87753ed6a5ebbc04ad58ab9a457b2fe403415b3a lrnassar Thu Jul 17 15:28:00 2025 -0700 Quietly retiring GBiB in favor of GBiC/docker, refs #35611 diff --git src/product/README.txt src/product/README.txt index 67cc87264b5..ae7c20ab66c 100644 --- src/product/README.txt +++ src/product/README.txt @@ -39,80 +39,55 @@ password-protected and loaded through https and restricted to UCSC's IP address, but has to be located on the web and accessible by the UCSC webserver. * For BLAT searches in your genome, you have to start a BLAT server yourself on a Unix server. * If your hub includes a high number of annotation files or HAL (multiple alignment) files and is located far from Santa Cruz, the display performance of assembly hubs may be slower than a local mirror. This issue can be resolved by using a UCSC mirror closer to the assembly hub (e.g. use genome-euro.ucsc.edu for assembly hubs located on servers in Europe, or genome-asia.ucsc.edu for those in Asia). Alternatively, you can improve performance by moving your hub data to a webspace provider closer to Santa Cruz or by using a content distribution network, where all content is mirrored and the closest location is chosen by your provider. -3. **Use Genome Browser in a Box** - - [Genome Browser in a Box](https://genome.ucsc.edu/goldenPath/help/gbib.html) (GBiB): - is a fully configured virtual machine that includes - Apache and MariaDB, and has behavior identical to the UCSC website. - GBiB loads genome data from the UCSC download servers on the fly. - Website and data updates are applied automatically every two weeks. By default, GBiB - uses the VirtualBox virtualization software, so it can be run on any - operating system, Windows, OSX and Linux. It does not require VirtualBox, - the virtual machine image can easily be converted to e.g., VMWare or HyperV. - For increased privacy, you can download the genomes and - annotation tracks you need and use your GBiB off-line even on a laptop. - - * Pros: - * Relatively simple to install: download and double-click. - * By default, software and data updates are managed remotely by UCSC, via an update script run every week. - * Best performance when rendering local BAM/bigWig/bigBed files. - * No Unix webserver needed, runs on any OS. - * For commercial users: easier click-through licensing compared to a full multi-seat, manual license. - * Cons: - * Requires the free VirtualBox software or a commercial Virtualization system. - * By default requires opening at least three outgoing ports to UCSC for MariaDB, Rsync downloads - and BLAT in your firewall. Once all data is downloaded, no open ports are needed. - * For maximum browsing speed, can require up to 2-6TB to store all genome annotation tracks, like a manual local installation. - -4. **Install locally with the Genome Browser installation script (GBIC)** +3. **Install locally with the Genome Browser installation script (GBIC)** We recommend this only if none of the above options fulfill your needs. Our [GBIC installation](https://genome.ucsc.edu/goldenpath/help/gbic.html) script will install a full local mirror of the UCSC website, for the assemblies you select. We support mirror site installations as time allows, and have many functional mirrors of the Genome Browser worldwide. For details, see the [section below](#installing-a-genome-browser-locally-with-the-gbic-installer). * Pros: * Relatively simple to install on a virtual machine or cloud instance: just run the script. * Best performance when rendering local BAM/bigWig/bigBed files. * For commercial users: easier click-through licensing compared to a full multi-seat, manual license. * Cons: * To keep up with changes in the Genome Browser, you will have to install linux packages and update the linux distribution yourself in the future and run the installation script with the 'update' command if you want to take advantage of new features in the Genome Browser. * Preferably run on a linux server that is not used otherwise. * By default requires opening at least three outgoing ports to UCSC for MariaDB and BLAT in your firewall. Once all data is downloaded and BLAT setup locally, no open ports are needed anymore. * For maximum browsing speed, can require up to 2-6TB to store all genome annotation tracks. -5. **Install manually yourself, by following installation instructions** +4. **Install manually yourself, by following installation instructions** We do provide [step-by-step instructions](https://genome.ucsc.edu/goldenpath/help/mirrorManual.html) for local installation, but do not recommend this, if any other system works for you. The internet also has various pages with instructions, but they are often out of date and may cause problems later. For details on manual instructions, see the [section below](#manual-installation-instructions). * Pros: * You will understand the complete setup of the Genome Browser. * For commercial users: license agreements can be customized to your needs. * Cons: * Not easy to setup, even for experienced Unix administrators. * Will probably require some support via the [genome-mirror](mailto:genome-mirror@soe.ucsc.edu) mailing list. * To keep up with changes in the Genome Browser, you will have to @@ -241,15 +216,46 @@ would be: udr rsync -avP hgdownload.soe.ucsc.edu::mysql/hg19/ /my/local/hg19/ [UDR]: https://github.com/LabAdvComp/UDR [Laboratory for Advanced Computing]: http://www.labcomputing.org/ [here]: http://hgdownload.soe.ucsc.edu/admin/udr # The genome-mirror mailing list For questions about installing and mirroring the UCSC Genome Browser, contact the UCSC mailing list [genome-mirror@soe.ucsc.edu](mailto:genome-mirror@soe.ucsc.edu). ** Messages sent to this address will be posted the moderated genome-mirror mailing list, which is archived on a SEARCHABLE PUBLIC [Google Groups forum](http://groups.google.com/a/soe.ucsc.edu/group/genome-mirror)**. + +# What happened to Genome Browser in a Box (GBiB)? + +Support for the Genome Browser in a Box (GBiB) product **product ended in 2025**. We recommend +use of the GBiC [dockerfile](/goldenPath/help/mirror.html#docker-installation-instructions) instead. +The information below is kept for historical purposes. + +1. **Use Genome Browser in a Box** + + [Genome Browser in a Box](https://genome.ucsc.edu/goldenPath/help/gbib.html) (GBiB): + is a fully configured virtual machine that includes + Apache and MariaDB, and has behavior identical to the UCSC website. + GBiB loads genome data from the UCSC download servers on the fly. + Website and data updates are applied automatically every two weeks. By default, GBiB + uses the VirtualBox virtualization software, so it can be run on any + operating system, Windows, OSX and Linux. It does not require VirtualBox, + the virtual machine image can easily be converted to e.g., VMWare or HyperV. + For increased privacy, you can download the genomes and + annotation tracks you need and use your GBiB off-line even on a laptop. + + * Pros: + * Relatively simple to install: download and double-click. + * By default, software and data updates are managed remotely by UCSC, via an update script run every week. + * Best performance when rendering local BAM/bigWig/bigBed files. + * No Unix webserver needed, runs on any OS. + * For commercial users: easier click-through licensing compared to a full multi-seat, manual license. + * Cons: + * Requires the free VirtualBox software or a commercial Virtualization system. + * By default requires opening at least three outgoing ports to UCSC for MariaDB, Rsync downloads + and BLAT in your firewall. Once all data is downloaded, no open ports are needed. + * For maximum browsing speed, can require up to 2-6TB to store all genome annotation tracks, like a manual local installation.