dee72cee166208ce54ff7f4c0c5baece0dc33331 brianlee Tue Sep 17 10:43:28 2019 -0700 Adding information about loading bams to gbib.html refs #24137 diff --git src/hg/htdocs/goldenPath/help/gbib.html src/hg/htdocs/goldenPath/help/gbib.html index c419294..4d25100 100755 --- src/hg/htdocs/goldenPath/help/gbib.html +++ src/hg/htdocs/goldenPath/help/gbib.html @@ -422,35 +422,46 @@ <div class="col-md-8"> <img src="../../images/gbib-shared.png" alt="GBiB shared" width="683" height="465"> </div> </div> <p> To check if your folders are shared, type this address into your web browser: <a href="http://127.0.0.1:1234/folders" target="_blank">http://127.0.0.1:1234/folders</a>. It should show all shared folders. To obtain the bigDataUrl of any of the files in your shared folders, right-click on any file and select "Copy link address". You can now paste this URL into the <a href="../../cgi-bin/hgCustom" target="_blank">Add Custom Tracks</a> page. Or, if you are uploading a track or assembly hub, right-click on your "hub.txt" file and select "Copy link address". You can now paste this URL into the box on the "My Hubs" tab of the <a href="../../cgi-bin/hgHubConnect" target="_blank">Track Data Hubs</a> page.</p> +<a name="loadBam"></a> <h3><em>Example: Loading a local BAM custom track</em></h3> <p> -Here is an example of a custom track that loads a local BAM file (to customize this for your own -use, replace the URL with a pasted URL from your own machine):</p> +Here is an example of a custom track in a shared test/ folder that loads a locally hosted +BAM file when pasted on the custom tracks page (select <em>My Data >> Custom Tracks</em> +in the Genome Browser menu): <pre><code>track type=bam name=BamExample bigDataUrl=http://127.0.0.1:1234/folders/test/bamExample.bam </code></pre> +<p> +To customize this URL for your own use, replace the URL with a pasted URL to files from your own +machine discoverable under the <em>My Data >> GBiB Shared Data Folder</em> in the Genome Browser menu. +Since the GBiB is configured so that the VirtualBox shared folder path can be placed directly into the +custom track page (via a line <code>udc.localDir=/folders</code> in the hg.conf file) and there +is software that knows files ending in <code>.bam</code> should be loaded as <code>type=bam</code>, +the link can be replaced with just a path to the file. For example, pasting the following on the +custom tracks page would also work:</p> +<pre><code>/folders/test/bamExample.bam </code></pre> <a name="Connectwithssh"></a> <h3>Connecting to GBiB with ssh</h3> <p> The GBiB terminal is a normal Linux command line interface. For easier use of the command line, you can connect to the GBiB machine from your computer with ssh. This may offer better speed and more functionality, such as support for copy/paste.</p> <p> To connect to GBiB with ssh, open a terminal on your computer and type: <code>ssh browser@localhost -p 1235</code>. You will be prompted for a password when attempting to access GBiB from your computer's command line. The password is "browser". Alternatively you can use <code>sudo</code> for root access, which does not require a password. Because stock Windows computers do not have ssh installed, Windows users will have to use the GBiB terminal or install a third-party ssh client for Windows, such as the free software <a href="http://putty.org" target="_blank">Putty</a>.</p>