fc01cb610a90c3ee353e9372b0d756ae8b0a2880 clmfisch Fri Dec 19 09:16:17 2025 -0800 Updating contact for external software diff --git src/hg/htdocs/store.html src/hg/htdocs/store.html index af4675138ba..71f37aeeb9a 100755 --- src/hg/htdocs/store.html +++ src/hg/htdocs/store.html @@ -1,405 +1,405 @@

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.

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: $7200
Cost per year per user: $1200 (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).
  • 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: $1200
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.

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.

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: $2400
Cost per year: $1200
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.
    • 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 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.

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. - - +

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: $1200
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 emalekos@ucsc.edu. + Please contact Eric Malekos at ericmalekos@gmail.com.