Hi Hiram, I forgot to ask you:
1- With your system of uploading CT directly into the DB, are we still able to use the Genome Browser Custom Track Session system? 2- Is this session system also manage through a database or is an independent system or is it linked to genome-wiki? 3- can we use the session system only locally? If yes, what do we need to use it? Thanks, Regards, Chris PS: maybe I should have open a new threads for these questions. -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: Friday, February 19, 2010 11:49 PM To: Christophe Legendre Cc: [email protected] Subject: Re: [Genome] Custom Track Adding and UCSC Genome Mirroring Good Evening: With your own local mirror of the genome browser you can load your tracks directly into the database. You do not need to load them as custom tracks. When you load local bigData files, the entry in the database is simply a local file name, it does not have to be a URL to an FTP or HTTP server. The loading sequence is like this: # create symLink from location where data file exists to a global # location for everything related to this database: ln -s `pwd`/localBigData.bam /gbdb/hg19/bbi/ # create the database table, a single column, the contents can be # this local file name, or a URL to an external resource hgsql hg19 -e 'drop table if exists localBigData; \ create table localBigData (fileName varchar(255) not null); \ insert into localBigData values ("/gbdb/hg19/bbi/localBigData.bam");' This will be a lot more convenient than trying to maintain the custom tracks database. See also: http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/README.trackD b http://genome-test.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/REA DME --Hiram [email protected] wrote: > Hello All, > > To date, when we want to add a custom track to the Genome Browser using > BAM file, we can enter in the bigDataURL field a HTTP or FTP location as > address where the BAM file and its pair-indexed file are. > > We are going to install locally a mirror of the UCSC Genome Browser. > > Then, we are going to create and add Custom Tracks to this mirror but > locally. > > Is there any possibility to give the address of file on a machine from a > local network (such as > /mymachine/bam_folder/MyBAMs/exp002/mybamfile.bam) into this bigDataUrl > field ? > > In the meantime, is it possible to customized the lifetime of the tracks > within the local Genome Browser Mirror in order to get more than 48 > hours storage? > > Thanks for your replies > > Best Regards, > > Dr Christophe LEGENDRE > > TGen, PHX, USA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
