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UCSC Genome Browser Store
All Software Products available below are free for non-commercial use by any Independent Researcher or Nonprofit Organization, as set forth in the End User License Agreement (EULA) (such use can be claimed during checkout).
Any other use requires purchase of a license, and certain products also require a one-time setup fee. Licenses for 50+ users may be eligible for Enterprise license terms; please contact us for more details. All use of Software Products is governed by the EULA, and capitalized terms on this page have the same meaning as set forth in the EULA.
Genome Browser in a Box (GBiB)
Cost for non-commercial use by nonprofit entity: Free
For all other use:
One time setup fee: $1000
Cost per year per user: $1100 (1 user minimum)
For all other use:
One time setup fee: $1000
Cost per year per user: $1100 (1 user minimum)
Genome Browser in a Box (GBiB) is a small, virtual machine version of the UCSC Genome Browser that can be run on your own laptop or desktop computer. Annotation data is loaded on demand through the Internet from UCSC or can be downloaded to your machine for faster access. Once GBiB is installed, you use a web browser to access the virtual server running on your own machine and add personal data files from your local hard disk. A more detailed description of this tool and how to use it is available at https://genome.ucsc.edu/goldenpath/help/gbib.html.
Terms and conditions (last modified 2022-01-31)
Size: 10.8 GB
System Requirements:
GBiB will run on most modern PCs and major operating systems that meet these basic requirements:
GBiB will run on most modern PCs and major operating systems that meet these basic requirements:
- The computer must support virtualization (common for most PCs sold after 2010).
- A compatible version of the VirtualBox Software must be installed. This software is free to use in many situations. See the VirtualBox wiki for licensing terms and conditions and installation instructions. We have tested and confirmed that GBiB works using version 4.3.6 or above. Note that you must have administrator rights for your computer to install VirtualBox.
- The computer disk must have at least 25 GB of free space (more if you plan to mirror many tracks).
- Your network firewall must allow connections on the following ports:
- Port 3306, used by MySQL. Without this, only mirrored tracks are shown.
- TCP port 873, used by rsync. Without this, you cannot download track data.
- The GBiB product includes executable versions of LINUX, Apache, and MySQL. Please follow the links to determine if you have the correct license for each of these open source programs
- The Online Mendelian Inheritance in Man (OMIM) content in the GBiB is copyrighted and owned by Johns Hopkins University. Use of the copyrighted material solely within GBiB is permitted. Redistribution or repackaging of the copyrighted material requires a license from Johns Hopkins University.
Product Includes:
- The Genome Browser in a Box setup program. This program:
- downloads the Genome Browser CGIs, HTML, and Javascript files
- configures the machine to download supporting data files from UCSC
- (optionally) downloads the UCSC command line tools to itself
- automatically updates software (including non-gb software) and data
- Pre-downloaded version of the hg19 database (not the full set but a majority of tables).
- Pre installed versions of Apache and MySQL.
Product does not Include:
- The UCSC Genome Browser source code.
- Virtual Machine software required to run GBiB.
Genome Browser in the Cloud (GBiC)
Cost for non-commercial use by nonprofit entity: Free
For all other use:
One time setup fee: $2000
Cost per year per user: $1000 (1 user minimum)
For all other use:
One time setup fee: $2000
Cost per year per user: $1000 (1 user minimum)
Genome Browser in the Cloud (GBiC) is a convenient program that automates the setup of a UCSC Genome Browser mirror, including the installation and setup of MariaDB and Apache servers. The program downloads and configures MySQL and Apache, then downloads the UCSC Genome Browser software to /usr/local/apache. The program can also be used to mirror full or partial assembly databases, keep up-to-date with the Genome Browser software, remove temporary files, and install the Kent command line utilities. You can use the GBiC program to install a Genome Browser mirror on any Linux based operating system, including your server, desktop/laptop, or cloud instance. The program overwrites the default Apache install location, and thus is intended to be run on machines/cloud instances that don’t already act as a web server. A more detailed description of this tool and how to use it is available from the GBiC User Guide. If you have questions about the script please send an email to the publicly archived Genome Browser Mirror mailing list: genome-mirror@soe.ucsc.edu.
Terms and conditions (last modified 2022-01-31)
Size: 68.4 KB
System Requirements:
The GBiC program will run on most Debian or RedHat based Linux operating systems, however there are a few additional considerations:
The GBiC program will run on most Debian or RedHat based Linux operating systems, however there are a few additional considerations:
- Your network firewall must allow connections on the following ports:
- Port 3306, used by MySQL/MariaDB. Without this, only locally mirrored tracks are shown.
- TCP port 873/9000, used by rsync/UDR. Without this, you cannot download the software or track data.
The GBiC product installs Apache and MySQL/MariaDB. Please follow the links to determine if you have the correct license for each of these open source programs.
- The tool has been tested on Ubuntu 14 & 16 LTS, CentOS 6 & 7, and Fedora 20. Other Linux distributions have not been tested yet and may not work correctly.
- The utility has been tested on virtual machines in Amazon’s EC2 (Centos 6 and Ubuntu 14) and Microsoft’s Azure (Ubuntu). Other cloud providers will likely work, but have not been tested.
- The minimum amount of disk space needed to load all data from UCSC on-the-fly is about 5GB, although temporary files will accumulate quickly after normal usage and take up more space. In order to fully mirror the hg19 assembly database locally, approximately 10 TB of disk space is needed, however most other organism databases are significantly smaller -- in the 5-10 GB range -- plus around 40 GB for associated GenBank data. This GenBank data will only be downloaded once.
- Around 4 GB of memory is required to display all of chromosome 1 on hg19. Most other assemblies will require significantly less memory.
Product Includes:
- The Genome Browser in the Cloud setup program. This program:
- downloads the Genome Browser CGIs
- installs Apache, MySQL (or MariaDB), and Ghostscript
- configures the machine to download supporting data files from UCSC
- (optionally) downloads the UCSC command line tools to itself
Product does not Include:
- The UCSC Genome Browser source code.
Genome Browser source code
Cost for non-commercial use by nonprofit entity: Free
For all other use:
One time setup fee: $6000
Cost per year per user: $1000 (5 users minimum)
For all other use:
One time setup fee: $6000
Cost per year per user: $1000 (5 users minimum)
The Genome Browser source code consists of all of the software files necessary to build and compile a full mirror site of the Genome Browser on your own server. Additionally, it builds more than 200 bioinformatics command-line utilities. You must also obtain and install Apache, MySQL and other software packages (see ‘system requirements’).
Terms and conditions (last modified 2022-01-31)
Size: 110 MB
System Requirements:
The following software packages are required for a full install of the Genome Browser. Please visit each link to determine if you are required to purchase or sign a license:
The following software packages are required for a full install of the Genome Browser. Please visit each link to determine if you are required to purchase or sign a license:
- A multiple-CPU machine with a Linux/Ubuntu/CentOS/Unix/MacOSX operating system
- Apache2.x - http web server
- gnu gcc, C code development system
- gnu make
- MySQL development system and libraries
- libpng runtime and development packages
- libssl runtime and development packages
Product Includes:
- A complete set of the cgi-bin files, HTML files, Javascript files, and database files needed to run a stock version of the UCSC Genome Browser.
- A complete set of source files required to build the UCSC Genome Browser, including .c and .h files, Javascript files, HTML files, makefiles, include files, libraries, database files, and instructions for building the UCSC Genome Browser from source.
- Installation instructions, including system requirements.
- A complete set of online user documentation (HTML format).
Product does not Include:
- Source or executables for the Blat Search tool.
- Genomic sequence or annotation data (this data may be freely downloaded from the UCSC Genome Browser website. (http://genome.ucsc.edu/downloads.html) or from many other publicly available sources on the internet, with restrictions outlined in the README files that accompany the data).
- The supporting software required to build, install and run the UCSC Genome Browser (e.g., C compilation environment, Apache server, MariaDB).
LiftOver program
Cost for non-commercial use by nonprofit entity: Free
For all other use:
Cost per year per user: $1000 (1 user minimum)
For all other use:
Cost per year per user: $1000 (1 user minimum)
The LiftOver program can be used to convert coordinate ranges between genome assemblies. This is a command-line tool, and supports forward/reverse conversions, batch conversions, and conversions between species. The LiftOver program requires a UCSC-generated over.chain file as input. Pre-generated files are available for selected assemblies from the downloads page.
Terms and conditions (last modified 2022-01-31)
LiftOver command-line program (LINUX 64-bit)
Size: 23.4 MB
Product Includes:
- Pre-compiled LiftOver standalone command line tool for LINUX or MacOSX.
Product does not Include:
- The UCSC Genome Browser source code.
- The over.chain data files.
LiftOver command-line program (Mac OSX 64-bit)
Size: 9.35 MB
Product Includes:
- Pre-compiled LiftOver standalone command line tool for LINUX or MacOSX.
Product does not Include:
- The UCSC Genome Browser source code.
- The over.chain data files.
Chain Files
Cost for non-commercial use by nonprofit entity: Free
For all other use:
Cost per year per user: $1000 (1 user minimum)
For all other use:
Cost per year per user: $1000 (1 user minimum)
Chain files can be used in tandem with the LiftOver program to convert coordinate ranges between genome assemblies. This license provides coverage for using all UCSC-generated chain files for that or any other purpose in accordance with the EULA.
Terms and conditions (last modified 2022-01-31)
Product does not Include:
- The UCSC Genome Browser source code.
- The LiftOver program.
Please address all questions and comments about the UCSC Genome Browser Store to genome-browser-store-group@ucsc.edu.