Install gbrowse

Go to ActiveState. Version 5. Once downloaded, launch the package, and it will install automatically. I believe it can be installed in ActiveState Perl 5. I don't know of a similar repo for ActiveState Perl 5. Please accept the default location for ActiveState Perl; this will make it easier to install GBrowse. You might want to wait until after you've played with the flat-file based implementation a bit and decide you need better performance.

Read this section only if you are on a Unix system and do not have root privileges. You will need to configure Apache to run out of your home directory. One way to do this is to install Apache from source code and to specify your home directory when you first configure it:. If you also see a "Port 80" directive, change it to read "Port You may not need to install Apache from scratch if your Unix distribution already has Apache installed.

What you will do is to create an Apache directory tree in your home directory and then start Apache using command-line arguments that tell it to start up from the home directory rather than its default system-wide directory. Now copy the system-wide httpd. You may need to search around a bit to find out where the system-wide httpd. You should search the httpd. If you see a Port directive, change it to read "Port ". Somewhere in httpd.

Replace both these sections with the following:. If Apache starts successfully, then this command will return silently. Otherwise, it will print an error message. To confirm that Apache is running from your home directory, create a file named index. The installation procedure will create a small in-memory database of yeast chromosome 1 and 2 for you to play with. To try the browser out, use your favorite browser to open:. Then try searching for "membrane trafficking.

This step takes you through populating the database with the full yeast genome. You can skip this step if you use the in-memory database for small projects. Note: This section refers to the user account under which Apache runs as "nobody" because that is the most common case. However, many systems use a different user account.

You will need an installation of MySQL for this section. Using the mysql command line, create a database called "yeast" in the synopsis above , and ensure that you have update and file privileges on it. The example above assumes that you have a username of "me" and that you will allow updates from the local machine only. It also gives all privileges to "me". You will need to provide the administrator's name and correct password for these commands to succeed.

The web server usually runs as nobody, and must be able to make queries on the database. Modify this as needed if the web server runs under a different account. The next step is to load the database with data. This is accomplished by loading the database from a tab-delimited file containing the genomic annotations in GFF format. If you requested that BioPerl scripts be installed during installation, they will also be found in your command path. For testing purposes, this distribution includes a GFF file with yeast genome annotations.

If the load is successful, you should see a message indicating that features were successfully loaded. Provided that the yeast load was successful, you may now run make test. This invokes a small test script that tests that the database is accessible by the "nobody" user and that the basic feature retrieval functions are working. You may also wish to load the yeast DNA, so that you can test the three-frame translation and GC content features of the browser.

Because of its size, the file containing the complete yeast genome is distributed separately and can be downloaded from:. You should now be able to browse the yeast genome.

Type the following URL into your favorite browser:. This will display the genome browser instructions and a search field. Type in "III" to start searching chromosome III, or search for "glucose" to find a bunch of genes that are involved in glucose metabolism. Usually there will be an informative error message in the error log. The most common problem is MySQL password or permissions problems. An increasing number of model organism databases are distributing genome annotation in GFF3 format.

An example of this format can be found at SGD. Although these files will load into the standard Bio::DB::GFF database, some of the features of GFF3 , such as the ability to represent multiple alternative splice forms as a single gene, will be lost. Create a GBrowse config file by copying one of the existing examples, and modify the top lines to read like the following:. The database should now be browsable. For example, if you are on a RedHat system, where the default Apache.

The backslashes are there to split the command across multiple lines. To make it easier when upgrading to new versions of the software,. Note that the configuration files are always placed in a subdirectory. You cannot change this. Similarly, the static files. The install script will detect. The same applies to the cascading stylesheet. However, neither. C subroutine for nucleotide alignments.

This will vastly improve the. You can always manually move the files around after install. When installing the static files, the install script also creates an. This directory is set to be world writable.

If you would prefer not to have a world. The first time you run Makefile. PL, a file named GGB. When Makefile. PL is run again, it will ask you. Read this section only if you are on a Unix system and do not have root.

You will need to configure Apache to run out of your home. One way to do this is to install Apache from source code and. If you also see a "Port 80" directive,. You may not need to install Apache from scratch if your Unix. What you will do is to create. Create an Apache directory and its subdirectories using the following.

Now copy the system-wide httpd. You may need to. You should search the httpd. If you see a Port. Somewhere in httpd. Delete the. Replace both these sections with the following:.

You can now start Apache from the command line using the "apachectl". If Apache starts successfully, then this command will return silently.

Otherwise, it will print an error message. More error messages may be. To confirm that Apache is running from your home directory, create a. You should then.

Now you can build and install gbrowse with the following incantation:. The installation procedure will create a small in-memory database of. To try the browser out, use. Try searching for "I" the name of the first chromosome of yeast , or a. Then try searching for "membrane. For your interest, the feature and DNA files for this database is. The configuration file is in the web. More configuration information and a short tutorial are located at:.

This step takes you through populating the database with the full yeast. You can skip this step if you use the in-memory database for.

Note for RedHat Linux users: note that if you are using the default. Therefore, everywhere 'nobody' occurs. In Bioperl versions 1. The example above assumes that you have a username of "me" and that. It also gives all. You may be comfortable with a more restricted set of. You will need to provide the administrator's name and.

The web. Modify this as needed if the web server runs under a different. The next step is to load the database with data. This is accomplished by. The Bioperl distribution comes with three. This will incrementally load a database, optionally initializing it. This script will work correctly even. It will then. Only suitable for use the very first time you create. The bulk loader. This will incrementally load a database. On UNIX systems, it will. Be careful, though, because this is an experimental.

You will find these scripts in the Bioperl distribution, in the. Earlier versions of the distribution. For testing purposes, this distribution includes a GFF file with yeast. If the load is successful, you should see a message indicating that. Provided that the yeast load was successful, you may now run "make. This invokes a small test script that tests that the database is. You may also wish to load the yeast DNA, so that you can test the.

You should now be able to browse the yeast genome. Type the following. This will display the genome browser instructions and a search field. Usually there will be. The most common problem.