40c4d8dae2dcdb5ce1793bcfa999fd753b1c861e max Tue Feb 6 07:05:20 2024 -0800 documenting the online/offline and dev options in GBIC, no ticket diff --git src/README src/README index be422cc..a9fa12e 100644 --- src/README +++ src/README @@ -41,30 +41,44 @@ are called from web pages or just want to make web pages. o - htmlPage - Read html pages, programatically submit html forms. o - memgfx - Creates a 256 color image in memory which can be drawn on, then saved as a .GIF file which can be encorperated into a web page. o - dnautils and dnaseq - Simple utilities on DNA. o - fa - Read/write fasta format files. o - basicBed - Functions for working with BED format files. o - psl - Functions for working with PSL (blat) format files. o - twoBit - Functions for working with twoBit DNA files. o - bPlusTree - Create/user B+ Tree indexes, the backbone of many databases. o - udc - URL Data Cache - code to locally cache remote files. +DEVELOPING FOR THE GENOME BROWSER + +To add features to the Genome Browser, you first need to setup your own Genome +Browser "Mirror", including Apache, MySQL databases, /gbdb data files, HTML and +Javascript and the C CGI programs. The easiest way by far is to get a fresh +Ubuntu/Rocky VM or container and run the GBIC installation script: +https://genome.ucsc.edu/goldenpath/help/gbic.html + +You can use the option "install" to set up a genome browser, the option +"mirror" to download a small database (e.g. yeast, sacCer3), use hg38 via +remote loading of the data from UCSC. Use the option "dev" to clone the kent +repo, install dependencies and build the code into the mirror you just +installed. + CODE CONVENTIONS INDENTATION AND SPACING: The code follows an indentation convention that is a bit unusual for C. Opening and closing braces are on a line by themselves and are indented at the same level as the block they enclose: if (someTest) { doSomething(); doSomethingElse(); } Each block of code is indented by 4 from the previous block. As per Unix standard practice, tab stops are set to 8, not 4