ffadd5a6ca32337c0f6eaaeefe8ef81aa47578c4 gperez2 Mon Apr 8 12:53:32 2024 -0700 Adding a Changing the default Genome Browser options section and made more edits to the docker page, refs #27056 diff --git src/hg/htdocs/goldenPath/help/docker.html src/hg/htdocs/goldenPath/help/docker.html index 89d4b94..5cde7bc 100755 --- src/hg/htdocs/goldenPath/help/docker.html +++ src/hg/htdocs/goldenPath/help/docker.html @@ -1,193 +1,234 @@ <!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="#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">Editing hg.conf</a></h6> +<h6><a href="#hg.conf">Customize your 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. You can package your genomics analysis pipeline or entire analysis environment on your local computer into a Docker container and move it 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 your 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> <h3>Obtaining a UCSC Genome Browser dockerfile</h3> <p>You can obtain a UCSC Genome Browser dockerfile 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 you downloaded the dockerfile, you can run docker build with the 't' option which allows you to name and optionally tag (format: "name:tag") the image. You can create an image 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, you can use the docker run command and the image with the -d option, which allows you to run the container in the background, whereas the default runs the container in the foreground. The -p option allows you to publish a container's port(s) to the host. The following command maps port 8080 on your 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>You can access the running container via http://localhost:8080</p> <p>You can run the the following command to list the running container: <pre><code>docker container ls</code></pre></p> <p>You can run the the following command to stop the running container: <pre><code>docker stop <container_name_or_id></code></pre></p> <p>You can run the the following command to remove the existing container: <pre><code>docker rm <container_name_or_id></code></pre></p> <h3>Using Docker Desktop to create a container</h3> <p>You can also use the the Docker Desktop user interface to run the container by going to the images tab and click the run button under Actions:</p> <div class="text-center"> <img 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 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 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 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 it allows you to mount 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, you can use the docker run command to start 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>You can copy files into the Docker volume or use a bind mount 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> You can run the execute command to list the file inside the running container: <pre><code>docker exec ucsc_genomebrowser_volume ls data</code></pre></p> <a id="updateGB"></a> -<h2>Updating the latest UCSC Genome Browser version</h2> +<h2>Updating the latest UCSC Genome Browser software</h2> +<h3>Access the shell of the Docker container</h3> <p>To update to the latest UCSC Genome Browser version, you will need to access the shell (command-line interface) of the Docker container running the UCSC Genome Browser. You can run the execute command inside a running Docker container with the -it options. The -i or --interactive option allows you to interact with the command being executed and keeps STDIN open even if not attached. This allows you to provide input to 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> -<p>You can then run the following command to update to the latest UCSC Genome Browser version: -<pre><code> bash root/browserSetup.sh update</code></pre></p> -<p>To update only the Genome Browser software, you can run the following command: +<h3>Update the Genome Browser software</h3> +<p>You can then run the following command to update the Genome Browser software: <pre><code> bash root/browserSetup.sh cgiUpdate</code></pre></p> +<h2>Customize your UCSC Genome Browser Docker container</h2> <a id="hg.conf"></a> -<h2>Editing hg.conf</h2> +<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>You can edit the hg.conf file by running the execute command inside a running Docker container with the -it options. The -i or --interactive option allows you to interact with the command being executed and keeps STDIN open even if not attached. This allows you to provide input to the command. The -t or --tty option allocates a pseudo-TTY and allows for a more interactive experience. You can use any common text editors such as vi, nano, and vim 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> +You can customize your track settings such as fonts, text size, and the default region, set default +tracks, or attach hubs and make them appear as your default settings. These settings will appear +every time you open the UCSC Genome Browser graphic display and will also appear after you reset +all your settings. This can be useful if you want to have hubs attached by default, change the +default assembly, or change the visibility of tracks.</p> +<p> +The first step is to create a <a href="#UsrAcct">Session</a> containing all desired display +options, hubs, tracks, and default region in your UCSC Genome Browser Docker container. +Open the shell on your UCSC Genome Browser Docker container. See the +<a href="#updateGB">Access the shell of the Docker container</a> section of this page. 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> +<p> +Drop the existing defaultCart table by running the following query:</p> +<pre> +mysql hgcentral -Ne "DROP TABLE defaultCart" +</pre> +<p> +Load the defaultCart.sql file as a table by running the following query:</p> +<pre> +mysql hgcentral < defaultCart.sql +</pre> +<p> +Insert your session to the default cart table by using your user name and the session name, which +was the session saved in the earlier step, and run the following query (add your userName):</p> +<pre> +mysql hgcentral -Ne "insert into defaultCart select contents from namedSessionDb where sessionName='nameOfSession' and userName='nameOfUser'" +</pre> +</p> + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->