ec7a214792ae943389d82a2d32d1774acf211b0b
jnavarr5
Mon Dec 28 15:28:30 2020 -0800
Escaping a single quote, refs #23297
diff --git src/product/installer/README.md src/product/installer/README.md
index c02407b..28ceadf 100644
--- src/product/installer/README.md
+++ src/product/installer/README.md
@@ -1,268 +1,268 @@
-% 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.
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\").
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
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.
For mirror-specific help, please contact the Mirror Forum as listed on our [contact page](../../contacts.html).
For an installation demonstration, see the [Genome Browser in the Cloud (GBiC) Introduction](https://www.youtube.com/watch?v=dcJERBVnjio)
video:
<p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/dcJERBVnjio?rel=0"
frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
allowfullscreen></iframe></p>
# How does the GBiC program work?
The GBiC program downloads the Genome Browser CGIs and sets up the central MySQL (MariaDB) database.
All potentially destructive steps require confirmation by the user (unless the `-b` batch mode
option is specified).
In particular, MySQL (MariaDB) and Apache are installed and set up with the right package manager
(yum or apt-get). A default random password is set for the MySQL (MariaDB) root user and added to
the `~/.my.cnf` file of the Unix root account. If you have already set up MySQL (MariaDB), you must
create the `~/.my.cnf` file. The program will detect this and create a template file for you. The
program also performs some minor tasks such as placing symlinks, detecting MariaDB, deactivating
SELinux, finding the correct path for your Apache install and adapting the MySQL (MariaDB) socket
config.
This will result in a Genome Browser accessible on localhost that loads its data through
genome-mysql.soe.ucsc.edu:3306 and hgdownload.soe.ucsc.edu:80. If your geographic location is not on
the US West Coast, the performance will be too slow for normal use, though sufficient to test that
the setup is functional. A special MySQL (MariaDB) server is set up in Germany for users in Europe.
You can change the `/usr/local/apache/cgi-bin/hg.conf` genome-mysql.soe.ucsc.edu lines to
genome-euro-mysql.soe.ucsc.edu in order to get better performance. You can then use the program to
download assemblies of interest to your local Genome Browser, which will result in performance at
least as fast as the UCSC site.
### Network requirements
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\":
```
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
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:
sudo bash browserSetup.sh -b install
To improve the performance of your Genome Browser, the program accepts the command
`minimal`. It will download the minimal tables required for reasonable
performance from places in the US and possibly others, e.g., from
Japan. Call it like this to trade space for performance and download a few
of the most used MariaDB tables for hg38:
sudo bash browserSetup.sh minimal hg38
If the Genome Browser is still too slow, you will have to mirror all tables of a
genome assembly. By default, rsync is used for the download. Alternatively you can use
UDR, a UDP-based fast transfer protocol (option: `-u`).
sudo bash browserSetup.sh -u mirror hg38
A successful run of `mirror` will also cut the connection to UCSC: no tables
or files are downloaded on-the-fly anymore from the UCSC servers. To change
the remote on-the-fly loading, specify the option `-o` (offline) or
`-f` (on-the-fly). If you are planning to keep sensitive data on your mirror,
you will want to disable on-the-fly loading, like so:
sudo bash browserSetup.sh -o
The full assembly download for hg19 is >7TB. Limit this
to 2TB or less with the `-t` option:
sudo bash browserSetup.sh -t noEncode mirror hg19
For a full list of `-t` options, see the [All GBiC options](#all-gbic-options) section or run the
program with no arguments.
To update all CGIs and fully mirrored assemblies, call the
tool with the `update` parameter like this:
sudo bash browserSetup.sh update
Minimal mirror sites (those that have partially mirrored an assembly) should not
use the `update` command, but rather just rerun the `minimal` command, so that only the minimal
tables are updated. For instance, if you have partially mirrored the hg19 and hg38 databases,
you may want to add this command to your crontab, perhaps running it every day, to keep your local
tables in sync with those at UCSC:
sudo bash browserSetup.sh minimal hg19 hg38
To update only the Genome Browser software and not the data, use the
`cgiUpdate` command:
sudo bash browserSetup.sh cgiUpdate
Software may break or not work correctly if the necessary data is not available.
Thus in most circumstances, we recommend you use the `mirror`, `update`, or `minimal` commands
instead of `cgiUpdate`.
You will also want to add a cleaning command to your crontab to remove
the temporary files that are created during normal Genome Browser usage. These accumulate
in `/usr/local/apache/trash` and can quickly consume significant space. A command like
this should be added to your crontab file:
sudo bash browserSetup.sh clean
If you find that you need the Kent command line utilities in addition to the Genome Browser, the
`addTools` command will install all the utilities into `/usr/local/bin`:
sudo bash browserSetup.sh addTools
A majority of these utilities require an `.hg.conf` file in the users home directory. For
an example of a minimal `.hg.conf` file, click
[here](http://genome-source.soe.ucsc.edu/gitlist/kent.git/blob/master/src/product/minimal.hg.conf).
If you find a bug, or if your Linux distribution is not supported, please contact
[genome-mirror@soe.ucsc.edu](mailto:genome-mirror@soe.ucsc.edu).
More details about the Genome Browser installation are available
[here](http://genome-source.soe.ucsc.edu/gitlist/kent.git/tree/master/src/product).
# All GBiC options
Here is the full listing of commands and options supported by the GBiC program:
```
browserSetup.sh [options] [command] [assemblyList] - UCSC genome browser install script
command is one of:
install - install the genome browser on this machine. This is usually
required before any other commands are run.
minimal - download only a minimal set of tables. Missing tables are
downloaded on-the-fly from UCSC.
mirror - download a full assembly (also see the -t option below).
No data is downloaded on-the-fly from UCSC.
update - update the genome browser software and data, updates
all tables of an assembly, like "mirror"
cgiUpdate - update only the genome browser software, not the data. Not
recommended, see documentation.
clean - remove temporary files of the genome browser older than one
day, but do not delete any uploaded custom tracks
addTools - copy the UCSC User Tools, e.g. blat, featureBits, overlapSelect,
bedToBigBed, pslCDnaFilter, twoBitToFa, gff3ToGenePred,
bedSort, ... to /usr/local/bin
parameters for 'minimal', 'mirror' and 'update':
<assemblyList> - download MySQL + /gbdb files for a space-separated
list of genomes
examples:
bash browserSetup.sh install - install Genome Browser, do not download any genome
assembly, switch to on-the-fly mode (see the -f option)
bash browserSetup.sh minimal hg19 - download only the minimal tables for the hg19 assembly
bash browserSetup.sh mirror hg19 mm9 - download hg19 and mm9, switch
to offline mode (see the -o option)
bash browserSetup.sh mirror -t noEncode hg19 - install Genome Browser, download hg19
but no ENCODE tables and switch to offline mode
(see the -o option)
bash browserSetup.sh update hg19 - update all data and all tables of the hg19 assembly
(in total 7TB)
bash browserSetup.sh cgiUpdate - update the Genome Browser CGI programs
bash browserSetup.sh clean - remove temporary files older than one day
All options have to precede the command.
options:
-a - use alternative download server at SDSC
-b - batch mode, do not prompt for key presses
-t - only download track selection, requires a value.
This option is only useful for Human/Mouse assemblies.
Download only certain tracks, possible values:
noEncode = do not download any tables with the wgEncode prefix,
except Gencode genes, saves 4TB/7TB for hg19
bestEncode = our ENCODE recommendation, all summary tracks, saves
2TB/7TB for hg19
main = only RefSeq/Gencode genes and common SNPs, total 5GB for hg19
-u - use UDR (fast UDP) file transfers for the download.
Requires at least one open UDP incoming port 9000-9100.
(UDR is not available for Mac OSX)
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.