ecb6ac9da06193c59e5a59dee24d6a02872eb407 mspeir Thu Sep 3 09:39:08 2026 -0700 store: fix the last two absolute links on the page Code review caught two links d8a3c66 missed. The gbic.html one in the GBiC firewall list is the same problem that commit fixed and gets the same fix: it is now relative, so it resolves against whichever copy of the page you are reading. The other is not the same problem. It was a bare URL in parentheses rather than a link, and genome.ucsc.edu/downloads.html is not a page in htdocs at all, it is a redirect to hgdownload. Making it relative would have given a 404 on every host including production. It now links to hgdownload.gi.ucsc.edu/downloads.html, matching the two other download links already on this page, and the sentence loses the stray period it had before the parenthetical. refs #37764 Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/htdocs/store.html src/hg/htdocs/store.html index 3c2ecbacff2..cd3b57e7686 100755 --- src/hg/htdocs/store.html +++ src/hg/htdocs/store.html @@ -1,497 +1,497 @@

UCSC Genome Browser Store

All products offered are free for personal and non-profit academic research use. Commercial use requires purchase of a license with setup fee and annual payment. A non-profit organization in service to a for-profit organization must purchase a commercial license, even if the latter already possesses a commercial product license.

During checkout, non-profit academic users will be given the option to declare that they are not using the products commercially and qualify for a free license.

Please address all questions and comments about the UCSC Genome Browser Store to genome-browser-store-group@ucsc.edu.

To make a purchase, or access download links as a personal or non-profit academic research use, please use our Google Form:

https://docs.google.com/forms/d/e/1FAIpQLScfrAUZiRQVCyUOymn5OITcKdcEkIOiFsLvXeCUX0hUrcsMDQ/viewform

Genome Browser source code

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
One time setup fee: $7,200
Cost per year per user: $1,200 (5 users minimum)
Cost for non-profit academic research use: Free
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:
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).
    • +
  • Genomic sequence or annotation data (this data may be freely downloaded from the UCSC Genome Browser downloads page 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

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
Cost per year: $1,200
Cost for non-profit academic research use: Free

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, which are licensed separately. See UCSC chain files below.

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, which are licensed separately. See UCSC chain files below.

UCSC chain files

Chain files, also known as over.chain files, describe how the coordinates of one genome assembly line up against those of another. They serve as input to the LiftOver program and the LiftOver web tool. UCSC produces these files with its own alignment pipeline, and they are the only files the LiftOver program accepts. Chain files are downloaded from the liftOver directory of each assembly on the downloads server, for example hgdownload.gi.ucsc.edu/goldenPath/hg38/liftOver/. Commercial use requires a license.
Terms and conditions
Cost per year per user: $1,200
Cost for non-profit academic research use: Free
Licensing notes:
  • A commercial license for chain files is granted on a per user basis, so it must be purchased for every person in your organization who uses the files.
  • A license is not transferable to another person without written permission from the University. See section 2.3 of the terms and conditions.
  • If a per user license does not fit how your organization works, for instance if the files are used in an automated pipeline rather than by named people, please write to genome-browser-store-group@ucsc.edu to discuss other arrangements.
Product includes:
  • A license to use the UCSC-generated over.chain files for commercial purposes. The files are downloaded from the UCSC downloads server.
Product does not include:
  • The LiftOver program, which is licensed separately.
  • The UCSC Genome Browser source code.

Genome Browser in the Cloud (GBiC)

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 MySQL (or 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
One time setup fee: $2,400
Cost per year: $1,200
Cost for non-profit academic research use: Free
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:
  • Your network firewall must allow connections on the following ports:
      -
    • Port 3306, used by MySQL/MariaDB. Without this, only locally mirrored tracks are shown.
      • +
    • 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 18/20/22/24 LTS, Rocky 9.5, and Fedora 30/35/41. 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 and Microsoft’s Azure. 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 10TB of disk space is needed, however most other organism databases are significantly smaller -- in the 5-10GB range -- plus around 40GB for associated GenBank data. This GenBank data will only be downloaded once.
  • Around 4GB 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 Docker image

The Genome Browser Docker image is a complete UCSC Genome Browser mirror in a container, with the Genome Browser software, an Apache web server, and a MariaDB database server all included. Everything runs inside the container, so the image does not touch the Apache or MySQL setup already on your machine. This makes it useful on a laptop, or on a server that already runs other web software. UCSC publishes a prebuilt image on Docker Hub as genomebrowser/server. It is rebuilt for every Genome Browser release, and one tag covers both Intel and Apple Silicon machines, so most people can pull the image rather than build it themselves. You can also build the image yourself on any system that runs Docker, including Windows, macOS, and Linux. Once the container starts, you open the mirror in a web browser at a port on your own machine. The container downloads track data from UCSC as you use it, and you can attach a Docker volume to keep your data and settings when the container restarts. A more detailed description of the image and how to use it is available from the Docker Help Page. If you have questions about the image please send an email to the publicly archived Genome Browser Mirror mailing list: genome-mirror@soe.ucsc.edu.
Terms and conditions
One time setup fee: $2,400
Cost per year: $1,200
Cost for non-profit academic research use: Free
System Requirements:
The image will run anywhere Docker itself runs, however there are a few additional considerations:
  • Docker Desktop, or the Docker engine, must be installed first. See the Docker documentation for your operating system.
  • Your network firewall must allow connections on TCP port 873, used by rsync. Without this, the container cannot download the Genome Browser software or track data.
  • You need a free port on the host machine to map to port 80 inside the container. Our examples use port 8080.
  • The image is built on Ubuntu 24 LTS and installs Apache and MariaDB inside the container. Please follow the links to determine if you have the correct license for each of these open source programs.
  • Plan on about 8GB of disk space for the image itself, separate from track data. Building the current Dockerfile produces around 5.6GB on disk, and the prebuilt image is a 2.6GB download that unpacks to around 7.4GB. 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 10TB of disk space is needed, however most other organism databases are significantly smaller -- in the 5-10GB range -- plus around 40GB for associated GenBank data. This GenBank data will only be downloaded once.
  • Around 4GB of memory is required to display all of chromosome 1 on hg19. Most other assemblies will require significantly less memory.
Product includes:
  • The UCSC Genome Browser Dockerfile. The image it builds:
    • downloads the Genome Browser CGIs
    • installs Apache and MariaDB inside the container
    • configures the container to download supporting data files from UCSC
    • starts both servers when the container runs
  • The prebuilt genomebrowser/server image on Docker Hub, which is the same image built for you and tagged with each Genome Browser release.
Product does not include:
  • The UCSC Genome Browser source code.
  • Docker itself, which must be installed separately.

CRISPOR

The CRISPOR software is an on-target and off-target predictor for picking CRISPR target sites. It can show the results on the UCSC Genome Browser and provides various helpers for designing primers, cloning sites and prepares files for the CRISPResso CRISPR validation software. The software runs in a Docker container.

See https://crispor.gi.ucsc.edu/ for more information.


Cost per year: $1,200

CRISPRware

CRISPRware can be used to design gRNAs for CRISPR experiments at the genomic or individual gene level. It can incorporate NGS data processed with common tools (e.g. Salmon or Kallisto) to design gRNAs that are particular to the cell line and conditions of interest.

See https://github.com/ericmalekos/crisprware for more information.

Cost per year: $1,200
Size: 108 MB
System Requirements:
Unix-like operating system with either Docker or conda for package installation. Developed and tested on Ubuntu 20 and 22. Minimally tested on MacOS.
To purchase CRISPRware
Please contact Eric Malekos at ericmalekos@gmail. com.