e6e1368336e28a3d336405cc8bd2cdc5480c1a9d jnavarr5 Thu Jun 25 17:34:02 2026 -0700 Fix typos in mirror README markdown that had drifted from the generated HTML, No RM. diff --git src/product/README.txt src/product/README.txt index 6a10ae08194..09dc1c6667b 100644 --- src/product/README.txt +++ src/product/README.txt @@ -157,31 +157,31 @@ MariaDB, the Genome Browser CGIs, temporary file removal and other topics, like data loading through proxies. The following external websites were not created by UCSC staff and are of varying quality, but may be helpful when installing on unusual platforms. * [Installation on Ubuntu](http://enotacoes.wordpress.com/2009/09/03/installing-a-minimal-ucsc-mirror-in-ubuntu-jaunty-64-bits/) * [Installation into a FreeBSD jail](http://www.bioinformatics.uni-muenster.de/download/ucsc), by Norbert Grundmann, Universitaet Muenster, Germany * [Compilation of the Kent source tree on OSX with fink](http://bergmanlab.ls.manchester.ac.uk/?p=32) by Casey Bergman, Manchester, UK * [Browser installation and new genome setup](http://www.oliverelliott.org/article/bioinformatics/tut_genomebrowser/), by Oliver Elliott, Columbia University, USA * [Installation notes in our wiki](http://genomewiki.ucsc.edu/index.php/Browser_Installation) # Using UDR to speed up downloads -[UDR] (UDT Enabled Rsync) is a download protocol that is very efficent +[UDR] (UDT Enabled Rsync) is a download protocol that is very efficient at sending large amounts of data over long distances. UDR utilizes rsync as the transport mechanism, but sends the data over the UDT protocol. UDR is not written or managed by UCSC. It is an open source tool created by the [Laboratory for Advanced Computing] at the University of Chicago. It has been tested under Linux, FreeBSD and Mac OSX, but may work under other UNIX variants. The source code can be obtained through [GitHub][UDR]. When using the GBIC installation program, the `-u` option will use UDR for all downloads. If you manually download data only occasionally, there is no need to change your method; continue to visit our download server to download the files you need. This new protocol has been put in place primarily to facilitate quick downloads of huge amounts of data over long distances. With typical TCP-based protocols like http, ftp, and rsync, the transfer speed @@ -194,58 +194,58 @@ using UDR vs. rsync, http or ftp. If you need help building the UDR binaries or have questions about how UDR functions, please read the documentation on the GitHub page and if necessary, contact the UDR authors via the GitHub page. We recommend reading the documentation on the UDR GitHub page to better understand how UDR works. UDR is written in C++. It is Open Source and is released under the Apache 2.0 License. In order for it to work, you must have rsync installed on your system. For your convenience, we offer a binary distribution of UDR for Red Hat Enterprise Linux 6.x (or variants such as CentOS 6 or Scientific Linux 6). You'll find both a 64-bit and 32-bit rpm [here]. Once you have a working UDR binary, either by building from source or by -installing the rpm, you can download files from either of our our +installing the rpm, you can download files from either of our download servers in a fashion similar to rsync. For example, using rsync, all of the MariaDB tables for the hg19 database can be downloaded using either one of the following two commands: rsync -avP rsync://hgdownload.soe.ucsc.edu/mysql/hg19/ /my/local/hg19/ rsync -avP hgdownload.soe.ucsc.edu::mysql/hg19/ /my/local/hg19/ Using UDR is very similar. The UDR syntax for downloading the same data 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 +will be posted to 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 +Support for the Genome Browser in a Box (GBiB) 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.