d8a3c66525910314ea3cdcc00b694138e769e699 mspeir Wed Sep 2 14:22:52 2026 -0700 store: make the internal links relative Every internal link on the page was written against https://genome.ucsc.edu, so on a sandbox or a mirror the page sent people to production instead of to the copy they were looking at. That bit us reviewing this ticket: the "Terms and conditions" links fetched the production EULA rather than the new one sitting next to the page. Eight links: the five EULA links, hgLiftOver, gbic.html and docker.html. The gbic.html link also had goldenpath in lowercase, which production tolerates but the tree does not, so it is now goldenPath like its neighbor. refs #37764 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/store.html src/hg/htdocs/store.html index 765201efc35..3c2ecbacff2 100755 --- src/hg/htdocs/store.html +++ src/hg/htdocs/store.html @@ -25,31 +25,31 @@ </p> <table class="table"> <tr> <td> <h2>Genome Browser source code</h2> <div class="product-details">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’).</div> <div class="product-eula"> - <a href="https://genome.ucsc.edu/store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> + <a href="store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> </div> <div class="product-price"> <strong>One time setup fee:</strong> $7,200<br> <strong>Cost per year per user:</strong> $1,200 (5 users minimum)<br> <strong><span style="color:red">Cost for non-profit academic research use:</span></strong> Free<br> </div> @@ -103,31 +103,31 @@ <table class="table"> <tr> <td> <h2>LiftOver program</h2> <div class="product-details">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 <a href="http://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">downloads page</a>.</div> <div class="product-eula"> - <a href="https://genome.ucsc.edu/store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> + <a href="store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> </div> <div class="product-price"> <strong>Cost per year:</strong> $1,200<br> <strong><span style="color:red">Cost for non-profit academic research use:</span></strong> Free<br> </div> @@ -182,46 +182,46 @@ </div> </td> </tr> </table> <a id="chainFiles"></a> <table class="table"> <tr> <td> <h2>UCSC chain files</h2> <div class="product-details">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 <a -href="https://genome.ucsc.edu/cgi-bin/hgLiftOver" target="_blank">LiftOver web +href="cgi-bin/hgLiftOver" target="_blank">LiftOver web tool</a>. 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 <a href="https://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">downloads server</a>, for example <a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/liftOver/" target="_blank">hgdownload.gi.ucsc.edu/goldenPath/hg38/liftOver/</a>. Commercial use requires a license.</div> <div class="product-eula"> - <a href="https://genome.ucsc.edu/store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> + <a href="store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> </div> <div class="product-price"> <strong>Cost per year per user:</strong> $1,200<br> <strong><span style="color:red">Cost for non-profit academic research use:</span></strong> Free<br> </div> @@ -257,37 +257,37 @@ </td> </tr> </table> <table class="table"> <tr> <td> <h2>Genome Browser in the Cloud (GBiC)</h2> <div class="product-details">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 <a href="https://genome.ucsc.edu/goldenpath/help/gbic.html" target="_blank">GBIC User Guide</a>. If you have questions about the script please send an email to the publicly archived Genome Browser Mirror mailing list: <a href="mailto:genome-mirror@soe.ucsc.edu" target="_blank">genome-mirror@soe.ucsc.edu</a>.</div> +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 <a href="goldenPath/help/gbic.html" target="_blank">GBIC User Guide</a>. If you have questions about the script please send an email to the publicly archived Genome Browser Mirror mailing list: <a href="mailto:genome-mirror@soe.ucsc.edu" target="_blank">genome-mirror@soe.ucsc.edu</a>.</div> <div class="product-eula"> - <a href="https://genome.ucsc.edu/store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> + <a href="store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> </div> <div class="product-price"> <strong>One time setup fee:</strong> $2,400<br> <strong>Cost per year:</strong> $1,200<br> <strong><span style="color:red">Cost for non-profit academic research use:</span></strong> Free<br> @@ -339,37 +339,37 @@ </ul> </div> </div> </td> </tr> </table> <table class="table"> <tr> <td> <h2>Genome Browser Docker image</h2> <div class="product-details">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 <a href="https://hub.docker.com/r/genomebrowser/server" target="_blank">genomebrowser/server</a>. 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 <a href="https://genome.ucsc.edu/goldenPath/help/docker.html" target="_blank">Docker Help Page</a>. If you have questions about the image please send an email to the publicly archived Genome Browser Mirror mailing list: <a href="mailto:genome-mirror@soe.ucsc.edu" target="_blank">genome-mirror@soe.ucsc.edu</a>.</div> +UCSC publishes a prebuilt image on Docker Hub as <a href="https://hub.docker.com/r/genomebrowser/server" target="_blank">genomebrowser/server</a>. 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 <a href="goldenPath/help/docker.html" target="_blank">Docker Help Page</a>. If you have questions about the image please send an email to the publicly archived Genome Browser Mirror mailing list: <a href="mailto:genome-mirror@soe.ucsc.edu" target="_blank">genome-mirror@soe.ucsc.edu</a>.</div> <div class="product-eula"> - <a href="https://genome.ucsc.edu/store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> + <a href="store/UCSC_GB_EULA.pdf" target="_blank">Terms and conditions</a> </div> <div class="product-price"> <strong>One time setup fee:</strong> $2,400<br> <strong>Cost per year:</strong> $1,200<br> <strong><span style="color:red">Cost for non-profit academic research use:</span></strong> Free<br>