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Generic Genome Browser Installation ^

GBrowse is distributed as binary packages for Windows and Macintosh OS X, and as source code for Unix systems.

1. WINDOWS INSTALL

Before installing on Windows systems, you will need to install ActiveState Perl and the Apache web server. You may also wish to install a database management system such as MySQL.

Install ActiveState Perl

Go to http://www.activestate.com, and download the product "ActivePerl." This is a little confusing because web site tries to point you to the commercial product, ASPN Perl. At the current time, the full download URL for ActivePerl is:

http://www.activestate.com/Products/Download/Download.plex?id=ActivePerl

Choose the "MSI" package for Windows. Once downloaded, launch the package, and it will install automatically.

Install the Apache web server

Go to http://httpd.apache.org/download.cgi . Select the most recent version of Apache, and choose the download marked "Win32 Binary (MSI Installer)." Once downloaded, launch the package and it will install automatically.

Install the MySQL database (optional)

Go to http://dev.mysql.com/downloads/mysql . Select and download the most recent version of the Windows package. Once the package is downloaded, you will need to unpack it with the WinZip program. Then launch the installer.

Install GBrowse

Apache and ActiveState Perl must be installed before you try this step. Launch the Windows command shell by choosing "Run..." and then typing "cmd". Once the command shell appears, type the following commands:

        ppm> rep add gmod http://www.gmod.org/ggb/ppm
        ppm> rep up gmod
        ppm> rep up gmod
        ppm> install DBD::mysql   (OPTIONAL)
        ppm> install Generic-Genome-Browser

The binary distribution of GBrowse is at http://www.gmod.org/ggb/ppm. Add this repository to the list of active repositories, and then move the repository to the top to ensure that you get the most up to date versions of the modules.

If you wish to use a MySQL database, install DBD::mysql if you have not already done so. Then install Generic-Genome-Browser.

At the end of the install, the automatic installation script will ask you to confirm the locations of your Apache conf (configuration), htdocs (document root) and cgi-bin (CGI executable) directories. Usually it will guess right, but if it doesn't, just type in the correct path.

When this is done, go to step (5) below.

2. MACINTOSH OS X INSTALL

NOTE: The MacOSX installer sited below is quite out of date. Until it is brought up to date, please use the SOURCE CODE INSTALL section below for Macs.

Go to the following URL:

    ftp://dev.wormbase.org/pub/people/tharris/macosx/packages

Find the most recent version of the GBrowse package. These files have the .dmg extension.

Once the package is downloaded, double click on it. The installer will handle everything else.

3. SOURCE CODE INSTALL

GBrowse runs on top of several software packages. These must be installed and configured before you can run GBrowse. Most preconfigured Linux systems will have some of these packages installed already.

A) MySQL -- http://www.mysql.com

The MySQL database is a fast open source relational database that is widely used for web applications. It is required for most real-live genome annotation projects. For small projects (a few thousands of annotated features), you can skip installing MySQL and use an in-memory database instead.

B) Apache Web Server -- http://www.apache.org

The Apache web server is the industry standard open source web server for Unix and Windows systems.

C) Perl 5.005 -- http://www.cpan.org

The Perl language is widely used for web applications. Version 5.6 is preferred, but 5.00503 or higher will work.

D) Standard Perl modules -- http://www.cpan.org

The following Perl modules must be installed for GBrowse to work. They can be found on the Comprehensive Perl Archive Network (CPAN):

        CGI                  (2.56 or higher)
        GD                   (2.07 or higher)
        CGI::Session         (4.03 or higher)
        DBI                  (any version)
        DBD::mysql           (any version)
        Digest::MD5          (any version)
        Text::Shellwords     (any version)
E) Bioperl version 1.5 or higher -- http://www.bioperl.org

GBrowse requires functionality that exists in bioperl-live (in the cvs repository). Please either use bioperl-live or Bioperl 1.5 when it comes out. Until then, there is a release candidate of Bioperl 1.5 that is thought to be stable with regard to GBrowse. It can be found at http://bioperl.org/DIST/bioperl-1.5.0-RC1.tar.gz. Other release candidates and the official 1.5 release of Bioperl can also be found in the http://bioperl.org/DIST/ directory when they are available.

Optional modules:

F) XML::Parser, XML::Writer, XML::Twig, XML::DOM

If these modules are present, the "Sequence Dumper" plugin will be able to produce GAME and BSML output. They can be downloaded from CPAN.

G) LWP

To load remote 3d party annotations. Available from CPAN.

H) Bio::Das

To display remote annotations using the Distributed Annotation System. The current version is available at http://www.biodas.org/download/Bio::Das/Bio-Das-0.92.tar.gz

I) MOBY

Needed by gbrowse_moby to fetch and display data from MOBY providers. Available from biomoby.org; obtain via anonymous cvs until it is released. Directions are at http://biomoby.open-bio.org/index.php/for-developers/get_code

J) GD::SVG

To save images as publication-quality editable images in Scalar Vector Graphics format. Available from CPAN.

Once the prerequisites are installed, download the most recent version of the Generic-Genome-Browser source code from:

   http://prdownloads.sourceforge.net/gmod

This will give you a .tar.gz file, which must be uncompressed and unpacked. Then run the following commands (in brief):

        perl Makefile.PL
        make
        make test (optional)
        make install UNINST=1

This will install the software in the default location under /usr/local/apache. See "Details" to change this, or to install gbrowse into your home directory. The 'UNINST=1' will insure that older versions of perl modules being installed will be removed to help prevent conflicts.

To further configure GBrowse, see CONFIGURE_HOWTO. To run GBrowse on top of Oracle and PostgreSQL databases see ORACLE_AND_POSTGRESQL. To run on top of a BioSQL database, see BIOSQL_ADAPTER_HOWTO. To run GBrowse on top of Gadfly, see README-berkeley-gadfly.

Details:

The browser consists of a CGI script named "gbrowse", a Perl module that handles some of the gory details, a small number of static image files, and a configuration directory that contains configuration files for each data source. By default, these will be installed in the following locations:

   CGI script:      /usr/local/apache/cgi-bin/gbrowse
   Static images:   /usr/local/apache/htdocs/gbrowse
   Config files:    /usr/local/apache/conf/gbrowse.conf
   The module:      -standard site-specific Perl library location-

You can change change the location of the installation by passing Makefile.PL one or more NAME=VALUE pairs, like so:

  perl Makefile.PL CONF=/etc HTDOCS=/home/html

This will cause the configuration files to be installed in /etc/gbrowse.conf and the static files to be installed in /home/html/gbrowse.

The following arguments are recognized:

   CONF            Configuration file directory
   HTDOCS          Static files directory
   CGIBIN          CGI script directory
   APACHE          Base directory for Apache's conf, htdocs and cgibin directories
   LIB             Perl site-specific modules directory
   BIN             Perl executable scripts directory
   NONROOT         If set to a non-zero value (e.g. NONROOT=1) then install
                      gbrowse in a way that does not require root access.
   DO_XS           Compile fast alignment algorithm (XS C extension)

For example, if you are on a RedHat system, where the default Apache installation uses /var/www/html for HTML files, /var/www/cgi-bin for CGI scripts, and /etc/httpd/conf for the configuration files, you should specify the following configuration:

  perl Makefile.PL HTDOCS=/var/www/html \
                   CONF=/etc/httpd/conf \
                   CGIBIN=/var/www/cgi-bin

(The backslashes are there to split the command across multiple lines only). To make it easier when upgrading to new versions of the software, you can put this command into a shell script.

As a convenience, you can use the configuration option APACHE, in which case the static and CGI files will be placed into APACHE/conf, APACHE/htdocs and APACHE/cgi-bin respectively, where APACHE is the location you specified on the command line:

  perl Makefile.PL APACHE=/home/www

Note that the configuration files are always placed in a subdirectory named gbrowse.conf. You cannot change this. Similarly, the static files are placed in a directory named gbrowse. The install script will detect if there are already configuration files in the selected directory and not overwrite them if so. The same applies to the cascading stylesheet file (gbrowse.css) located in the gbrowse subdirectory. However, neither the GIF files in the "buttons" subdirectory nor the plugin modules in the gbrowse.conf/plugins directory are checked before overwriting them, so be careful to copy the new copies somewhere safe if you have modified them.

The DO_XS flag, if true (perl Makefile.PL DO_XS=1), will compile a small C subroutine for nucleotide alignments. This will vastly improve the performance of the gbrowse_details script when displaying alignments. To use this feature, you will need a C compiler.

You can always manually move the files around after install. See CONFIGURE_HOWTO for details.

When installing the static files, the install script also creates an empty directory named "tmp". This directory is set to be world writable so that the GBrowse server can use it to manage temporary image files that it creates on the fly. If you would prefer not to have a world writable directory on your system, simply change the ownership and permissions to allow the web server account to write into it. The directory is located in /usr/local/apache/htdocs/gbrowse/tmp by default.

The first time you run Makefile.PL, a file named GGB.def will be created your file path settings. When Makefile.PL is run again, it will ask you whether you wish to reuse the settings stored in the file.

4. INSTALLING INTO YOUR HOME DIRECTORY

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:

   % cd apache_x.xx.xx
   % ./configure --prefix=$HOME/apache
   % make
   % make install

This will place Apache into your home directory under ~/apache. You should then edit ~/apache/conf/httpd.conf and replace the directive:

  Listen 80

with

  Listen 8000

so that Apache will listen for connections to the unprivileged port 8000 rather than the usual port 80. If you also see a "Port 80" directive, change it to read "Port 8000." You'll now be able to talk to Apache using URLs like http://your.host.edu:8000/.

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.

Create an Apache directory and its subdirectories using the following series of commands:

  % cd ~
  % mkdir apache
  % mkdir apache/conf
  % mkdir apache/logs
  % mkdir apache/htdocs
  % mkdir apache/cgi-bin

Now copy the system-wide httpd.conf into ~/apache/conf. You may need to search around a bit to find out where the system-wide httpd.conf lives (try running the command "locate httpd.conf):

  % cp /etc/httpd/conf/httpd.conf ~/apache/conf

Now open up ~/apache/conf/httpd.conf with a text editor and add the following four directives, replacing $HOME with the full path to your home directory (for example "/home/fred"):

  Listen       8000
  ServerRoot   $HOME/apache
  DocumentRoot $HOME/apache/htdocs
  SetEnv       PERL5LIB $HOME/lib  

You should search the httpd.conf file for older versions of these directives, and delete them if they're there. If you see a Port directive, change it to read "Port 8000".

Somewhere in httpd.conf there will be a ScriptAlias directives, as well as a <Directory> section that refers to "cgi-bin". Delete the ScriptAlias directive and the entire <Directory> section through to the </Directory> line. Replace both these sections with the following:

 ScriptAlias /cgi-bin/ "cgi-bin/"

 <Location "/cgi-bin">
    AllowOverride None
    Options None
    Order allow,deny
    Allow from all
 </Location>

You can now start Apache from the command line using the "apachectl" script:

 % /usr/sbin/apachectl -d ~/apache -k start

If Apache starts successfully, then this command will return silently. Otherwise, it will print an error message. More error messages may be found in ~/apache/logs/error_log.

To confirm that Apache is running from your home directory, create a file named index.html and copy it into ~/apache/htdocs. You should then be able to open a browser, connect to http://localhost:8000/, and see the index.html file that you just created.

Now you can build and install gbrowse with the following incantation:

 % cd Generic-Genome-Browser-X.XX
 % perl Makefile.PL APACHE=~/apache LIB=~/lib BIN=~/bin NONROOT=1
 % make
 % make install

When you are prompted to load gbrowse using http://localhost/gbrowse, use http://localhost:8000/gbrowse instead.

5. TRY THE BROWSER OUT

The installation procedure will create a small in-memory database of yeast chromosome 1 for you to play with. To try the browser out, use your favorite browser to open:

  http://localhost/cgi-bin/gbrowse

Try searching for "I" (the name of the first chromosome of yeast), or a gene such as NUT21 or TCF3. Then try searching for "membrane trafficking."

For your interest, the feature and DNA files for this database is located in the web server's document root at gbrowse/databases/yeast_chr1. The configuration file is in the web server's configuration directory under gbrowse.conf/yeast1.conf.

More configuration information and a short tutorial are located at:

   http://localhost/gbrowse

6. POPULATING THE DATABASE (MySQL)

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 (see section 6).

Synopsis:

  mysql -uroot -p password -e 'create database yeast'

  mysql -uroot -p password -e 'grant all privileges on yeast.* to me@localhost'
  mysql -uroot -p password -e 'grant file on *.* to me@localhost'
  mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost'

  bp_bulk_load_gff.pl -d yeast sample_data/yeast_data.gff

Details:

Note for RedHat Linux users: note that if you are using the default installed Apache, the user that apache runs as is 'apache' as opposed to the otherwise standard 'nobody'. Therefore, everywhere 'nobody' occurs in these directions, replace it with 'apache'.

In Bioperl versions 1.3 or later (not released as of August 2003), this script is named bp_bulk_load_gff.pl.

You will need a MySQL database in order to start using GBrowse. 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 may be comfortable with a more restricted set of privileges, but be sure to provide at least SELECT, UPDATE and INSERT privileges. You will need to provide the administrator's name and correct password for these commands to succeed.

In addition, grant the "nobody" user the SELECT privilege. 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. The Bioperl distribution comes with three tools for loading Bio::DB::GFF databases:

1 bp_load_gff.pl

This will incrementally load a database, optionally initializing it if it does not already exist. This script will work correctly even if the MySQL server is located on another host.

2 bp_bulk_load_gff.pl

This Perl script will initialize a new Bio::DB::GFF database with a fresh schema, deleting anything that was there before. It will then load the file. Only suitable for use the very first time you create a database, or when you want to start from scratch! The bulk loader is as much as 10x faster than bp_load_gff.pl, but does not work in the situation in which the MySQL database is running on a remote host.

3 bp_fast_load_gff.pl

This will incrementally load a database. On UNIX systems, it will activate a fast loader that makes the speed almost the same as the bulk loader. Be careful, though, because this is an experimental piece of software.

You will find these scripts in the Bioperl distribution, in the subdirectory scripts/Bio-DB-GFF. Earlier versions of the distribution will have these files directly in the scripts/ subdirectory.

For testing purposes, this distribution includes a GFF file with yeast genome annotations. The file can be found in the test_data subdirectory. If the load is successful, you should see a message indicating that 13298 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:

  http://prdownloads.sourceforge.net/gmod/yeast.fasta.gz?download

Load the file with this command:

  bp_load_gff.pl -d yeast -fasta yeast.fasta.gz </dev/null

(or, if you are on a windows system:

  bp_load_gff.pl -d yeast -fasta yeast.fasta.gz

and hit ^Z when the script pauses.)

You should now be able to browse the yeast genome. Type the following URL into your favorite browser:

  http://name.of.your.host/cgi-bin/gbrowse/yeast

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.

*IF YOU GET AN ERROR* examine the Apache server error log (depending on how Apache was installed, it may be located in /usr/local/apache/logs/, /var/log/httpd/, /var/log/apache, or elsewhere). Usually there will be an informative error message in the error log. The most common problem is MySQL password or permissions problems.

7. LOADING OTHER DATA SETS

Genome feature tables for the major model organisms and human can be found at www.gmod.org in the downloads section, but these files are not guaranteed to be up to date.

Each model organism database has its own flat file format for representing the data. For the most up to date information, you should download these files and process them into GFF format. Currently, all of the model organism databases require some tweaking of the flat files, but the bioperl distribution includes several small perl scripts to make this easier. These scripts are optionally installed when you install Bioperl. You'll find them in the bioperl scripts/Bio-DB-GFF directory if you didn't install them directly.

They are:

  process_gadfly.pl     For FlyBase D. melanogaster flat files
  process_sgd.pl        For SGD S. cerevisiae flat files
  process_wormbase.pl   For WormBase C. elegans flat files

In Bioperl 1.3, these scripts are named bp_process_gadfly.pl, and so forth.

Run the script with the -h option to get some data-specific help:

  % process_gadfly.pl -h

The bp_process_wormbase.pl script requires the AcePerl package, which is available from CPAN. It is not strictly necessary to run this script because the unaltered GFF files distributed from WormBase are compatible with GBrowse. process_wormbase.pl supplements the information with the physical positions of genetic markers, GenBank accession numbers and functional descriptions of gene products.

For configuration files that will work with each of these databases, look in contrib/conf_files (or in http://localhost/gbrowse/contrib/conf_files). Simply copy the appropriate configuration file into your gbrowse.conf directory, and edit the database name as appropriate.

You might also be interested in the load_genbank.pl script, which is installed when you install GBrowse. You can give this script a list of Genbank or EMBL accession numbers and it will automatically download the indicated entries and load them into a MySQL database. You can also load flat files in Genbank or EMBL format.

For human gene models, we suggest you use the ucsc_genes2gff.pl script, which operates on the files downloadable from the UCSC genome browser.

The sample configuration file 08.genbank.conf (located in contrib/conf_files) is appropriate for data loaded with load_genbank.pl.

8. LOADING DNA

To display the DNA sequence and to run sequence-dependent glyphs such as the three-frame translation, you will need to load the DNA as well as the annotations. The DNA must be formatted as a series of one or more FASTA-format files in which each entry in the file corresponds to a top-level sequence such as a chromosome pseudomolecule. You can then run the bp_load_gff.pl or bp_bulk_load_gff.pl script using the -fasta argument. For example, if the yeast genome is contained in a FASTA file named yeast.fa, you would run the command:

  bp_bulk_load_gff.pl -d yeast -fasta yeast.fa sample/yeast_data.gff

Alternatively, you may put several FASTA files into a directory, and provide the directory name as the argument to -fasta.

(The yeast DNA is too large to be included in this distribution, but you can get a copy of it from ftp://genome-ftp.stanford.edu/pub/yeast/)

Run "bp_bulk_load_gff.pl -h" to see usage instructions.

Newer versions of GFF (the so-called "GFF2.5" and "GFF3" formats) include the DNA at the bottom of the file, following the sequence annotations. If you are loading one of these GFF files, the DNA will be recognized automatically and loaded by any of the loaders.

9. CREATING YOUR OWN GENOME DATABASE

See the file doc/pod/CONFIGURE_HOWTO.pod for information on how to create new databases from scratch, add new browser tracks, and how to get the browser to dump the DNA from the region currently under display.

10. MAKING THE BROWSER RUN FASTER

Three factors are major contributors to the length of time it takes to load a gbrowse page:

  1. Loading the Perl interpreter and parsing BioPerl and all the other Perl libraries that gbrowse uses.
  2. Query speed on the database
  3. The conversion at the Perl layer of database data into BioPerl objects for rendering.

To improve (1), I recommend that you install the mod_perl module for Apache. (http://perl.apache.org). By configuring an Apache::Registry directory and placing gbrowse inside it (rather than in the default cgi-bin directory). The overhead for loading Perl and its libraries are eliminated, thereby increasing the performance of the script noticeably.

Be aware that there is a bad interaction between the Apache::DBI module (often used to speed up database accesses) and Bio::DB::GFF. This will cause the GFF dumper plugin to fail intermittently. GBrowse does not need Apache::DBI to achieve performance increases under mod_perl and it is suggested that you disable Apache::DBI. If you cannot do this, then you should remove the file GFFDumper.pm from the gbrowse.conf/plugins directory.

Database query performance (2) is also a major factor. If you are using MySQL as the backend, you will see dramatic performance increases by increasing the amount of memory available to the key buffer, sort buffer, table cache and other in-memory data structures. I suggest that you replace the default MySQL configuration file (usually stored in /etc/my.cnf) with one of the large-memory sample configuration files provided in the support-files subdirectory of the MySQL distribution. Of course, if you tell MySQL to use more memory than you have, then performance will degrade again.

Finally, there is a slowdown when gbrowse converts the results of database SQL queries into renderable biological objects. This becomes particularly noticeable when there are lots of multi-segment objects to be displayed. You can work around this slowdown by using semantic zooming (see CONFIGURE_HOWTO). Otherwise, there's not much that can be done about this short of buying a faster machine. The GMOD team is working hard to reduce this performance hit.

11. MAKING THE SERVER RUN SAFER

Whenever you are running a server-side Web script using information provided by a web client, there is a risk that maliciously-formatted data provided by the use will trick the server-side script into performing some unintentional action, such as modifying a file on the server. Perl's "taint" checks are designed to catch places in the code where such malicious data could cause harm, and GBrowse has been tested extensively with these taint checks activated.

Because of taint checks' noticeable impact on performance, they have been turned off in the distributed version of gbrowse. If you wish to reactivate the extra checking (at the expense of a performance hit), go to the file "gbrowse" located in the Web scripts directory and edit the top line of the file to read:

  #!/usr/bin/perl -w -T

The -T switch turns on taint checks.

If you are running GBrowse under mod_perl, add the following line to the httpd.conf configuration file:

  PerlTaintCheck  On

This will affect all mod_perl scripts globally.

12. BIOPERL VERSIONS

GBrowse is evolving quickly, and some of its features are dependent on new features in Bioperl 1.4.0. If you are having trouble making GBrowse run, make sure you are using Bioperl 1.4.0!

13. THE GBROWSE_IMG SCRIPT

The gbrowse_img CGI script (a new feature as of version 1.41), is a stripped-down version of gbrowse which just generates images. It is suitable for incorporating into <img> tags in order to make a thumbnail of a region of interest. The thumbnail can then be linked to the full-featured gbrowse. Here is an example of how this works using the WormBase site:

  <a href="http://www.wormbase.org/db/seq/gbrowse/wormbase?name=mec-3">
    <img src="http://www.wormbase.org/db/seq/gbrowse_img/wormbase?name=mec-3;width=200">
  </a>

This will generate a 200-pixel inline image of the region. Clicking on the image will link to the fully-navigable gbrowse script.

You can also use gbrowse_img to superimpose temporary features (like BLAST hits) on the existing genome features.

Read docs/gbrowse_img.txt DOES NOT EXIST for the CGI parameters and other instructions. A copy of these instructions in HTML form will be generated when gbrowse_img is called without any arguments. Type http://your.host/cgi-bin/gbrowse_img into your favorite web browser.

14. PLUGINS

Gbrowse has a plugin architecture which makes it easy for third-party developers to expand its functionality. The plugins are Perl .pm files located in the directory gbrowse.conf/plugins/. To install plugins, simply copy them into this directory. To uninstall, remove them.

If you wish to install your own or third party plugins, it is suggested that you create a separate directory outside the gbrowse.conf/ hierarchy in which to store them and then to indicate the location of these plugins using the plugin_path setting:

  plugin_path = /usr/local/gbrowse_plugins

This setting should be somewhere in the [GENERAL] section of the relevant gbrowse configuration file.

15. THE GENBANK/EMBL PROXY

Sample configuration number 5 ("05.embl.conf") corresponds to an experimental pass-through proxy for Genbank. At least in theory, if you enter a landmark that isn't recognized, gbrowse will go to EMBL using the bioperl BioFetch facility, parse the record, and enter it into the local database. This allows you to browse arbitrary Genbank/EMBL/Refseq entries.

You are free to experiment with this, but don't expect it to be entirely reliable. To get it to work, you must:

  1. Make sure you are using Bioperl 1.02 (or a patched version of 1.01)
  2. Create a local database named "embl" and initialize it this way:
  3. Set up permissions for this database so that "nobody@localhost" has SELECT, INSERT, UPDATE and DELETE privileges
  4. Initialize the database for use with this command:
      % bp_load_gff.pl -c -d embl </dev/null

    (if you are on a windows system, just leave out the </dev/null)

  5. If you need to use a proxy to access remote web sites, uncomment the -proxy line in the conf file, and adjust the URL of the proxy as appropriate.
  6. Go to http://localhost/cgi-bin/gbrowse/embl. Search for a Genbank or embl accession number, such as CEF58D5

16. UPDATING THE BROWSER WITHOUT REENTERING YOUR DIRECTORY SETTINGS

When updating GBrowse to a new version of the software, you can configure it using your preferred directory settings by making a backup copy of the file GGB.def that was generated the first time you installed GBrowse and using `cat GGB.def` as the argument to Makefile.PL. Here is the recipe:

  cp Generic-Genome-Browser-1.40/GGB.def Generic-Genome-Browser-1.41/GGB.def
  cd Generic-Genome-Browser-1.41/
  perl Makefile.PL `cat GGB.def`
  make
  make install

17. REMOVING OUT-OF-DATE IMAGE FILES

As GBrowse runs, it creates temporary image files in the gbrowse tmp directory (typically /usr/local/apache/htdocs/gbrowse/tmp). These image files are relatively small, but if you run GBrowse for a long time they may begin consuming significant amounts of disk space. The following Unix shell commands will remove old image files:

  cd /usr/local/apache/htdocs/gbrowse/tmp
  find . -type f -atime +20 -print -exec rm {} \;

You might want to run this command under cron, but be aware that since the image files are owned by user "nobody", you must install this command in the cron script for "nobody" or "root."

18. KNOWN BUGS

Currently there is one known bug. The navigation buttons do not operate properly when the client is using Internet Explorer 5.1 on a Macintosh and accessing gbrowse running on a MacOS X server running Apache. Other combinations of clients and servers work properly.

19. FEATURE WISH LIST (updated April, 2004)

  - Configure data sources on a track-by-track basis.
  - A configurable synteny viewer.

If you are interested in working on any of these features, please contact the developers at the address given in the next section.

20. SUPPORT AND BUG REPORTS

Please send requests for help to gmod-gbrowse@lists.sourceforge.net. There is also a formal bug tracking and feature request system in place at http://www.gmod.org/

Have fun!

Lincoln Stein & the GMOD team lstein@cshl.org

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