08320469134fa85d4162a1927ed3659af7e2fbe3
mspeir
  Mon Apr 28 18:57:20 2025 -0700
adding note about update command being compatible with db names and add lines about GBiC+Docker that were not in the .md file, refs #25120

diff --git src/product/installer/README.md src/product/installer/README.md
index 91ced6388ac..0962c6fad28 100644
--- src/product/installer/README.md
+++ src/product/installer/README.md
@@ -1,27 +1,28 @@
 % Genome Browser in the Cloud User's Guide
 
 # What is Genome Browser in the Cloud?
 
 The Genome Browser in the Cloud (GBiC) program is a convenient tool that automates the setup of a
 UCSC Genome Browser mirror. The GBiC program is for users who want to set up a full mirror of the 
 UCSC Genome Browser on their server/cloud instance, rather than using 
 [Genome Browser in a Box](gbib.html) (GBIB) 
 or our public website. Please see the 
 [Installation of a UCSC Genome Browser on a local machine (mirror)](mirror.html#considerations-before-installing-a-genome-browser)
 page for a summary of installation options, including the pros and cons of using a mirror
-installation via the GBiC program vs. using GBiB.
+installation via the GBiC program vs. using GBiB. GBiC can also be used as a Docker container.
+See our [Docker help page](docker.html) for more information.
 
 The program works by setting up MySQL (MariaDB), Apache, and Ghostscript, and then copying the
 Genome Browser CGIs onto the machine under `/usr/local/apache/`. Because it also deactivates the
 default Apache htdocs/cgi folders, it is best run on a new machine, or at least a host that is not
 already used as a web server. The tool can also download full or partial assembly databases,
 update the Genome Browser CGIs, and remove temporary files (aka "trash cleaning").
 
 The GBiC program has been tested and confirmed to work with Ubuntu 18/20/22/24 LTS,
 Rocky 9.5, and Fedora 30/35/41.
 
 It has also been tested on virtual machines in Amazon EC2 (Centos) and Microsoft Azure (Ubuntu).
 
 If you want to load data on the fly from UCSC, you need to select the 
 data centers "US West (N. California)" (Amazon) or "West US" (Microsoft) for best performance. 
 Other data centers (e.g. East Coast) will require a local copy of the genome assembly, which 
@@ -151,30 +152,35 @@
 which may result in errors if your CGIs and 2bit files have not been updated to the latest version.
 
 The full assembly download for hg19 is >7TB. Limit this
 to 2TB or less with the `-t` option: 
 
     sudo bash browserSetup.sh -t noEncode mirror hg19
 
 For a full list of `-t` options, see the [All GBiC options](#all-gbic-options) section or run the 
 program with no arguments.
 
 To update all CGIs and fully mirrored assemblies, call the
 tool with the `update` parameter like this: 
 
     sudo bash browserSetup.sh update
 
+The `update` parameter can also be used to update the data for a single assembly by providing the
+UCSC assembly name (e.g. rn6, bosTau6, equCab3):
+
+    sudo bash browserSetup.sh update bosTau9
+
 Minimal mirror sites (those that have partially mirrored an assembly) should not 
 use the `update` command, but rather just rerun the `minimal` command, so that only the minimal
 tables are updated. For instance, if you have partially mirrored the hg19 and hg38 databases,
 you may want to add this command to your crontab, perhaps running it every day, to keep your local 
 tables in sync with those at UCSC:
 
     sudo bash browserSetup.sh minimal hg19 hg38
 
 To update only the Genome Browser software and not the data, use the
 `cgiUpdate` command: 
 
     sudo bash browserSetup.sh cgiUpdate
 
 Software may break or not work correctly if the necessary data is not available. 
 Thus in most circumstances, we recommend you use the `mirror`, `update`, or `minimal` commands