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.
-The program works by setting up MySQL, Apache, and Ghostscript, and then copying the Genome
+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 with Ubuntu 14/16 LTS, Centos 6/6.7/7.2, and Fedora 20.
It has also been tested on virtual machines in Amazon EC2 (Centos 6 and Ubuntu 14) 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 @@ -55,129 +55,129 @@
Download the GBiC program from the UCSC Genome Browser store.
Run the program as root, like this:
sudo bash browserSetup.sh install
-The install command downloads and configures Apache, MySQL and Ghostscript, copies the Genome Browser
+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:
-The GBiC program downloads the Genome Browser CGIs and sets up the central MySQL database. All
+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 and Apache are installed and set up with the right package
+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 root user and added to the ~/.my.cnf file of the Unix root account.
-If you have already set up MySQL, you must create 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 SELinux, finding the correct path for your Apache install
-and adapting the MySQL socket config.
+and adapting the MySQL (MariaDB) socket config.
This will result in a Genome Browser accessible on localhost that loads its data
through genome-mysql.soe.ucsc.edu:3306 and hgdownload.soe.ucsc.edu:80. If
your geographic location is not on the US West Coast, the performance will be too slow for normal
-use, though sufficient to test that the setup is functional. A special MySQL server is
+use, though sufficient to test that the setup is functional. A special MySQL (MariaDB) server is
set up in Germany for users in Europe. You can change the /usr/local/apache/cgi-bin/hg.conf
genome-mysql.soe.ucsc.edu lines to genome-euro-mysql.soe.ucsc.edu in order to get better
performance. You can then use the program to download
assemblies of interest to your local Genome Browser, which will result in performance at least
as fast as the UCSC site.
Your network firewall must allow outgoing connections to the following servers and ports:
The first argument of the program is called command in the following section of this document.
The first command that you will need is install, which installs the Genome Browser dependencies,
-binary files and basic MySQL infrastructure:
+binary files and basic MySQL (MariaDB) infrastructure:
sudo bash browserSetup.sh installThere are a number of options supported by the GBiC program. In all cases, options must be specified before the command.
The following example correctly specifies the batch mode option to the program:
sudo bash browserSetup.sh -b install
To improve the performance of your Genome Browser, the program accepts the command
minimal. It will download the minimal tables required for reasonable
performance from places in the US and possibly others, e.g., from
Japan. Call it like this to trade space for performance and download a few
-of the most used MySQL tables for hg38:
+of the most used MariaDB tables for hg38:
sudo bash browserSetup.sh minimal hg38
If the Genome Browser is still too slow, you will have to mirror all tables of a
genome assembly. By default, rsync is used for the download. Alternatively you can use
UDR, a UDP-based fast transfer protocol (option: -u).
sudo bash browserSetup.sh -u mirror hg38
A successful run of mirror will also cut the connection to UCSC: no tables
or files are downloaded on-the-fly anymore from the UCSC servers. To change