > To find more information on those file types please take a look at > > this > > page: > > > > http://genome.ucsc.edu/FAQ/FAQformat.html > > > > I hope this information is useful. If you have further questions, > > please contact the mailing list: [email protected]. > > > > Vanessa Kirkup Swing > > UCSC Genome Bioinformatics Group > > > > > > ---------- Forwarded message ---------- > > From: Diego F. Pereira <[email protected]> > > Date: Thu, Sep 15, 2011 at 9:23 AM > > Subject: [Genome] Hg19 tables > > To: [email protected] > > > > > > Good morning, > > > > By reviewing the Hg19 database, I found several wgEncode tables that > > have just 2 fields (i.e. fileName and Field0). > > > > I would like to ask you what type of information they contain or where > > I can find some info about them. > > > > > > > > Best Regards, > > > > Diego > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
