For a quick work-around since this isn't a genome that actually needs this particular database, try simply creating an empty database:
$ hgsql -e "create database proteins040315;" mysql If that doesn't work, download the actual protein databases, from, for example: ftp://hgdownload.cse.ucsc.edu/mysql/proteins040315/ or text dumps: ftp://hgdownload.cse.ucsc.edu/goldenPath/proteinDB/proteins040315/database/ or rsync rsync -avz --progress rsync://hgdownload.cse.ucsc.edu/mysql/proteins/040315/ or sync -avz --progress rsync://hgdownload.cse.ucsc.edu/goldenPath/proteinDB/proteins040315/database/ It may need the other protein databases too. --Hiram Jaysheel Bhavsar wrote: > Hi Hiram, > I am not sure if that is what need to be done hear, I am not yet > familiar with the browsers working. When it get to the "base" level of the > view, and click on a region of the bed file that I uploaded, I get the > following error message > > Couldn't connect to database proteins040315 on xxxx.edu as yyyy. Unknown > database 'proteins040315' > > (xxxx= host name, and yyyy=usename for mysql) > > how are the proteinsX tables create? I understand that system is looking for > proteins040315 database because that is what 'default' points to in gdbPdb > table. > > Does this help? > > Thank you > Jay > > On Apr 1, 2010, at 11:57 AM, Hiram Clawson wrote: > >> Good Morning Jay: >> >> It isn't clear what you are referring to here. >> >> Do you say you have protein sequences that you want to load into the genome >> browser ? >> >> To do that, you need to align the proteins to the genome with an aligner, >> for example blat. Once you have those positions as psl files, you can load >> the psl file as a track in the genome browser. >> >> --Hiram >> >> Jaysheel Bhavsar wrote: >>> Hi guys, >>> I am very new at this genome viewer business, so please bare with me if >>> I don't have the terminology or understanding of the inner workings. I >>> need to get genome browser up and running for genome that we have in the >>> lab. I have been able to get a local copy of genome browser up and >>> running, and have been able to add a custom track, along with gc5Base, and >>> wiggle info as described here >>> (http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database). >>> Everything seem to work as expected (I haven't played around with all the >>> options in trackDb.ra, but that will come later). >>> Issue 1: >>> Now the issue is that I am not able to get to the actually proteins/seq >>> for the tracks loaded. From what I understand I can create an entry in >>> gdbPdb, which seems straight forward (insert statement with org db name >>> like hg18 and proteinsX name). But I can't see find information as to what >>> needs to be in proteinesX database. I wasn't able find a utility or hgX >>> loader script either (unless I missed it). Could someone please point me >>> in the right direction, as to how to upload my protein/seq data. >>> Issue 2: >>> I have some metadata associated with each chromosome that I loaded into >>> db, is there a way to show that info on the browser? I have a tab >>> delimited file of protein id, gotermId and go annotations. >>> Thank you Jay > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
