e5759993329b6e609e9ab825991a90283e714088 mspeir Wed Sep 9 11:17:57 2026 -0700 Help pages: fix broken internal links and restore anchors people still cite, refs #38062 Three groups of anchor problems on the help and FAQ pages. Broken internal links, five pages: posters.html listed a 2022 section that does not exist (no 2022 posters), api.html listed REST and JSON separately after the two sections were merged, docker.html pointed at a #UsrAcct section that is not on that page, FAQgenes.html had a capitalized #ncbiRefSeq where the anchor is #ncbiRefseq, and the genomes.txt settings rows in trackDbHub.v3.html carried no anchors so its own "genome" link missed. Retired anchors that are still cited in twenty years of answers on the genome list. Content moved to its own page and the old anchor was deleted rather than left behind, so the citations land at the top of the page. Reattached seven numeric FAQformat anchors to the Topics entry linking to each format's page. BED, PSL, GFF and GTF were removed from the custom track page in 2012 and never added back to its list of supported formats; added them with the old anchors, which fixes customTrack.html and hgTracksHelp.html together since both include customTrackText.html. Also restored #lines there, and #Session on hgTrackHubHelp.html and #link4 on FAQlink.html. Section anchors on six pages that had none, so a support answer can link to one part of them: bam.html, hic.html, bedgraph.html, ftp.html, net.html and trackDbIndexBb.html. Skipped quickLiftChain.html, oligoMatch.html and cutters.html, which are track description fragments included into the details page rather than standalone pages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/help/docker.html src/hg/htdocs/goldenPath/help/docker.html index bef13673a50..edbc28b09b1 100755 --- src/hg/htdocs/goldenPath/help/docker.html +++ src/hg/htdocs/goldenPath/help/docker.html @@ -1,277 +1,277 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Docker help page" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Docker Help Page</h1> <h2>Contents</h2> <h6><a href="#docker">What is Docker?</a></h6> <h6><a href="#installingDocker">How to Install Docker Desktop?</a></h6> <h6><a href="#dockerUCSCgb">Using Docker Desktop for UCSC Genome Browser</a></h6> <h6><a href="#dockerHub">Using the Prebuilt UCSC Genome Browser Image</a></h6> <h6><a href="#buildImage">Building the Image Yourself</a></h6> <h6><a href="#dockerVolume">Create a Docker Volume for Data Persistence</a></h6> <h6><a href="#updateGB">Updating the Latest UCSC Genome Browser Version</a></h6> <h6><a href="#hg.conf">Customize a UCSC Genome Browser Docker Container</a></h6> <!-- ========== What is Docker? ============================== --> <a id="docker"></a> <h2>What is Docker?</h2> <p> Docker is a platform for developing, testing and running applications. Docker can be used to run genomics tools and manage software such as the UCSC Genome Browser. Docker offers consistency across different computers and environments by packaging everything needed including specific software versions and configurations into a self-contained unit called a container. <h3>Container</h3> <p> A container is software that packages up code and all its dependencies to run an application quickly and reliably from one computing environment to another. A container is isolated from other containers and a Docker container can be run on a developer's local laptop, virtual machines, on cloud providers, or other combinations of environments. A genomics analysis pipeline or entire analysis environment can be packaged to a local computer into a Docker container and moved to a cluster or a cloud server. See also: <a href="https://docs.docker.com/get-started/" target=_blank>Use containers to Build, Share and Run applications</a> <h3>Image</h3> <p> A Dockerfile is a text file that provides instructions to build an image. The Dockerfile is written in <a href="https://docs.docker.com/build/guide/intro/#the-dockerfile" target=_blank>Dockerfile syntax</a>. A docker image is a read-only template with instructions and everything needed to run an application for the container. See also: <a href="https://docs.docker.com/get-started/" target=_blank>Overview of the get started guide</a> </p> <a id="installingDocker"></a> <h2>How to Install Docker Desktop?</h2> <h3>Windows</h3> <ul> <li>Go to the <a href="https://docs.docker.com/desktop/install/windows-install/" target=_blank>Install Docker Desktop on Windows</a> page</li> <li>Check <a href="https://docs.docker.com/desktop/install/windows-install/#system-requirements" target=_blank>system requirements</a></li> <li><a href="https://docs.docker.com/desktop/install/windows-install/#install-docker-desktop-on-windows" target=_blank>Install Docker interactively or from the command line</a> </ul> <h3>macOS</h3> <ul> <li>Go to the <a href="https://docs.docker.com/desktop/install/mac-install/" target=_blank>Install and run Docker Desktop on Mac</a> page</li> <li>Check <a href="https://docs.docker.com/desktop/install/mac-install/#system-requirements" target=_blank>system requirements</a></li> <li><a href="https://docs.docker.com/desktop/install/mac-install/#install-and-run-docker-desktop-on-mac" target=_blank>Install Docker interactively or from the command line</a></li></ul> <h3>Linux</h3> <ul> <li>Go to the <a href="https://docs.docker.com/desktop/install/linux-install/#supported-platforms" target=_blank>Install Docker Desktop on Linux</a> page and select Linux distribution</li> <li>Check <a href="https://docs.docker.com/desktop/install/linux-install/#system-requirements" target=_blank>system requirements</a></li> <li>Follow <a href="https://docs.docker.com/desktop/install/linux-install/#generic-installation-steps" target=_blank>Generic installation steps</a> </ul> <a id="dockerUCSCgb"></a> <h2>Using Docker Desktop for UCSC Genome Browser</h2> <p>Start Docker Desktop after installation is complete:</p> <ul> <li><b>Windows</b>: start Docker Desktop from the Start menu <li><b>macOS</b>: start Docker Desktop from the Applications folder <li><b>Linux</b>: start the Docker service by running the following command on the terminal: <pre><code>sudo systemctl start docker</pre></code> </ul> <a id="dockerHub"></a> <h2>Using the Prebuilt UCSC Genome Browser Image</h2> <p> UCSC publishes a ready-made Genome Browser image on Docker Hub as <a href="https://hub.docker.com/r/genomebrowser/server" target=_blank>genomebrowser/server</a>. The image is rebuilt for every Genome Browser release and tagged with the version number, for example <code>v502</code>. The <code>latest</code> tag always points at the most recent release, and a single tag covers both Intel and Apple Silicon machines. Most people should pull this image rather than build the Dockerfile themselves, since pulling takes a few minutes where a build takes considerably longer.</p> <p> The following commands download the image and start a container, mapping port 8080 on the host machine to port 80 in the container:</p> <pre><code>docker pull genomebrowser/server docker run -d --name ucsc_genomebrowser_container -p 8080:80 genomebrowser/server</code></pre> <p>The Genome Browser is then available at http://localhost:8080</p> <p>To pull a specific release rather than the most recent one, add the version tag:</p> <pre><code>docker pull genomebrowser/server:v502</code></pre> <p> Plan on about 8GB of disk space for the image itself. The download is around 2.6GB and unpacks to around 7.4GB. Track data is downloaded from UCSC as you use the browser and needs space beyond that. See the <a href="#dockerVolume">Create a Docker Volume for Data Persistence</a> section below for keeping that data between container restarts.</p> <p> Build the image from the Dockerfile instead if you need to change how it is built, for instance to add other software or to change the Genome Browser configuration at build time. The next sections describe how to do that.</p> <a id="buildImage"></a> <h2>Building the Image Yourself</h2> <h3>Obtaining a UCSC Genome Browser Dockerfile</h3> <p>The UCSC Genome Browser dockerfile can be obtained from the <a href="https://github.com/ucscGenomeBrowser/" target=_blank>UCSC Genome Browser Github</a> by using the wget command:</p> <pre><code>wget https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/product/installer/docker/Dockerfile</code></pre> <h3>Creating a Image</h3> <p> Once the dockerfile has been downloaded, running the docker build with the 't' option allows the naming and the optional tag (format: "name:tag") of the image. The image can be created by running the following command in the same directory where the dockerfile is located:</p> <pre><code>docker build . -t user_name/ucsc_genomebrowser_image</code></pre> <h3>Creating a Container</h3> <p>After the image has been created, running the docker run command and the image with the -d option allows the container to be run in the background, whereas the default runs the container in the foreground. The -p option publishes a container's port(s) to the host. The following command maps port 8080 on the host machine to port 80 in the container and names the container using the -name option: <pre><code>docker run -d --name ucsc_genomebrowser_container -p 8080:80 user_name/ucsc_genomebrowser_image</code></pre></p> <p>Accessing the running container via http://localhost:8080</p> <p>Running the following command will list the running container: <pre><code>docker container ls</code></pre></p> <p>Running the following command stops the running container:: <pre><code>docker stop <container_name_or_id></code></pre></p> <p>Running the following command removes the existing container:: <pre><code>docker rm <container_name_or_id></code></pre></p> <h3>Using Docker Desktop to Create a Container</h3> <p>The Docker Desktop user interface can be used to run the container by going to the images tab and clicking the run button under Actions:</p> <div class="text-center"> <img alt="Docker Desktop Images tab showing the Genome Browser mirror container image" src="../../images/docker_image.png" style="width:50%;max-width:1083px"> </div> <p>Click Optional settings in the "Run a new container" pop-up window:</p> <div class="text-center"> <img alt="Docker run dialog with the Optional Settings section expanded" src="../../images/docker_optional_settings.png" style="width:50%;max-width:1083px"> </div> <p>Enter a Container name and a Host port in the "Run a new container" popup window:</p> <div class="text-center"> <img alt="Docker container settings panel with container name and host port fields" src="../../images/container_settings.png" style="width:20%;max-width:1083px"> </div> <p>Click the link with the Host port to go to the running container via localhost:</p> <div class="text-center"> <img alt="Docker container logs showing the running Genome Browser with a clickable port link" src="../../images/container_logs.png" style="width:60%;max-width:1083px"> </div> <a id="dockerVolume"></a> <h2>Create a Docker Volume for Data Persistence</h2> <p> A Docker volume allows the data to be persistent (long-lasting) after the container restarts and mount to a host directory or another container's data volume into the UCSC Genome Browser container. </p> <p>The following command creates a new volume named ucsc_genomebrowser_volume that containers can consume and store data in:</p> <pre><code>docker volume create ucsc_genomebrowser_volume</code></pre></p> <p> After creating the volume named ucsc_genomebrowser_volume, running the docker run command starts the UCSC Genome Browser container using the user_name/ucsc_genomebrowser_image image and the -v option to mount the volume created in the previous step.</p> <pre><code>docker run -d --name ucsc_genomebrowser_volume -p 8080:80 -v ucsc_genomebrowser_volume:/data user_name/ucsc_genomebrowser_image</code></pre></p> <p>Files can be copied into the Docker volume or a bind mount can be used to link a host directory containing data to the /data directory inside the container. The following command copies a file to the data directory inside the container:</p> <pre><code>docker cp file.txt ucsc_genomebrowser_volume:/data</code></pre></p> <p>Running the execute command will list the file inside the running container:</p> <pre><code>docker exec ucsc_genomebrowser_volume ls data</code></pre></p> <a id="updateGB"></a> <h2>Updating the Latest UCSC Genome Browser Software</h2> <h3>Access the Docker Container's Shell</h3> <p>Updating the latest UCSC Genome Browser version will require access to the Docker container running shell (command-line interface) of the UCSC Genome Browser. The execute command can be run inside a running Docker container with the -it options. The -i or --interactive option allows interaction with the command being executed and keeps STDIN open even if not attached. This will allow input to be provided for the command. The -t or --tty option allocates a pseudo-TTY and allows for a more interactive experience. The following example shows how to run exec command and the -it options: <pre><code>docker exec -it <container_name_or_id> /bin/bash</code></pre></p> <h3>Update the Genome Browser Software</h3> <p>Running the following command updates the Genome Browser software: <pre><code> bash root/browserSetup.sh cgiUpdate</code></pre></p> <h2>Customize a UCSC Genome Browser Docker Container</h2> <a id="hg.conf"></a> <h3>Editing hg.conf</h3> <p>The hg.conf file is a file that has information on how to connect to MariaDB, the location of the other directories and various other settings.</p> <p> The hg.conf file can be edited by running the execute command inside a running Docker container with the -it options. The -i or --interactive option allows interaction with the command being executed and keeps STDIN open even if not attached. This will allow input to be provided for the command. The -t or --tty option allocates a pseudo-TTY and allows for a more interactive experience. Any common text editors such as vi, nano, and vim can be used with the execute command and the -it options. The following example shows how to edit the hg.conf file using vi: <pre><code>docker exec -it <container_name_or_id> vi /usr/local/apache/cgi-bin/hg.conf</code></pre></p> <a id="defaults"></a> <h3>Changing the Default Genome Browser Options</h3> <p>Track settings such as fonts, text size, default tracks, attached hubs, and the default region can be customized and set as the default settings. These settings will appear every time the UCSC Genome Browser graphic display is opened and will also appear after a reset of all user settings. This can be useful when working with a different assembly than hg38, having track hubs automatically attached, or changing the visibility of tracks.</p> <ul> - <li>The first step is to create a <a href="#UsrAcct">Session</a> containing all desired display + <li>The first step is to create a <a href="hgSessionHelp.html#Create">Session</a> containing all desired display options, hubs, tracks, and default region in the UCSC Genome Browser Docker container. Open the UCSC Genome Browser Docker container shell. See the <a href="#updateGB">Access the Docker Container's Shell</a> section of this page.</li> <li>Create a new file, 'defaultCart.sql', to make a new MySQL table. Add the following to the defaultCart.sql file: <pre> #The default cart CREATE TABLE defaultCart ( contents longblob not null # cart contents );</pre></li> <li>Drop the existing defaultCart table by running the following query: <pre> mysql hgcentral -Ne "DROP TABLE defaultCart" </pre></li> <li>Load the defaultCart.sql file as a table by running the following query:</p> <pre> mysql hgcentral < defaultCart.sql </pre></li> <li>Insert the session to the default cart table by using the user name and the session name, which was the session saved in the earlier step, and run the following query (add userName): <pre> mysql hgcentral -Ne "insert into defaultCart select contents from namedSessionDb where sessionName='nameOfSession' and userName='nameOfUser'" </pre></li> <li>Finally, make sure the following line is in your hg.conf file. This file is found in the cgi-bin directory, e.g. cgi-bin/hg.conf. <pre> defaultCartName=defaultCart </pre></li> </ul> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->