36f54a92956a350a2e61453b47c52e4286a1f942 max Thu Mar 12 07:10:13 2020 -0700 adding more details to gbic.html refs #25123 diff --git src/hg/htdocs/goldenPath/help/gbic.html src/hg/htdocs/goldenPath/help/gbic.html index 37a1bd6..1fa286e 100755 --- src/hg/htdocs/goldenPath/help/gbic.html +++ src/hg/htdocs/goldenPath/help/gbic.html @@ -130,39 +130,41 @@ <ul> <li>US server: TCP port 873 on hgdownload.soe.ucsc.edu (128.114.119.163)</li> <li>European server: TCP port 873 on hgdownload-euro.soe.ucsc.edu (129.70.40.99)</li> </ul></li> <li>Download HTML descriptions on the fly: <ul> <li>US server: TCP port 80 on hgdownload.soe.ucsc.edu (128.114.119.163)</li> <li>European server: TCP port 80 on hgdownload-euro.soe.ucsc.edu (129.70.40.99)</li> </ul></li> </ul></p> <a name="partition"></a> <h3>Root file system too small for all data</h3> <p> If you need to move data to another partition because the root file system is too small for all -of the assembly's data, the following steps will help complete the installation. First, create the -following directories and then make symlinks to the directory that will contain the data: +of the assembly's data, the following steps will help complete the installation. First, do a minimal +installation with the browserSetup.sh script as described below, using just the "install" argument. +Then make symlinks to the directory that will contain the data, e.g. if your biggest filesystem +is called "/big": <pre> -mkdir /home/xxx/storage1/gbdb -mkdir /home/xxx/storage1/mysql - -ln -s /home/xxx/storage1/mysql /var/lib/mysql -ln -s /home/xxx/storage1/gbdb /gbdb +sudo mv /var/lib/mysql /big/ +sudo mv /gbdb /big/ +sudo ln -s /big/mysql /var/lib/mysql +sudo ln -s /big/gbdb /gbdb </pre> +Then use the "mirror" or "minimal" arguments to browserSetup.sh to rsync over the majority of the data. </p> <a name='gbic-commands'></a> <h2>GBiC Commands</h2> <p> The first argument of the program is called <code>command</code> in the following section of this document. The first command that you will need is <code>install</code>, which installs the Genome Browser dependencies, binary files and basic MySQL (MariaDB) infrastructure: </p> <pre><code>sudo bash browserSetup.sh install</code></pre> <p> There are a number of options supported by the GBiC program. In all cases, options must