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Manual installation of the UCSC Genome Browser on a Unix server

Contents

Software Requirements
Hardware and disk space requirements
Overview of the Genome Browser directories and databases
Installing the UCSC Genome browser
MySQL Setup
Adding a custom genome to the browser
Modifying the source code
Custom Track Database
Debugging the CGI binaries
Local Git repository
Proxy support
Adding tracks to the browser
The UDC local cache directory
Activating CRAM support for the Genome Browser.

Software Requirements

Optional:

It is best to install these packages with your standard operating system package management tools:

Hardware and disk space requirements

We currently use the following hardware to support our website:

The UCSC Genome Browser website experiences over one million hits per day. Your hardware requirements may be much less demanding and will depend upon how much traffic you expect for your mirror.

Annotation database size differs a lot between the assemblies: The full size of the hg19 database in 2016 is 6 TB, for ce2 it is 5GB. It also depends on the tracks: The size of the hg19 annotations can be reduced to 2TB if you do not download any ENCODE tracks. The size of only the main gene and SNP annotations is around 5GB for hg19 and hg38. To increase download speed, there are two download servers located in North America and Europe, hgdownload and hgdownload-euro.

You can use the following command to get the size of the files for all of the assemblies, but it can also be modified to give the size for a particular assembly: 

rsync -hna --stats rsync://hgdownload.soe.ucsc.edu/gbdb/ | egrep "Number of files:|total size is"

For example, to get the size of all of the files for hg19, you would use either of the following commands: 

rsync -hna --stats rsync://hgdownload.soe.ucsc.edu/gbdb/hg19/ | egrep "Number of files:|total size is"
rsync -hna --stats rsync://hgdownload-euro.soe.ucsc.edu/gbdb/hg19/ | egrep "Number of files:|total size is"

After running that command, you should see output like this: 

Number of files: 54886
total size is 6515.70G  speedup is 5181080.38 (DRY RUN)

The next commands will give you the size of the entire mySQL database, but can be changed to get the size for a particular assembly: 

rsync -hna --stats rsync://hgdownload.soe.ucsc.edu/mysql/ | egrep "Number of files:|total size is"
rsync -hna --stats rsync://hgdownload-euro.soe.ucsc.edu/mysql/ | egrep "Number of files:|total size is"

Overview of the Genome Browser directories and databases

We strongly recommend to place our CGI programs in /usr/local/apache/cgi-bin. The htdocs root directory for html files should then be in /usr/local/apache/htdocs. All Genome Browser components called from Apache get their settings from the central configuration file /usr/local/apache/cgi-bin/hg.conf. Among others, the location and the username/password for the MySQL server is specified there.

When a web browser requests a Genome Browser page, typically /cgi-bin/hgTracks, Apache executes this CGI program. The programs then read information about the installed genome assemblies and the current user session from the database hgcentral. For each genome assembly, there is a separate MySQL database (e.g. hg38). Some types of data are kept as indexed binary files outside of MySQL, they are located in /gbdb, e.g. /gbdb/hg38. The location of the /gbdb directory can be changed with a setting in hg.conf. Some types of data are not specific for a genome, these are kept in the MySQL databases hgFixed, proteome and visiGene.

To load data into the genome browser databases, you need a configuration file ~/.hg.conf in your home directory with the MySQL username/password and one of the loader programs, e.g. hgLoadBed.

Installing the UCSC Genome browser

Scripts to perform all of the functions below can be found in the directory here: src/products/scripts/

Confirm the following:

  1. Apache web server is installed and working, http://localhost/ provides the Apache default home page from your machine NOTE: The browser static html web pages require the Apache XBitHack option to be enabled to allow SSI html statements to function. Add 'Options +Includes' for your html directory, your httpd.conf file entry looks like: 

    XBitHack on
<Directory /usr/local/apache/htdocs>
Options +Includes
</Directory>

    You can test your Apache cgi-bin/ directory by copying the script src/product/scripts/printEnv.pl into it.

  2. MySQL database is installed and working

    mysql -u browser -pgenome -e 'show tables;' mysql

    MySQL can be run from the command line, and the tables from the database mysql can be displayed.

    MySQL development package is installed (mysql-devel on RedHat) The directory: /usr/include/mysql/ has the mysql .h files And the library: /usr/lib/mysql/libmysqlclient.a exists (your exact pathnames may vary depending upon your installation)

    Set MySQL database access permissions. The examples mentioned in the README.mysql.setup instructions will allow this setup to function as described here.

    To setup the example user accounts as mentioned in these instructions, run the script:

    ex.MySQLUserPerms.sh

  3. Find the location of your Apache WEB server DocumentRoot and cgi-bin directory. Typical locations are: /var/www and /usr/local/apache, /var/www/html, /var/www/cgi-bin The directory where these are located is referred to as WEBROOT in this documentation: 

    WEBROOT=/var/www
export WEBROOT

    The browser WEB pages and cgi-bin binaries expect these two directories to be next to each other in ${WEBROOT} since referrals in html are often: "../cgi-bin"

    The browser should function even if WEBROOT is in a different directory from the primary Apache web root. In this case, the three directories: html cgi-bin and trash should be at the same level in this other WEBROOT. For example: 

        /some/other/directory/path/html/
    /some/other/directory/path/cgi-bin/
    /some/other/directory/path/trash/

    Symlinks to the trash directory should exist from the html directory. As so: 

        /some/other/directory/path/html/trash -> ../trash

    The actual trash directory can be somewhere else. If it is not in your Apache /var/www/trash/ directory, then create that symlink as well as the html/trash symlink. For example /var/www/trash -> /some/other/directory/trash /var/www/html/trash -> /some/other/directory/trash

  4. Create html, cgi-bin and trash directories: 

    mkdir ${WEBROOT}/html
mkdir ${WEBROOT}/cgi-bin
chmod 755 ${WEBROOT}/cgi-bin

    (this chmod 755 will prevent suexec failures that are indicated by "Premature end of script headers" errors in the Apache error_log. Your cgi binaries should also be 755 permissions.) 

    mkdir ${WEBROOT}/trash
chmod 777 ${WEBROOT}/trash
ln -s ${WEBROOT}/trash  ${WEBROOT}/html/trash

    The browser creates .png (and other) files in the trash directory. The 'chmod 777' allows the Apache WEB server to write into that directory.

    A cron job should be set to periodically clean the files in trash. See also, the two scripts here: src/product/scripts/trashCleanMonitor.csh src/product/scripts/trashCleaner.csh

  5. Download static WEB page content: See also: src/product/scripts/updateHtml.sh

  6. Copy CGI binaries: This set of binaries are for x86_64 types of Linux machines. Both rsync commands accomplish the same task, querying either the North American or European download server. If you need to instead build binaries for your platform, follow the instructions in: README.building.source See also: src/product/scripts/kentSrcUpdate.sh 

    rsync -avP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
    rsync -avP rsync://hgdownload-euro.soe.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/

  7. Create hgcentral database and tables. This is the primary gateway database that allows the browser to find specific organism databases. See also: scripts/fetchHgCentral.sh to fetch a current copy of hgcentral.sql 

    mysql -u browser -pgenome -e "create database hgcentral;"
mysql -u browser -pgenome hgcentral < hgcentral.sql

    Please note, it is possible to create alternative hgcentral databases. For example, for test purposes. In this case use a unique name for the hgcentral database, such as "hgcentraltest", and it can be specified in the hg.conf file as mentioned in the next step. To create a second copy of the hgcentral database: 

    mysql -u browser -pgenome -e "create database hgcentraltest;"
mysql -u browser -pgenome hgcentraltest < hgcentral.sql

  8. Create the hg.conf file in ${WEBROOT}/cgi-bin/hg.conf to allow the CGI binaries to find the hgcentral database

    Use the file here: ex.hg.conf as the beginning template for your system:

    Copy the sample hg.conf: 

    cp ex.hg.conf ${WEBROOT}/cgi-bin/hg.conf

    Please edit this hg.conf file and set any parameters required for your installation. Use the comments in that file as your guide.

    Browser developers will want a copy of this file in their home directory with mode 600 and named: ~/.hg.conf

    These copies may have different db.user specification to allow developers write access to the database. See also: README.mysql.setup

  9. Load databases of interest. See also: README.QuickStart

    src/product/scripts/activeDbList.sh src/product/scripts/minimal.db.list.txt src/product/scripts/loadDb.sh

    And discussion in scripts/README about whether you can use directly the MySQL binary database files, or if you need to download goldenPath database text dumps and load them into the database.

    An alternative to loading the database tables from text files, is to directly rsync the MySQL tables themselves from either the North American or European download servers and place them in your MySQL /var/ directory. These tables are much larger than the text files due to the sizes of indexes created during a table load, but it can save a lot of time since the data loading step is quite compute intensive. Typical rsync commands for an entire database (e.g. ce4) would be something like: 

    rsync -avP --delete --max-delete=20 rsync://hgdownload.soe.ucsc.edu/mysql/ce4/ /var/lib/mysql/ce4/
    rsync -avP --delete --max-delete=20 rsync://hgdownload-euro.soe.ucsc.edu/mysql/ce4/ /var/lib/mysql/ce4/

  10. Download extra databases to work with a full genome assembly such as human/hg38: hgFixed go140213 proteins140122 sp140122 Construct symlinks in your MySQL data directory to use database names: go proteome uniProt for these database directories: 

    $ ls -og proteome go uniProt
lrwxrwxrwx 1  8 Feb 26 11:39 go -> go140213
lrwxrwxrwx 1 14 Mar 27 12:01 proteome -> proteins140122
lrwxrwxrwx 1  8 Mar 27 12:01 uniProt -> sp140122

$ ls -ld go140213 proteins140122 sp140122
drwx------ 2 mysql mysql 4096 Feb 26 10:57 go140213
drwx------ 2 mysql mysql 4096 Aug 19 08:08 proteins140122
drwx------ 2 mysql mysql 4096 Mar 26 13:01 sp140122

    These file names are data stamped YYMMDD to indicate changes over time as they are updated with new builds of the UCSC gene track. When a new UCSC gene track is released, fetch new databases and change the symlink.

  11. Copy the gbdb data to /gbdb - See also: scripts/fetchFullGbdb.sh scripts/fetchMinimalGbdb.sh

  12. The browser should now appear at the URL: http://localhost/

    Check your Apache error_log file for hints to solving problems.

  13. BLAT server setup: The blatServers table in the database hgcentral needs to have a fully qualified host name specified in the 'host' column.

    Educational and non-profit institutions are allowed to use blat free of charge. Commercial installations of the browser require a license for blat. See also: http://kentinformatics.com/index.html and: http://genome.ucsc.edu/license/ In the source tree: src/gfServer/README.blat

  14. Useful links:

    http://genomewiki.ucsc.edu/index.php/Category:Mirror_Site_FAQ

    There are numerous README files in the source tree on a variety of specific subjects, e.g.: 

    ./src/README
./src/product/README.*
./src/hg/makeDb/trackDB/README
./src/hg/makeDb/doc/make*.txt

  15. Apache configuration:

    To lock down your trash directory from scanning via "indexes" enter the following in your httpd.conf: 

    <Directory "/var/www/html/trash">
Options MultiViews
AllowOverride None
Order allow,deny
Allow from all
</Directory>

    The specified directory name is your apache: DocumentRoot/trash e.g. /usr/local/apache/htdocs/trash

MySQL Setup

  1. Enable "LOAD DATA LOCAL INFILE":

    Set these in /etc/my.cnf or /etc/mysql/my.cnf: 

    [mysqld]
local-infile=1

[client]
local-infile=1

  2. MySQL Storage Engine:

    In recent versions of MySQL, the default storage engine has changed from myisam to innodb. However the myisam engine should be used with the UCSC Genome Browser.

    Set it in /etc/my.cnf or /etc/mysql/my.cnf: 

    [mysqld]
default-storage-engine=MYISAM

    Always restart your mysql server after making changes to these configuration files.

  3. Users: There are three cases of identity to consider when providing access to the MySQL system for the browser CGI binaries and browser developers:

    1. A MySQL user that needs read-only access to the genome databases. The browser CGI binaries require read-only access to the genome databases.
    2. A MySQL user that has write permissions to one database. The CGI binaries require write permissions to one particular database (hgcentral) for maintaining user's cart information to store the user's browser cookie settings.
    3. A MySQL user that has general write permissions to all browser and genome databases to be used by developers

    The cgi-bin binaries obtain the first two of these MySQL identities from the text file: $WEBROOT/cgi-bin/hg.conf

    Developers of the browser databases obtain their MySQL identities from a text file in their home directory: ~/.hg.conf Note the initial dot in the name: .hg.conf This file in a user's directory will specify a higher-privileged user to allow read/write access to the MySQL databases. This file must be set to mode 600 to provide security of the user and password to the database: 

    $ chmod 600 ~/.hg.conf

    All kent source code commands use this file to access the MySQL databases. Since this file contains password information it requires the permissions to be set at 600 to keep it secret. The kent source code commands will enforce this access and not function unless it is set at 600 permissions.

    Therefore you will want to create three different MySQL users for these purposes.

    The examples listed below are implemented in the shell script: src/product/scripts/ex.MySQLUserPerms.sh You can execute that script to set up these example users.

    An example full read/write access user: "browser", is created with the following procedure.

    For the following it is assumed that your root account has access to the mysql database. You should be able to perform the following: 

    $ export SQL_PASSWORD=mysql_root_password
$ mysql -u root -p${SQL_PASSWORD} -e "show tables;" mysql

    Create a MySQL user called "browser" with password "genome" and give access to selected MySQL commands for the following list of databases. When you add other databases, you will need to add these permissions to your databases. This procedure of adding permissions specifically for a set list of databases is a more secure method than allowing the MySQL "browser" user to have access to any database.

    ( MySQL version 5.5 requires the LOCK TABLES permission here ) ( FILE, CREATE, DROP, ALTER, LOCK TABLES, CREATE TEMPORARY TABLES on ${DB}.* ) 

    for DB in cb1 hgcentral hgFixed hg38 proteins140122 sp140122 go140213 uniProt go proteome
do
    mysql -u root -p${SQL_PASSWORD} -e "GRANT SELECT, INSERT, UPDATE, DELETE, \
    FILE, CREATE, DROP, ALTER, CREATE TEMPORARY TABLES on ${DB}.* \
    TO browser@localhost \
    IDENTIFIED BY 'genome';" mysql
done

    The above granted permissions are recommended for browser developers. The WEB browser CGI binaries need SELECT, INSERT and CREATE TEMPORARY TABLES permissions. For example, you should create a special user for the browser genome databases only. In this example, user: "readonly" with password: "access" 

    for DB in cb1 hgcentral hgFixed hg38 proteins140122 sp140122 go140213 uniProt go
 proteome
do
    mysql -u root -p${SQL_PASSWORD} -e "GRANT SELECT \
        on ${DB}.* TO \
        readonly@localhost IDENTIFIED BY 'access';" mysql
done

    Create a database to hold temporary tables: 

    mysql -u root -p${SQL_PASSWORD} -e "create database hgTemp"

mysql -u root -p${SQL_PASSWORD} -e "GRANT SELECT, INSERT, \
    CREATE TEMPORARY TABLES \
    on hgTemp.* TO \
    readonly@localhost IDENTIFIED BY 'access';" mysql

    A third MySQL user should be created with read-write access to only the hgcentral database. For example, a user: "readwrite" with password: "update" 

    for DB in hgcentral
do
    mysql -u root -p${SQL_PASSWORD} -e "GRANT SELECT, INSERT, UPDATE, DELETE, \
        CREATE, DROP, ALTER on ${DB}.* TO readwrite@localhost \
        IDENTIFIED BY 'update';" mysql
done

    The cgi-bin binaries obtain their MySQL identities from the hg.conf file in the cgi-bin directory. The file in this directory: src/product/ex.hg.conf demonstrates the use of the "readonly" user for genome database access and the "readwrite" user for hgcentral database access.

  4. The hgsql command: Developers can access the browser databases via the 'hgsql' command which can be built in the source-tree at:

    kent/src/hg/hgsql/

    This 'hgsql' command provides a convenient front-end to the standard 'mysql' command by reading the user's ~/.hg.conf file to provide access to the browser databases with the appropriate identity. Each user creates a ~/.hg.conf file (same format as the above mentioned cgi-bin/hg.conf file) and the specified database user identity is used for accesses to the browser databases.

    This same function of reading ~/.hg.conf for database access is built into all the source-tree binaries which modify the genome databases.

    The above example hg.conf could be used as a user's ~/.hg.conf file with the change of db.user, db.password, central.user, and central.password to be the fully permitted read-write user: 

    db.user=browser
db.password=genome
central.user=browser
central.password=genome
central.db=hgcentral

    To test this access with your ~/.hg.conf file in place: 

    hgsql -e "show tables;" hgcentral
hgsql -e "show grants;" hgcentral

  5. Configuring MySQL SSL connections:

    MySQL is typically compiled with SSL capability from OpenSSL or yaSSL. To see if your server supports ssl, login to mysql and run this command: 

    mysql> show variables like '%ssl%';
+---------------+----------+
| Variable_name | Value    |
+---------------+----------+
| have_openssl  | DISABLED |
| have_ssl      | DISABLED |
| ssl_ca        |          |
| ssl_capath    |          |
| ssl_cert      |          |
| ssl_cipher    |          |
| ssl_crl       |          |
| ssl_crlpath   |          |
| ssl_key       |          |
+---------------+----------+

    If your mysql was compiled with SSL support, which is true of virtually all mysql packages being provided today, you can easily enable SSL by adding settings to /etc/my.cnf: 

    -------
my.cnf:
-------

[mysqld]
ssl
ssl-key=/somepath/server-key.pem
ssl-cert=/somepath/server-cert.pem
ssl-ca=/somepath/ca.pem
ssl-capath=/somepath/
ssl-cipher=DHE-RSA-AES256-SHA:AES128-SHA
# mysql 5.6.3 or later
ssl-crl=/someCrlPath/some-crl.pem
ssl-crlpath=/someCrlPath/
# mysql5.7 or later require all connections to be encrypted
require_secure_transport server

    After making changes to my.cnf, be sure to restart your mysqld service.

    The key means private key here, and should be kept secured. The cert is a certificate acting like a public key, signed by a trusted authority (CA).

    If a key and cert are available, that means you can authorize. And it proves the key exists. The key is not sent to the other party. The cert is. If a ca is available it can show what certs to trust.

    You do not need all the settings, but some versions of mysql do not activate SSL unless at least one of these is found: key, cert, ca, capath, cipher If you configure a key for the server or client, you will also provide its cert.

    We cannot teach you how to create SSL certificates here. There are many websites including mysql that have information about making keys and certs and ca.

    If you just add the ssl option to the top, it will try to use SSL, or make it available.

    The ca is the certificate authority cert that you are using. It could be just a local self-signed authority you made up, or it can be a commercial authority like veriSign. This typically is used to sign the certificate for the server and users. The capath is a directory where ca-certs exist (OpenSSL only).

    The crl is a certificate revocation list. (OpenSSL only). The crlpath is a directory where revocation lists exist (OpenSSL only). This crl options are a new feature in 5.6.3, not sure it works right yet.

    After making a key for the server, and signing a cert for it with ca, you can create SSL connections.

    Do not specify a passphrase when creating your server keys.

    The cipher setting is a colon-separated list of SSL ciphers that are supported.

    The security files like certs etc. that are specified in the above settings must be readable by the unix account that mysqld runs under, default is "mysql".

    SELinux or apparmor may block access to certain locations. /etc/mysql is the default location for .pem files on some platforms.

    yaSSL, which is still often used with the MySQL Community Edition, expects keys to be in the PKCS #1 format and doesn't support the PKCS #8 format used by OpenSSL 1.0 and newer. You can convert the key to the old format using openssl rsa: openssl rsa -in key_in_pkcs1_or_pkcs8.pem -out key_in_pkcs1.pem

    yaSSL requires that all components of the CA certificate tree be contained within a single CA certificate file and that each certificate in the file has a unique SubjectName value. To work around this limitation, concatenate the individual certificate files comprising the certificate tree into a new file and specify that file as the value of the --ssl-ca option. For example, 

    cd my-certs-dir
cat ca-cert.pem server-cert.pem (etc) > yaSSL-ca-cert.pem
chmod +r yaSSL-ca-cert.pem

    Now use my-certs-dir/yaSSL-ca-cert.pem for certificate authority (ca) for clients.

    These are the SSL settings which can be placed into your hg.conf for CGIs or .hg.conf for utility programs: 

    db.key=/sompath/someuser-key.pem
db.cert=/sompath/someuser-cert.pem
db.ca=/somepath/ca.pem
db.caPath=/somepath
db.crl=/someCrlPath/some-crl.pem
db.crlPath=/someCrlPath/
db.verifyServerCert=1
db.cipher=DHE-RSA-AES256-SHA:AES128-SHA

    The key and certificate for "someuser" above are signed by a ca.

    The verifyServerCert setting if it exists tells the client to verify that the CN field in the server's cert matches the hostname to which it is connecting. This prevents Man-In-the-Middle attacks.

    The caPath and crlPath options only work with OpenSSL.

    The example shows the most common use for the profile "db". But the SSL settings work with any profile in the hg.conf file.

    Of course you can stick SSL settings into your [client] section of my.cnf, but the CGIs and utils would not see them. Only mysql and hgsql would see them.

    Configuring SSL requirements for mysql user accounts:

    You can tell mysql to require SSL for a user's account like this: 

    GRANT ALL PRIVILEGES ON *.* TO 'someuser'@'%'
  REQUIRE SSL;

    You can tell mysql to use SSL for a user's account and to further require the client to use their key and x509 certificate to connect by saying: 

    GRANT ALL PRIVILEGES ON *.* TO 'someuser'@'%'
  REQUIRE x509;

    There are more-specific requirements that may be added: 

    GRANT ALL PRIVILEGES ON *.* TO 'someuser'@'%'
  REQUIRE SUBJECT '/C=US/ST=CA/L=Santa Cruz/O=YourCompany/OU=YourDivision/CN=someuser/emailAddress=someuser@YourCompany.com'
      AND ISSUER  '/C=US/ST=CA/L=Santa Cruz/O=YourCompany/OU=YourDivision/CN=YourCompanyCA/emailAddress=admin@YourCompany.com'
      AND CIPHER  'DHE-RSA-AES256-SHA';

    You can see the cert details like this: openssl x509 -in /somepath/someuser-cert.pem -text

    In later versions of MySQL, it is a requirement that the CN of the CA cert must DIFFER from the CN of the user and server certs.

    Further MySQL SSL documentation is available from https://dev.mysql.com/doc/refman/5.6/en/using-encrypted-connections.html

Adding a custom genome to the browser

Please note that setting up an assembly hub is a lot easier than adding a genome to a local mirror.

The browser can be made to operate with a bare minimum of tables for the purpose of demonstrating the CGI binaries are functioning.

The only tables you need to load for this are:

  1. all tables in the hgcentral database
  2. six tables in the human genome

Create an empty hgcentral database: 

$ hgsql -e "create database hgcentral;" mysql

Load all tables into the hgcentral database. Copy all the mysql data files from either the North American or European download server 

rsync -avP rsync://hgdownload.soe.ucsc.edu/mysql/hgcentral/ .
rsync -avP rsync://hgdownload-euro.soe.ucsc.edu/mysql/hgcentral/ .

directly into the MySQL data area for your hgcentral database. (something usually like /var/lib/mysql/hgcentral/)

Or load this database with mysql/hgsql commands and the hgcentral.sql text file dump of these tables from: 

rsync -avP rsync://hgdownload.soe.ucsc.edu/genome/admin/hgcentral.sql .
rsync -avP rsync://hgdownload-euro.soe.ucsc.edu/genome/admin/hgcentral.sql .

And then six tables for the latest human database.

The gateway page always needs a minimum human database in order to function even if the browser is being built for the primary purpose of displaying other genomes. This default can currently be changed in the source tree in src/hg/lib/hdb.c (to be done: specify this default in hg.conf file)

Start with an empty database, for example hg18: 

hgsql -e "create database hg18;" mysql

Again, copy the MySQL files directly from one of the download servers, for example, hg18: 

rsync -avP rsync://hgdownload.soe.ucsc.edu/mysql/hg18/ .
rsync -avP rsync://hgdownload-euro.soe.ucsc.edu/mysql/hg18/ .

(beware, this is several TB of data) into your MySQL data area. Or load these tables from the text SQL dumps from: 

rsync -avP rsync://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ .
rsync -avP rsync://hgdownload-euro.soe.ucsc.edu/goldenPath/hg18/database/ .

(beware, this is several TB of data)

The minimal set of tables required are: 

grp
trackDb
hgFindSpec
chromInfo
gold
gap

With this set of six tables the gateway page will begin to function and the browser page and table browser will function. Other browser functions are not ready yet without additional tables and databases. This is a bare minimum just to demonstrate the CGI binaries are working.

This will all work even without copying any files for the /gbdb/ data area, although most functions will not work, such as fetching the DNA sequence from a browser view. The DNA sequence for an assembly is found in, for example hg18: /gbdb/hg18/nib/chr*.nib Some assemblies have all the DNA sequence in a single .2bit file, for example: /gbdb/mm8/mm8.2bit

Modifying the source code

If you want to make changes to the source code, contact us first via the mailing list, to make sure that there is no option in development or an undocumented way to solve your problem.

If you need to change the code, make sure to isolate your changes into a single function, if possible. Using git, merge your branch into our "beta" branch, ideally for every release, then recompile. If your changes could be useful for someone else, and you are getting tired of updating them to keep up with our changing code base, consider submitting them as a pull request, so we can integrate it into the main code base and you do not have to worry about updating them anymore.

Once you have git setup properly, merging your changes into our current release should be as easy as this: 

git pull # get new version
git checkout beta # switch to our stable branch
git merge myChangesBranch # merge your changes into the beta branch
make -j 20 cgi-alpha # compile and put CGIs into /usr/local/apache/cgi-bin

Custom Track Database

A new feature of the genome browser as of March 2007 is the ability to use a data base for custom tracks. Up to this date, custom track data has been kept in files in the /trash/ct/ directory. This article discusses the steps required to enable this function.

  1. Summary configuration

  2. Host and database name

    For performance and security considerations, the MySQL host for the custom track database can be a separate machine from the ordinary MySQL host that usually serves up the assembly databases or the hgcentral database. It is not required that the custom track database be on a separate MySQL server. The specification of the host machine is placed in the /cgi-bin/hg.conf file, for example a host machine called "ctdbhost":

    customTracks.host=ctdbHost

    The database name used on this host is fixed at customTrash which is a define in the source tree file hg/inc/customTrack.h

    Edit /cgi-bin/hg.conf configuration items:

    The following items must be specified in /cgi-bin/hg.conf to enable this function: 

    customTracks.host=ctdbhost
customTracks.user=ctdbuser
customTracks.password=ctdbpasswd
customTracks.useAll=yes

    Establish this user account and password in MySQL with db and user privileges:

    Select, Insert, Update, Delete, Create, Drop, Alter, Index for example with your MySQL root user account: 

    hgsql -hctdbhost -uroot -p -e \
    "GRANT SELECT,INSERT,UPDATE,DELETE,CREATE,DROP,ALTER,INDEX" \
    on customTrash.* TO ctdbuser@yourWebHost IDENTIFIED by 'ctdbpasswd';" mysql

    Optionally, a temporary read-write directory used during database loading can be specified: 

    customTracks.tmpdir=/data/tmp

    The default for this is /data/tmp and should be created with read/write/delete access for the Apache server effective user. It should be on a local filesystem for best access speed, not via NFS.

  3. Database loaders:

    The database loaders used to load custom tracks are the standard loader commands found in the source tree, hgLoadBed, hgLoadWiggle and wigEncode. They are installed into /cgi-bin/loader/ with a 'make cgi' from the source tree directory kent/src/hg/ These loaders are used by the cgi binaries hgCustom, hgTracks, and hgTables to load custom tracks into the database. They are operated in an exec'd pipeline fashion, the code details can be see in src/hg/lib/customFactory.c

  4. Command line access:

    Since the MySQL host may be different than your ordinary MySQL host, you will need to create a unique $HOME/.ct.hg.conf file to be used in the case where you want to manipulate this separate database with the kent source tree command line tools. This unique .ct.hg.conf is merely a copy of your normal .hg.conf file but with a different host/username/password specified: 

    db.host=ctdbhost
db.user=ctdbuser
db.password=ctdbpasswd
central.db=hgcentral

    Remember to set the privileges on this hg.conf file at 600: 

    chmod 600 $HOME/.ct.hg.conf

    To enable the use of this file for subsequent command line operations, set the environment variable HGDB_CONF to point to this file, for example in the bash shell: 

    export HGDB_CONF=$HOME/.ct.hg.conf

    With that in place, you can examine the contents of the customTrash database: 

    hgsql -e "show tables;" customTrash

    This unique hg.conf file will also be used by the cleaner command dbTrash

  5. Cleaner script

    The database and the temporary data directory /data/tmp need to be kept clean. This is similar to the current cleaner script you have running on your /trash filesystem. In this case there is a specific source tree utility used to access and clean the database. The temporary data directory /data/tmp would stay clean if each and every loaded custom track was successfully loaded. In the case of badly formatted or illegal data submitted for the custom track, the database loaders do not remove their temporary files from /data/tmp This /data/tmp directory can be kept clean with, for example, an hourly cron job that performs: 

    find /data/tmp -type f -amin +10 -exec rm -f {} \;

    This would remove any file not accessed in the past 10 minutes.

    The database cleaner command dbTrash should be run as a cron job encapsulated in a shell script something like this, which maintains a record of items cleaned to enable later analysis of custom track database usage statistics: 

    #!/bin/sh

DS=`date "+%Y-%m-%d"`
YYYY=`date "+%Y"`
MM=`date "+%m"`
export DS YYYY MM

mkdir -p /data/trashLog/ctdbhost/${YYYY}/${MM}
RESULT="/data/trashLog/ctdbhost/${YYYY}/${MM}/${DS}.txt"
export RESULT

/cluster/bin/x86_64/dbTrash -age=48 -drop -verbose=2 > ${RESULT} 2>&1

    Running this once a day will remove any tables not accessed within the past 48 hours. The dbTrash command is found in the source tree in kent/src/hg/dbTrash

    The /trash directory can be kept clean with the following two commands, one to implement an 8 hour expiration time on most files, the second to implement a 48 hour expiration time on custom track files: 

    find /trash \! \( -regex "/trash/ct/.*" -or -regex "/trash/hgSs/.*" \) \
    -type f -amin +480 -exec rm -f {} \;
find /trash \( -regex "/trash/ct/.*" -or -regex "/trash/hgSs/.*" \) \
    -type f -amin +2880 -exec rm -f {} \;

  6. metaInfo and history

    You will note two special and persistent tables in the customTrash database: metaInfo and history. The metaInfo table records a time of last use for each custom track table and a useCount for statistics. The time of last use is used by the cleaner utility dbTrash to expire older tables. The history table is the same as the history table in the normal assembly databases. The loader commands, hgLoadBed and hgLoadWiggle record into the history table each time they load a track. The cleaner command dbTrash also records in the history table statistics about what it is removing.

  7. Turning On Considerations

    Please note, if there are currently existing custom tracks in /trash/ct/ files, at the time of adding the configuration items to /cgi-bin/hg.conf/ those existing tracks will be converted to database versions upon their next use by the user. Therefore, to enable this function on the round-robin WEB servers, we will need to do the update to /cgi-bin/hg.conf in as much a simultaneous manner as possible. Perhaps something like a shell script to do eight background rsync's all at the same time.

  8. Use of trash files with the database on

    When the custom tracks database is in use, there are still small files kept in /trash/ct which become the reference pointers to the actual database tables belonging to that custom track. The standard trash cleaner script should still be kept running to clean these files.

  9. Known difficulties

    For the case of a custom track submission that contains more than one track set of data, in the case where one of the sets of data is illegal and causes a loading problem, even though some sets of data may have loaded successfully, the submitting user will see an error about the corrupted data, and they would need to correct their data submission to get all tracks successfully loaded.

    It remains to be seen just how good the error reporting system is for illegal data.

Debugging the CGI binaries

The typical sign of trouble is an Error 500 display in your web browser when accessing the CGI binaries, and the following message in your Apache error log: 

[Fri Mar 25 11:02:40 2005] [error] Premature end of script headers: hgTracks

This is usually a simple configuration problem. Items to verify:

  1. the hg.conf file in the cgi-bin directory specifies the correct user names and passwords for MySQL database access. See also: README.mysql.setup
  2. The cgi-bin directory is set to permissions 755 and not 775 or 777 When permissions are too permissive for this directory, Apache errors out with suexec permission violations.
  3. Verify change history of the database hgcentral. Rarely, changes in this database require corresponding changes in the source code. Make sure your code and version of hgcentral are synchronized. Newer versions of hgcentral database with old source code are OK. The problem is when you have new source code that expects new features in hgcentral.

If these items are OK, then you can check the actual operation of a cgi binary. Go to the source tree directory of the cgi binary, for example hgTracks: 

kent/src/hg/hgTracks

In this directory, run a 'make compile' to produce a binary that is left in this directory. This binary can be run from the command line: 

./hgTracks

By itself with no arguments, it should produce the default tracks display HTML page for the Human genome. This assumes you have set up your $HOME/.hg.conf file to allow access to the MySQL databases. (See also: README.mysql.setup). A binary execution failure should be obvious at this stage of the game. If it exits because of SIGSEGV we can run it under a debugger for specifics. More on this below.

If the problem is specific to a particular set of tracks being displayed, or particular genomes or options, command line arguments can be given to these CGI binaries to provide the URL inputs that a CGI binary would normally see.

To prepare the binaries for operation under a debugger, go to the src/inc directory and edit the common.mk configuration file. Change "COPT=-O" to read: "COPT=-g" GNU gcc will allow "-O" with "-g", and some bugs will only exhibit themselves with -O on. However the optimizations with -O can sometimes confuse the debugger's sense of location due to optimization rearrangement of code. Also eliminate the -Wuninitialized option from the HG_WARN definition to avoid constant warnings about that being incompatible with -g.

Rebuild the source tree: 

cd kent/src
make clean
make libs
cd hg/hgTracks
make compile

The hgTracks binary will now have all symbol information in it and it can be operated under a debugger such as ddd (or gdb, etc...).

For the case of specific options or tracks causing problems, to find the full set of options in effect for the failure case, when your WEB browser is at the Error 500 display page, edit the displayed URL in your WEB browser to call the cgi binary cartDump: http://html/cgi-bin/cartDump

This will display all environment variables in effect at the time of the crash. Most of the track display options that are marked as "hide" can be ignored. That is their default setting already. The important ones are the db, position, and specific options for the track under consideration. The command line can be formatted just as if it was a URL string. For example: 

./hgTracks "db=hg17&trackControlsOnMain=0&position=chr4:56214201-56291736"

Or with spaces between the arguments: 

./hgTracks db=hg17 trackControlsOnMain=0 position=chr4:56214201-56291736

Remember to protect special characters on the command line from shell interpretation by appropriate quoting.

At this point, running under a debugger, with a command line for specific options, a crash of the binary should give you some clue about the problem by checking the stack backtrace to see what function is failing. It is highly doubtful you will be finding problems in the source code for the crashes. The almost universal cause for failure are the data inputs to the binaries. For example, violations of the SQL structures expected from the database tables. Missing data files in the /gbdb/ hierarchy, and so forth.

If you are developing code for special track displays, the most common form of problem is a memory violation while using some of the specialized structures, hash lists, etc. Your stack backtrace will usually highlight these situations.

In order to determine the URL being used by the browser CGIs to pass to in the debugger, you need to force the browser to use GET http requests rather than POST. Try adding &formMethod=GET to an URL. Not all forms pay attention to that input, but when they do it generally looks like this:

hPrintf("

tex", getScriptName(), cartUsualString(cart, "formMethod", "POST"));

If you add &formMethod=GET and a subsequently fetched form is still posting, you might need to alter the "<FORM..." statement to use the cartUsualString.

The hg18 hgTracks config page generates a GET URL that is too long for FireFox, so after debugging hgTables, you will probably want to add &formMethod=POST to an URL (or clear cart, load session etc).

One thing that does not work with GET is "upload file" inputs.

Local Git repository

Use the following procedures to create your own personal copy of the kent source tree where you can have your own edits that are not part of the development at UCSC. This is useful for mirror sites that have their own customizations in the source tree for local circumstances.

Install Git software version 1.6.2.2 or later. See the Git Community Handbook installation (http://book.git-scm.com/2_installing_git.html) and setup (http://book.git-scm.com/2_setup_and_initialization.html) instructions, as well as our Installing git (http://genomewiki.ucsc.edu/index.php/Installing_git) Genomewiki page.

Start an initial Git local repository: 

git clone git://genome-source.soe.ucsc.edu/kent.git

or, if a firewall prevents git daemon port 9418, use: 

git clone http://genome-source.soe.ucsc.edu/kent.git

The kent source tree will be imported to the current working directory in a directory named ./kent/.

Track the beta branch at UCSC repository: Most users want to use the beta branch, which has tested, released versions of the browser. To create a beta tracking branch: 

cd kent
git checkout -t -b beta origin/beta

The -b creates a local branch with name "beta", and checks it out. The -t makes it a tracking branch, so that 'git pull' brings in updates from origin/beta, the "real" beta branch in our public central read-only repository.

To get the latest UCSC release, from anywhere within the kent source tree: 

git pull

Updates: UCSC generally updates the origin/beta branch every three weeks. If you are updating database tables for a mirror site, we recommend that you update the source at the same time, as source code is sometimes modified to include operations on new columns that have been added to database tables.

See also: the README files in the source tree directory src/product/README.*. For instructions on keeping local tracks separate from UCSC Genome Browser tracks, see src/product/README.trackDb.

Proxy support

net.c now has support for http(s) proxy servers which may be required by some installations to get through the firewall to external resources such as (but not limited to) for example bigWig or bigBed data via custom track bigDataUrl.

One must add the setting "httpProxy", "httpsProxy", "ftpProxy" to hg.conf

httpProxy=http://someProxyServer:3128 httpsProxy=http://someProxyServer:3128 ftpProxy=ftp://127.0.0.1:2121

If the proxy server requires BASIC authentication

httpProxy=http://user:password@someProxyServer:3128 httpsProxy=http://user:password@someProxyServer:3128

where user and password may need URL-encoding if they contain special characters such as ":" and "@".

If you wish to exclude domains from proxying, create a comma-separated list of domain-suffixes.
If a domain ends with an entry from this list, the proxy will be skipped.

noProxy=ucsc.edu,mit.edu

(The httpProxy and httpsProxy URLs should use http protocol, not https. One reason for this is that https sessions would end up doubly-encoded.)

If you are debugging your proxy configuration, you can use this hg.conf setting to turn on logging to stderr.

logProxy=on

It is not meant to be left on in production. Your proxy server should have its own logging features.

net.c also responds to environment variables http_proxy, https_proxy, ftp_proxy, no_proxy and log_proxy.

Adding tracks to the browser

See also:

A track needs two items to make it exist in the browser:

  1. A database table with the track data
  2. An entry in a database table: trackDb_localTracks Built from track specifications in your trackDb.ra file. Please note the description of trackDb.ra entries in the source tree: src/hg/makeDb/trackDb/README The correspondence between the database table and the trackDb.ra definition is in the name used on the 'track' line in the trackDb.ra file. Your database table name is used on the 'track' definition line.

Almost all of the database tables have specific loader programs to load the track data. The loader programs also verify the data before it is added to the table, and they create the proper indexes on the table to allow efficient display by the genome browser.

By far the most common format of track data is the BED format. See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 for a description of BED file formats.

A typical BED file format is loaded into a database table with the loader: hgLoadBed For example, to load the data from the file: data.bed into the table named: bedExample 

hgLoadBed hg17 bedExample data.bed

There are a variety of file formats: GFF, GTF, PSL, WIG, MAF as well as a variety of specialized data types. All the loader programs can be seen in the source tree as subdirectories in: src/hg/makeDb/ 

cd src/hg/makeDb
ls -d hg*

The build instructions for the browser code do not include instructions for building all of the loaders, or other utilities in the kent source tree. This is because there are literally hundreds of utilities, 345 at last count, that are not needed for ordinary browser development. In most cases a developer will need only a couple of the loaders and utilities. Since the libraries were built for the CGI binaries, to build any utility or loader, simply go into its directory and run a 'make'

For our purposes here, we need for example, for BED format tracks:

  1. hgLoadBed
  2. hgTrackDb
  3. hgFindSpec

To build the three loaders mentioned, go to the three directories: 

src/hg/makeDb/hgTrackDb/
src/hg/makeDb/hgFindSpec/
src/hg/makeDb/hgLoadBed/

And run a 'make' in each one. The resulting binary is placed in: \(HOME/bin/\)MACHTYPE This binary directory should be in your PATH, or make this directory be a symlink to some binary directory that is in your PATH and you have write permission to.

With those three loader programs built, you can now load BED format tracks, and build the trackDb_localTracks table as mentioned next.

The hgTrackDb and hgFindSpec loaders are used to build the trackDb and hgFindSpec tables in the database. Older instructions used to mention using the trackDb file hierarchy in the source tree. This is no longer necessary and is not recommended. You can certainly obtain example trackDb entries from the source tree hierarchy: src/hg/makeDb/trackDb/ in any of the *.ra files. And you will need to refer to the README file in that directory for information about options you can use with each track type. To work independently of the UCSC source tree, establish your own trackDb.ra files outside the UCSC source tree in a directory of your choice under your control. Then, to load them into the database, run the hgTrackDb command with this simple makefile in the directory where your .ra file exists: 

trackDbSql=/path/to/kent/source/tree/src/hg/lib/trackDb.sql
DB=hg19

all::
        hgTrackDb . ${DB} trackDb_localTracks ${trackDbSql} .

This hgTrackDb command reads your trackDb.ra file and converts it into row entries for each track specified in it into row contents in this new table trackDb_localTracks.

The DB= specification is your database of interest, this example: hg19 This loads your local specific table trackDb_localTracks in the database. This name trackDb_localTracks is not special, just different than the ordinary trackDb table. It should have some meaning to anyone in your environment and not be the same name as any UCSC database table. The two '.' arguments in the command above refer to directory names. Since you have no hierarchy of levels in this single directory, unlike in the source tree trackDb hierarchy, the '.' arguments refer to the current directory.

To direct the genome browser to this table to use as extra trackDb definitions, add to the specification in your cgi-bin/hg.conf file: 

db.trackDb=trackDb_localTracks,trackDb

Beware of the specified order of the tables if there are tracks by the same name in each table. Any definitions for tracks in trackDb_localTracks will override any definitions for the same named tracks in trackDb. You could thus override the standard definitions for tracks from the trackDb table. Your usual case will be that your tracks are unique to your local installation.

See also: new assistant scripts as of March 2010 in the src/product/scripts/ directory here to fetch and build the source tree.

Older instructions about building the source tree remain valid:

If you really do want to build all the utilities and all database loaders, perform the following 'make' commands in your source tree: 

cd src
make clean
make libs
cd hg
make
cd ../utils
make

This builds everything cleanly, all CGI binaries, all database loaders, all utilities. Perform this sequence each time you do a 'git pull' on your source tree. The 'make clean' step is especially important since the makefile hierarchy does not have built in dependencies and will not rebuild items that depend upon each other. The traditional dependency on the source tree libraries is taken care of because a make in any directory that produces a binary will always re-link the binary every time, thus always picking up any potentially new library.

The UDC local cache directory

The udcCache allows tracks that are either installed tracks or custom tracks of the above mentioned types to cache data that they have already fetched via URL. This allows data to reside elsewhere and only download the parts needed on demand. The datablocks are usually compressed and have an efficient random access index. They are accessed from a remote location via URLs such as HTTP, HTTPS, FTP.

By default, udcCache stores files in /tmp/udcCache

However, you may include the following in your hg.conf and then let your regular trash cleaning scripts clean out the old udcCache automatically as well: 

# directory for temporary bbi file caching
udc.cacheDir=../trash/udcCache

Notice that this path is relative to your cgi executable directory which is the current directory when the cgi starts up. On some systems this directory is called cgi-bin/.

Activating CRAM support for the Genome Browser.

The UCSC Genome Browser is capable of displaying tracks from both the BAM and CRAM file formats. While BAM tracks provide all of the required data within the file, however, CRAM tracks depend on external "reference sequence" files (see http://www.ebi.ac.uk/ena/software/cram-toolkit for more information about the CRAM format). A bit of information on how the Browser works with these files is included below. For installation instructions, skip to the numbered steps at the end of this file.

The directory that Genome Browser CGIs check for CRAM reference files is set with the cramRef setting in hg.conf. For example, the following setting is used on our production servers: 

cramRef=/userdata/cramCache

When loading tracks from the CRAM file format, CGIs will look for reference sequences in that directory. The filename of each reference sequence should be the MD5 or SHA1 checksum of the reference sequence as described at http://www.ebi.ac.uk/ena/software/cram-reference-registry. If a CGI is unable to find the reference sequence file for a CRAM track, it will next check the cramRef/pending/ directory to see if a request for that reference sequence has already been made, and the cramRef/error/ directory to see if a previous attempt at downloading that reference sequence resulted in an error. If none of those files are found, the CGI will then create a request file in the cramRef/pending/ directory. The name of the request file will be the MD5 or SHA1 sequence checksum, as specified in the CRAM data file. The contents of the request file will be the URL to download that reference sequence. A separate tool can then be used to download reference sequences listed in the pending/ directory and place them into cramRef/.

Steps to set up CRAM track support:

  1. Add the hg.conf setting cramRef. The value should be the path (relative or absolute) to a directory where CRAM reference sequences are stored.

  2. Inside the cramRef directory create subdirectories called "pending" and "error". The apache user must have read/write permissions for the pending/ directory, and at least read permissions for the cramRef/ and error/ directories.
    If you plan to manually load all CRAM reference sequences for your tracks into the cramRef directory, track support is now complete. If you prefer to have reference sequences automatically downloaded and placed in that directory (e.g., for user-submitted custom tracks), continue to step 3.

  3. Add a cron job to run a script that parses files in the cramRef/pending/ directory, downloads the corresponding reference sequence files, and places those sequence files in cramRef/. Error messages during file retrieval should be placed in cramRef/error/. An example script is provided in this repository at kent/src/product/scripts/fetchCramReference.sh. The account that runs this script must have read/write permissions for the cramRef/, cramRef/pending/, and cramRef/error/ directories.

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