3091ba51499288c02b9bafb87b6ae937320c6344 max Mon Feb 1 08:20:52 2021 -0800 adding note about what the uniprot other track contains to uniprot docs, refs #26889 diff --git src/product/README.QuickStart src/product/README.QuickStart deleted file mode 100644 index ade5c33..0000000 --- src/product/README.QuickStart +++ /dev/null @@ -1,73 +0,0 @@ - -Getting a browser up and running quickly in a minimal state -(see also: http://genomewiki.ucsc.edu/index.php/Browser_installation) - -The browser can be made to operate with a bare minimum of tables -for the purpose of demonstrating the CGI binaries are functioning. - -The only tables you need to load for this are: - -1. all tables in the hgcentral database -2. six tables in the human genome - -Create an empty hgcentral database: -$ hgsql -e "create database hgcentral;" mysql - -Load all tables into the hgcentral database. -Copy all the mysql data files from - rsync -avP rsync://hgdownload.soe.ucsc.edu/mysql/hgcentral/ . -directly into the MySQL data area for your hgcentral database. -(something usually like /var/lib/mysql/hgcentral/) -(or load this database with mysql/hgsql commands and the hgcentral.sql - text file dump of these tables from: - rsync -avP rsync://hgdownload.soe.ucsc.edu/genome/admin/hgcentral.sql . - (or: http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql) -) - -And then six tables for the latest human database. -The gateway page always needs a minimum human database in order -to function even if the browser is being built for the primary -purpose of displaying other genomes. This default can currently -be changed in the source tree in src/hg/lib/hdb.c -(to be done: specify this default in hg.conf file) - -Start with an empty database, for example hg18: -$ hgsql -e "create database hg18;" mysql - -Again, copy the MySQL files directly from the download -server, for example hg18: - rsync -avP rsync://hgdownload.soe.ucsc.edu/mysql/hg18/ . - (beware, this is an immense amount of data) -into your MySQL data area. Or load these tables from the text SQL -dumps from: - rsync -avP rsync://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ . - (beware, this is an immense amount of data) - -The minimal set of tables required are: -grp -trackDb -hgFindSpec -chromInfo -gold -gap - -The gap table is an example of the split table concept for performance -purposes. It consists of the tables: chr*_gap which is a total -of 49 tables just for the gap track. (3 * 49 = 147 MySQL data files) - -(each MySQL data table is three files: .MYD .MYI and .frm files) - -With this set of six tables the gateway page will -begin to function and the browser page and table browser -will function. Other browser functions are not ready yet without -additional tables and databases. This is a bare minimum just to -demonstrate the CGI binaries are working. - -This will all work even without copying any files for the /gbdb/ -data area, although most functions will not work, such as fetching -the DNA sequence from a browser view. The DNA sequence for -an assembly is found in, for example hg18: /gbdb/hg18/nib/chr*.nib -Some assemblies have all the DNA sequence in a single .2bit file, -for example: /gbdb/mm8/mm8.2bit - -====================================================================