(Redirected from GBrowse Linux HOWTO
This page contains detailed installation instructions for installing GBrowse 1.x, suitable for use on Linux and other Unix-like platforms. It also contains performance and maintenance hints useful for all systems.
Note that these instructions are specific to GBrowse 1.x versions. See the installation instructions for GBrowse 2.x.
See also the following OS-specific instructions:
One of the easiest ways to install GBrowse is with the network installer
script, gbrowse_netinstall.pl
The install script has a few useful options:
-h|--help Show this message
-d|--dev Use the development version of both GBrowse
and bioperl from GitHub
--bioperl_dev Use the development version of BioPerl from GitHub
--gbrowse_dev Use the development version of GBrowse from GitHub
--build_param_str=<args> Use this string to set Makefile.PL parameters
such as CONF or PREFIX for GBrowse
installation
--install_param_str=<args>
Use this string to predefine 'make install'
parameters such as CONF or PREFIX for
GBrowse installation
--gbrowse_path Path to GBrowse tarball (will not download
GBrowse); Assumes a resulting
'Generic-Genome-Browser' directory
--bioperl_path Path to BioPerl tarball (will not download
BioPerl); Assumes a resulting'bioperl-live'
directory
--skip_start Don't wait for 'Enter' at program start
--skip_bioperl Don't fetch and install BioPerl; assumes a
working bioperl is already installed
So, for example, if you want to install the most recent developments in GBrowse and BioPerl, you can do this:
sudo perl gbrowse_netinstall.pl -d
This option is useful for getting new options just added to GBrowse (for example, the Balloon pop up windows added before the release of GBrowse 1.69) or for getting a new BioPerl that has recent bugs fixed.
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.
The Apache web server [1] is the industry standard open source web server for Unix and Windows systems.
The MySQL database [2] 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.
The Perl language [3] is widely used for web applications. You will need version 5.8.6 or higher.
The following Perl modules must be installed for GBrowse to work. They can be found on the Comprehensive Perl Archive Network (CPAN) [4]:
The BioPerl project [5] is a set of Perl modules for working with common bioinformatics applications. GBrowse requires BioPerl version 1.6 or greater.
For full details on installing BioPerl, see http://www.bioperl.org
Note that in addition to the above Perl modules required by GBrowse, BioPerl has its own set of required Perl modules. The BioPerl install process (‘perl Build.PL’ within the bioperl-live directory) will try to automatically install these modules for you. However, it may help you to keep track of potential errors if you install them separately first (using CPAN, for example). They are: Data::Stag | IO::String | DB_File | Scalar::Util | ExtUtils::Manifest | Test::More | Module::Build | Test::Harness | CPAN
Optionally: Test::Pod | Statistics::Frequency | XML::LibXML::Reader | Bio::ASN1::EntrezGene | Bio::Ext::Align | Inline::MakeMaker | Bio::SeqIO::staden::read | Ace | Spreadsheet::ParseExcel | Math::Random | Graph | SVG::Graph | SOAP::Lite | GraphViz | Array::Compare | Convert::Binary::C | Algorithm::Munkres | Set::Scalar | Spreadsheet::WriteExcel | XML::SAX::Writer | Clone | XML::DOM::XPath | PostScript::TextBlock
Previously, Bio::Graphics and Bio::DB::Das::Chado were a part of BioPerl but since version 1.6.0, they have been split out into a separate package. They can be installed from the CPAN shell like any other Perl module.
The following Perl modules are not needed for a functional GBrowse install. We recommend that you install them as needed to obtain additional features.
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.
LWP
To load remote 3d party annotations. Available from CPAN.
Bio::Das
To display remote annotations using the Distributed Annotation
System.
The current version is available at CPAN:
http://search.cpan.org/~lds/Bio-Das/ and can be
installed from the cpan shell.
BioMOBY
Needed by gbrowse_moby to fetch and display data from BioMOBY providers.
Available from biomoby.org; obtain via anonymous cvs until it is
released. Directions are at
http://www.biomoby.org/GettingTheCode.html.
GD::SVG
To save images as publication-quality editable images in Scalar Vector
Graphics format. Available from CPAN.
Bio::SCF File::Temp io-lib(v1.7+)
Needed by the sequencing trace glyph to parse SCF files and display the
trace graph. The io-lib library can be downlowded from https://sourceforge.net/project/showfiles.php?group_id=100316&package_id=108243
which is part of the Staden Package
https://sourceforge.net/projects/staden/.
Math::FFT Statistics::Descriptive
Needed by the Spectrogram plugin to calculate Fast Fourier Transforms.
This module is available from CPAN.
Bio::PrimerDesigner, Math::Round, primer3
Needed by the PrimerDesigner plugin. The perl modules are available from
CPAN. The linux primer3 binary is packaged with the Bio::PrimerDesigner
distribution. The binary (or source code) can also be obtained from
http://frodo.wi.mit.edu/primer3/primer3_code.html. If
you are using this plugin, the primer3 binary must be installed in
/usr/local/bin and named ‘primer3’. If it is installed in another path,
edit the following section in the PrimerDesigner plugin:
use constant BINARY => 'primer3';
use constant BINPATH => '/usr/local/bin';
For Intel-based Macintoshes, you may need to be a bit careful about the DBD libraries you install. Joan Pontius reports that you must use the 32-bit MySQL server and DBD::mysql version 2.9007 in order for the preinstalled Perl to work nicely with MySQL. You can get the correct DBD::mysql version at 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 for your platform. See Installation 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.pod. To run GBrowse on top of Oracle and PostgreSQL databases see ORACLE_AND_POSTGRESQL.pod. To run on top of a BioSQL database, see BIOSQL_ADAPTER_HOWTO.pod. Note that these are in Perl “POD” format. To get rid of the formatting instructions, save to disk and run “perldoc CONFIGURE_HOWTO.pod”
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. The correct locations of these CGI script, configuration directory and static files depend on how Apache was installed on your system, which varies from operating system to operating system, and are controlled by the following installation options:
| Setting | Default | Description |
|---|---|---|
| CONF | The system wide Apache configuration directory (e.g. /etc/httpd/ in Centos 5.2). | CONF is the directory in which you will place the gbrowse configuration files. A directory called gbrowse.conf will be created under this location to contain the GBrowse configuration files. |
| HTDOCS | The system wide Apache document root (e.g. /var/www/html/ in Centos 5.2). | The document root in which the HTML files for your web server reside. The static GBrowse HTML files will be created in a subdirectory under this location. |
| GBROWSE_ROOT | gbrowse | The location under HTDOCS in which you would like GBrowse’s static files (stylesheets, images, documentation, etc.) to be stored. For example, if you specify “HTDOCS=/var/www/html” and “GBROWSE_ROOT=genomes/gbrowse” then the static files will be stored at “/var/www/html/genomes/gbrowse”. |
| CGIBIN | The system wide Apache cgi-bin (e.g. /var/www/cgi-bin/ in Centos 5.2). | The Perl scripts responsible for generating the dynamic content will be created in a subdirectory under this location. |
| APACHE | none | A convenience option that defines CONF, HTDOCS and CGIBIN as APACHE/conf, APACHE/htdocs and APACHE/cgi-bin respectively. |
| LIB | The system wide Perl library path | The Perl modules that are part of GBrowse are created under this location. This location will be added to Perl’s INC path, telling GBrowse where to look for these Perl modules. Note, if you see errors like “Can’t locate Bio/Graphics.pm in @INC (@INC contains: …”, you probably need to set the servers $PERL5LIB to match the one you used at install time. |
| BIN | ? | Perl executable scripts directory - but I don’t know what that means! |
Some additional configuration settings include:
| Setting | Default | Description |
|---|---|---|
| YES | 0 | Don’t talk, do. Accept the defaults for all settings (in addition to those provided). |
| NONROOT | 0 | If set to a non-zero value (e.g. NONROOT=1) then install gbrowse in a way that does not require root access (in theory). |
| DO_XS | 1 | Compile fast alignment algorithm (XS C extension). If you have a C compiler and wish to compile the XS extensions, set DO_XS=1. Currently all this does is to speed up the multiple alignment plugin. |
| SELINUX | 0 | Avoid the message to warn you about SELinux that appears when SELinux could be a problem. |
You can manually set these locations by passing Makefile.PL one or more NAME=VALUE pairs, like so:
perl Makefile.PL CONF=/etc HTDOCS=/home/html
Fortunately, this isn’t usually necessary. The Makefile.PL script attempts to guess the appropriate directory locations for your system, but sometimes you will have to specify them manually. For example, if you are on an unusual system, where the Apache installation uses /opt/www/html for HTML files, /opt/run/cgi-bin for CGI scripts, and /etc/httpd/conf for the configuration files, you should specify the following configuration:
perl Makefile.PL HTDOCS=/opt/www/html \
CONF=/etc/httpd/conf \
CGIBIN=/opt/run/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.pod 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 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.
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.
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:
http://localhost/cgi-bin/gbrowse
Try searching for “chrI” (the name of the first chromosome of yeast), or a gene such as NUT21 or TEL01L. 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 HTDOCS/GBROWSE_ROOT/databases/yeast_chr1+2. The configuration file is in the web server’s configuration directory under CONF/gbrowse.conf/yeast.conf.
More configuration information and a short tutorial are located at:
http://localhost/gbrowse
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.
mysql -uroot -ppassword -e 'create database yeast'
mysql -uroot -ppassword -e 'grant all privileges on yeast.* to me@localhost'
mysql -uroot -ppassword -e 'grant file on *.* to me@localhost'
mysql -uroot -ppassword -e 'grant select on yeast.* to nobody@localhost'
bp_bulk_load_gff.pl -d yeast sample_data/yeast_data.gff
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. Mac OSX uses “www”, Fedora Core uses “apache” and Ubuntu uses “www-data.” In the instructions that follow, replace ‘nobody’ with the appropriate Apache account name.
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 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:
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.
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.
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 software relies on features
that are unevenly implemented across platforms. For example, it does not
work correctly on Mac OSX.
You will find these scripts in the BioPerl distribution, in the
subdirectory scripts/Bio-DB-GFF. 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. 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
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.
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. We suggest instead that you use a Bio::DB::SeqFeature::Store database.
Here is a quick recipe.
Get a GFF3 file (available from SGD, WormBase, FlyBase and many other
sites) and save it as genome.gff3.
mysql -uroot -p password -e 'create database genomegff3'
mysql -uroot -p password -e 'grant all privileges on genomegff3.* to me@localhost'
mysql -uroot -p password -e 'grant select on genomegff3.* to nobody@localhost'
bp_seqfeature_load.pl -d genomegff3 -f -c genome.gff3
Create a GBrowse config file by copying one of the existing examples, and modify the top lines to read like the following:
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=genomegff3
-user nobody
The database should now be browsable. For more details, see GFF3.
Go to the individual model organism database’s web sites to find the GFF3 (or GFF2) format files you need. A few notable sites are:
WormBase (C. elegans and related nematodes)
ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/gff/c_elegans.current.annotations.gff2.gz
SGD (S. cerevisiae)
ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/
FlyBase (D. melanogaster)
ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/
Other MODs - please feel free to add your download URLs here
In addition, the bin/ subdirectory of the GBrowse distribution
contains a series of scripts to convert annotation files in various
formats into GFF3 (or GFF2) format. For example, the
ucsc_genes2gff.pl script will convert gene models in Table Browser
format files from
http://www.genome.ucsc.edu into GFF3
format. load_genbank.pl will download and load sequence annotation
files in GenBank format from NCBI. The sample configuration file
08.genbank.conf (located in contrib/conf_files) is appropriate for
data loaded with load_genbank.pl.
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.
GFF3 allow you to include FASTA sequence 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.
See the GBrowse Configuration HOWTO 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.
Three factors are major contributors to the length of time it takes to load a gbrowse page:
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.
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.
The gbrowse_img CGI script 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:
http://www.wormbase.org/db/seq/gbrowse_img/wormbase?name=mec-3;width=200
This will generate a 200-pixel inline image of the region.
You can also use gbrowse_img to superimpose temporary features (like BLAST hits) on the existing genome features.
If the script is called without CGI arguments, it will generate usage instructions. Select http://your.host/cgi-bin/gbrowse_img to see this internal documentation.
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.
Sample configuration number 5 (“05.embl.conf”) corresponds to a 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.
This functionality is not well supported, nor widely used, but here is a recipe for giving it a try:
% bp_load_gff.pl -c -d embl
As GBrowse runs, it creates temporary image files in the gbrowse tmp directory (typically 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 HTDOCS/gbrowse/tmp
find . -type f -atime +20 -print -exec rm {} \;
Be sure to replace HTDOCS with the path to your web server HTML document root directory.
You might want to run this command under cron, but be sure that the user that the cron job runs under has the proper permissions. You may need to install it in root’s cron script.
Please report bugs to the GMOD project bug tracking system. Email support is available by sending requests for help to gmod-gbrowse@lists.sourceforge.net.
Have fun!
Lincoln Stein & the GMOD team