- - - -
-
- Visit our Video Page.
-
- 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) or our public website. Please see the Installation of a UCSC Genome Browser on a local machine (mirror) page for a summary of installation options, including the pros and cons of using a mirror -installation via the GBiC program vs. using GBiB. GBiC can also be used as a Docker container. See -the Docker help page for more information. +installation via the GBiC program vs. using GBiB. GBiC can also be used as a Docker container. +See our Docker help page 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.
@@ -75,50 +75,41 @@sudo bash browserSetup.sh install
The install command downloads and configures Apache, MySQL (MariaDB) and Ghostscript, copies the
Genome Browser CGIs, and configures the mirror to load data remotely from UCSC. The install
command must be run before any other command is used.
For mirror-specific help, please contact the Mirror Forum as listed on our contact page.
For an installation demonstration, see the Genome Browser in the Cloud (GBiC) Introduction
-video:
-
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-
-
-
- Visit our Video Page.
-
-
Visit our YouTube channel for more videos. -
- +video:+ + +
+
The GBiC program downloads the Genome Browser CGIs and sets up the central MySQL (MariaDB) database.
All potentially destructive steps require confirmation by the user (unless the -b batch mode
option is specified).
In particular, MySQL (MariaDB) and Apache are installed and set up with the right package manager
(yum or apt-get). A default random password is set for the MySQL (MariaDB) root user and added to
the ~/.my.cnf file of the Unix root account. If you have already set up MySQL (MariaDB), you must
create the ~/.my.cnf file. The program will detect this and create a template file for you. The
program also performs some minor tasks such as placing symlinks, detecting MariaDB, deactivating
@@ -247,30 +238,37 @@
sudo bash browserSetup.sh -t noEncode mirror hg19
For a full list of -t options, see the 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: