2ff8201b43ce7f5a9f66c9bf81842ba9f5002b75 lrnassar Wed Feb 10 17:54:02 2021 -0800 Doc'ing new defaultCart feature for GBiB. Also removed a note about a broken link, the link is only broken since it leads to a local GBiB. It works as expected if there is a GBiB running. refs #26938 diff --git src/hg/htdocs/goldenPath/help/gbib.html src/hg/htdocs/goldenPath/help/gbib.html index 65816a2..6e979a9 100755 --- src/hg/htdocs/goldenPath/help/gbib.html +++ src/hg/htdocs/goldenPath/help/gbib.html @@ -3,30 +3,31 @@ <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1> Genome Browser in a Box User's Guide</h1> <h2>Contents</h2> <h6><a href="#What">What is Genome Browser in a Box (GBiB)?</a></h6> <h6><a href="#GetStarted">Getting Started: Setting up Genome Browser in a Box</a></h6> <h6><a href="#UsingGbib">Using Genome Browser in a Box</a></h6> <h6><a href="#GbibMirroring">Improving speed and performance</a></h6> <h6><a href="#UpdatingGbib">Updating Genome Browser in a Box</a></h6> <h6><a href="#YourTracks">Viewing your own data</a></h6> +<h6><a href="#CustomizingGbib">Customizing your GBiB</a></h6> <h6><a href="#SharingGBIB">Sharing Genome Browser in a Box with others</a></h6> <h6><a href="#UsrAcct">User accounts and sessions</a></h6> <h6><a href="#Trouble">Troubleshooting common problems</a></h6> <h6><a href="#Commands">Genome Browser in a Box commands</a></h6> <h6><a href="#License">Licensing information</a></h6> <hr> <p> <strong>Other resources:</strong> <ul><strong> <li><a class="toc" href="http://genome.ucsc.edu/blog/genome-browser-in-a-box-gbib-origins/" target="_blank">UCSC blog post about GBiB</a></li> <li><a class="toc" href="https://www.youtube.com/watch?v=1DzZZgB1gvQ" target="_blank">GBiB introductory video</a></li> </strong></ul> @@ -518,37 +519,98 @@ byte-range requests, they cannot be transmitted over the Internet to view in the browser. For GEO files, try the ftp location first. If you find the files of interest are giving byte-range request errors, then one option is to download the files and locally load them from your own laptop. With GBiB you can download these files to a local shared folder and then browse them. In the following example the URL of the bigWig (.bw) file was obtained for the wget by right clicking the http link for this <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1186795">GSM1186795</a> example, that only displays data on chrM and chrX.</p> <pre><code>ssh browser@localhost -p 1235 (to enter GBiB from your computer terminal, password: browser) cd /folders sudo wget "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM1186795&format=file&file=GSM1186795%5FDZ012%5FTRA1%5FN2L3%5Ftr27%5Fce10%5FBTm1x200n%2Ebw" -O GSM1186795.bw </code></pre> <p> The file can then be found in the GBiB's <a href="http://127.0.0.1:1234/folders/"><code>http://127.0.0.1:1234/folders/</code></a> location, or loaded with a direct link to the files location:</p> -<!-- FIX ME -- THIS URL DOESN'T WORK --> + <pre><code><a href="http://127.0.0.1:1234/cgi-bin/hgTracks?db=hg19&hgt.customText=http://127.0.0.1:1234/folders/GSM1186795.bw&position=chrM" target="_blank">http://127.0.0.1:1234/cgi-bin/hgTracks?db=hg19&hgt.customText=<strong>http://127.0.0.1:1234/folders/GSM1186795.bw</strong>&position=chrM</a></code></pre> <p> (NOTE: In this above example, the <strong>ftp location</strong> now has byte-range requests supported so the <strong>GEO ftp link</strong> can be loaded on the browser).</p> +<a name="CustomizingGbib"></a> +<h2>Customizing your GBiB</h2> + +<a name="Fonts"></a> +<h3>Enabling additional font styles</h3> +<p> +In order to enable the use of additional fonts in the tracks display, the following lines +need to be need to be added to the <code>hg.conf</code> file:</p> +<pre> +freeType=on +freeTypeDir=/usr/share/fonts/type1/gsfonts +</pre> +<p> +The file can be found in the following location:</p> +<pre> +/usr/local/apache/cgi-bin/hg.conf +</pre> +<p> +The fonts can then be change by pressing the <strong>configuration</strong> located below the +image on the tracks display.</p>. + +<a name="Defaults"></a> +<h3>Changing the default Genome Browser options on a GBiB</h3> +<p> +GBiB supports changes to some default settings such as assembly, attached hubs, fonts, text size, +etc. Changing these defaults means that any time a new user goes to the mirror, or whenver +all user settings are reset, the custom options will be enabled. This can be useful in cases +when it is desirable to have hubs attached by default, to change the default assembly or +visibility display, etc.</p> +<p> +The first step is to create a <a href="#UsrAcct">Session</a> containing all desired display +options, hubs, etc. Then a file will be created from within the GBiB that contains the +command to create a new MySQL table: <strong>defaultCart</strong>. See the +<a href="#Connectwithssh">Connect with ssh</a> section of this page for help logging into +your GBiB. Contents of new file <strong>defaultCart.sql</strong>:</p> +<pre> +#The default cart +CREATE TABLE defaultCart ( + contents longblob not null # cart contents +); +</pre> +<p> +The table can then be loaded:</p> +<pre> +mysql hgcentral < defaultCart.sql +</pre> +<p> +Finally, the contents of the desired session can be entered into the new table.</p> +<pre> +mysql hgcentral -Ne "insert into defaultCart select contents from namedSessionDb where sessionName='nameOfSession' and userName='nameOfUser'" +</pre> +</p> +Where <strong>nameOfSession</strong> is the name of the created session and +<strong>nameOfUser</strong> is the name of the user the session was created under. Keep +in mind that only the top entry in that table will be used to pull default variables, so +in order to change the new defaults (or to remove the new dedaults) first you will want +to delete the table contents:</p> +<pre> +mysql hgcentral -Ne "delete from defaultCart" +</pre> + <a name="SharingGBIB"></a> <h2>Sharing Genome Browser in a Box with others</h2> <p> By default, GBiB can be accessed only from the machine on which it is installed. This is done to prevent others from accessing your data. You can, however, make your GBiB instance available for use by others. To open up external access to GBiB:</p> <ol> <li> Shut down the GBiB machine (<a href="#GbibStop">Stopping GBiB</a>).</li> <li> Select the browserbox machine in the VirtualBox left-hand menubar.</li> <li> Select <em>Machine >> Settings</em> in the VirtualBox menu to display the Settings window.</li> <li>