90c7c79830fcf633543d0fdb16fdbc21f1ae6e6f max Fri Apr 21 02:42:26 2023 -0700 #Preview2 week - bugs introduced now will need a build patch to fix various doc fixes related to bigDataIndex, no redmine, email and galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3 diff --git src/hg/htdocs/goldenPath/help/bam.html src/hg/htdocs/goldenPath/help/bam.html index 694cf6f..ef9482a 100755 --- src/hg/htdocs/goldenPath/help/bam.html +++ src/hg/htdocs/goldenPath/help/bam.html @@ -61,31 +61,31 @@ <li> If the file URL ends with .bam and the BAM index file URL ends with .bam.bai, you can paste the URL directly into the <a href="../../cgi-bin/hgCustom">custom track</a> management page, click submit and view in the Genome Browser. The track name will then be the name of the file. If you want to configure the track name and descriptions or the URLs are not as described, you will need to create a <a href="hgTracksHelp.html#TRACK">track line</a>, as shown below in step 7.</li> <li> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. The most basic version of the "track" line will look something like this: <pre><code> track type=bam name="My BAM" bigDataUrl=<em>http://myorg.edu/mylab/my.sorted.bam</em></code></pre> Again, in addition to <em>http://myorg.edu/mylab/my.sorted.bam</em>, the associated index file <em>http://myorg.edu/mylab/my.sorted.bam.bai</em> must also be available at the same location. If not, you can specify the URL with the - <code>bigDataUrl=<em>http://myorg.edu/mylab/my.sorted.bam.bai</em></code></li> + <code>bigDataIndex=<em>http://myorg.edu/mylab/my.sorted.bam.bai</em></code></li> <li> Paste the custom track line into the text box in the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a>, click submit and view in the Genome Browser.</li> </ol> <h3>Parameters for BAM custom track definition lines</h3> <p> All options are placed in a single line separated by spaces. In the example below, the lines are broken only for readability. If you copy/paste this example, you must remove the line breaks. Click <a href="examples/bamExample.txt">here</a> for a text version that you can paste without editing.</p> <pre><code> <strong>track type=bam bigDataUrl=</strong><em>http://...</em> <strong>pairEndsByName=</strong><em>.</em> <strong>pairSearchRange=</strong><em>N</em>