d8d9e8bc8fa214d169bc3011359fbe9bfd6b7c08 jnavarr5 Tue Jan 5 17:06:01 2021 -0800 Removing the escaped characters to clean up the markdown file (github README) refs #23297 diff --git src/product/installer/README.md src/product/installer/README.md index 8125efc..847685c 100644 --- src/product/installer/README.md +++ src/product/installer/README.md @@ -1,40 +1,40 @@ -% Genome Browser in the Cloud User\'s Guide +% Genome Browser in the Cloud User's Guide # What is Genome Browser in the Cloud? The Genome Browser in the Cloud (GBiC) program is a convenient tool that automates the setup of a UCSC Genome Browser mirror. The GBiC program is for users who want to set up a full mirror of the UCSC Genome Browser on their server/cloud instance, rather than using [Genome Browser in a Box](gbib.html) (GBIB) or our public website. Please see the [Installation of a UCSC Genome Browser on a local machine (mirror)](mirror.html#considerations-before-installing-a-genome-browser) page for a summary of installation options, including the pros and cons of using a mirror -installation via the GBiC program vs\. using GBiB. +installation via the GBiC program vs. using GBiB. The program works by setting up MySQL (MariaDB), Apache, and Ghostscript, and then copying the Genome Browser CGIs onto the machine under `/usr/local/apache/`. Because it also deactivates the default Apache htdocs/cgi folders, it is best run on a new machine, or at least a host that is not already used as a web server. The tool can also download full or partial assembly databases, -update the Genome Browser CGIs, and remove temporary files (aka \"trash cleaning\"). +update the Genome Browser CGIs, and remove temporary files (aka "trash cleaning"). The GBiC program has been tested with Ubuntu 14/16 LTS, Centos 6/6.7/7.2, and Fedora 20. It has also been tested on virtual machines in Amazon EC2 (Centos 6 and Ubuntu 14) and Microsoft Azure (Ubuntu). If you want to load data on the fly from UCSC, you need to select the -data centers \"US West (N. California)\" (Amazon) or \"West US\" (Microsoft) for best performance. -Other data centers (e.g\. East Coast) will require a local copy of the genome assembly, which +data centers "US West (N. California)" (Amazon) or "West US" (Microsoft) for best performance. +Other data centers (e.g. East Coast) will require a local copy of the genome assembly, which requires 2TB-7TB of storage for the hg19 assembly. Note that this exceeds the current maximum size of a single Amazon EBS volume. # Quick Start Instructions Download the GBiC program from the [UCSC Genome Browser store](https://genome-store.ucsc.edu/). Run the program as root, like this: sudo bash browserSetup.sh install The `install` command downloads and configures Apache, MySQL (MariaDB) and Ghostscript, copies the Genome Browser CGIs, and configures the mirror to load data remotely from UCSC. The `install` command must be run before any other command is used. @@ -75,43 +75,43 @@ Your network firewall must allow outgoing connections to the following servers and ports: * MySQL (MariaDB) connections, used to load tracks not local to your computer: * US server: Port 3306 on genome-mysql.soe.ucsc.edu (128.114.119.174) * European server: Port 3306 on genome-euro-mysql.soe.ucsc.edu (129.70.40.120) * Rsync, used to download track data: * US server: TCP port 873 on hgdownload.soe.ucsc.edu (128.114.119.163) * European server: TCP port 873 on hgdownload-euro.soe.ucsc.edu (129.70.40.99) * Download HTML descriptions on the fly: * US server: TCP port 80 on hgdownload.soe.ucsc.edu (128.114.119.163) * European server: TCP port 80 on hgdownload-euro.soe.ucsc.edu (129.70.40.99) ### Root file system too small for all data 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, 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\": +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": ``` sudo mv /var/lib/mysql /big/ sudo mv /gbdb /big/ sudo ln -s /big/mysql /var/lib/mysql sudo ln -s /big/gbdb /gbdb ``` -Then use the \"mirror\" or \"minimal\" arguments to browserSetup.sh to rsync over the majority of +Then use the "mirror" or "minimal" arguments to browserSetup.sh to rsync over the majority of the data. # GBiC Commands The first argument of the program is called `command` in the following section of this document. The first command that you will need is `install`, which installs the Genome Browser dependencies, binary files and basic MySQL (MariaDB) infrastructure: sudo bash browserSetup.sh install There are a number of options supported by the GBiC program. In all cases, options must be specified before the command. The following example correctly specifies the batch mode option to the program: @@ -253,16 +253,16 @@ This option will download a udr binary to /usr/local/bin -o - switch to offline-mode. Remove all statements from hg.conf that allow loading data on-the-fly from the UCSC download server. Requires that you have downloaded at least one assembly, using the '"download"' command, not the '"mirror"' command. -f - switch to on-the-fly mode. Change hg.conf to allow loading data through the internet, if it is not available locally. The default mode unless an assembly has been provided during install -h - this help message ``` # Credits * Max Haeussler for writing the program. * Christopher Lee for testing and QA. * Daniel Vera (bio.fsu.edu) for his RHEL install notes. -* Bruce O\'Neill, Malcolm Cook for feedback. +* Bruce O'Neill, Malcolm Cook for feedback.