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GBrowse Ubuntu HOWTO

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NOTE: As of the 11.10 release of Ubuntu, there is a .deb package for GBrowse (it's usable on Debian machines as well, but I don't know the details of what repository needs to be activated to get GBrowse via apt-get on Debian).

ANOTHER NOTE: the current version of GBrowse in that deb package is fairly old (2.38 versus the current 2.55); below I'll outline using apt-get to get all of the prerequisites for GBrowse but use cpan to install GBrowse.

To install GBrowse on a recent Ubuntu distribution, just do this:

 sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2

And then point your browser at http://localhost/gbrowse2.

The content below will be left in place for older distributions.

Note: You may need to start the apache server once you have run the above installation

sudo /etc/init.d/apache2 start
  • If you plan to use a MySQL database, you may need to install mysql
sudo apt-get install mysql-server

Using apt-get just to get the prereqs

If you execute this command:

 sudo apt-get install gbrowse

You'll get a list of all of the required packages that GBrowse wants to install, like this (but hit N when asked if you want to continue!):

 amap-align bedtools bioperl bioperl-run bowtie bwa
 infernal javascript-common kalign libace-perl libalgorithm-c3-perl 
 libalgorithm-munkres-perl libapache-dbi-perl libapache2-mod-perl2 
 libapache2-reload-perl libarray-compare-perl libb-hooks-endofscope-perl 
 libbio-asn1-entrezgene-perl libbio-graphics-perl libbio-perl-perl 
 libbio-perl-run-perl libbio-scf-perl libbit-vector-perl libbsd-resource-perl 
 libcarp-clan-perl libcgi-session-perl libclass-c3-perl libclass-c3-xs-perl
 libclass-load-perl libclass-load-xs-perl libconvert-binary-c-perl 
 libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl 
 libdate-manip-perl libdbd-sqlite3-perl libdevel-globaldestruction-perl 
 libdevel-partialdump-perl libdevel-symdump-perl libeval-closure-perl 
 libfreezethaw-perl libgd-svg-perl libgraph-perl libgraphviz-perl 
 libheap-perl libjcode-pm-perl libjs-prototype libjs-scriptaculous 
 liblist-moreutils-perl libmath-derivative-perl libmath-spline-perl 
 libmldbm-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl
 libnamespace-clean-perl libole-storage-lite-perl libpackage-deprecationmanager-perl
 libpackage-stash-perl libpackage-stash-xs-perl libparams-classify-perl 
 libparams-util-perl libparse-recdescent-perl libpostscript-perl libset-scalar-perl
 libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl
 libstaden-read1 libstatistics-descriptive-perl libsub-exporter-perl 
 libsub-identify-perl libsub-install-perl libsvg-graph-perl libsvg-perl 
 libtree-dagnode-perl libtry-tiny-perl libunicode-map-perl libvariable-magic-perl 
 libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl 
 libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-regexp-perl
 libxml-sax-writer-perl libxml-xpathengine-perl libyaml-syck-perl samtools 
 sim4 wise wwwconfig-common libjson-perl libterm-readkey-perl libcapture-tiny-perl
 libmodule-build-perl apache2 build-essential

You can copy this list of packages and place them in a text editor and remove the new lines. In vim, I just hit "J" until the list is one large line. IF gbrowse is in that list, remove it. Then I can take that list and paste it into a long apt-get command:

 sudo apt-get install amap-align bedtools bioperl bioperl-run bowtie bwa infernal javascript-common kalign libace-perl libalgorithm-c3-perl libalgorithm-munkres-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libarray-compare-perl libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-graphics-perl libbio-perl-perl libbio-perl-run-perl libbio-scf-perl libbit-vector-perl libbsd-resource-perl libcarp-clan-perl libcgi-session-perl libclass-c3-perl libclass-c3-xs-perl libclass-load-perl libclass-load-xs-perl libconvert-binary-c-perl libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdbd-sqlite3-perl libdevel-globaldestruction-perl libdevel-partialdump-perl libdevel-symdump-perl libeval-closure-perl libfreezethaw-perl libgd-svg-perl libgraph-perl libgraphviz-perl libheap-perl libjcode-pm-perl libjs-prototype libjs-scriptaculous liblist-moreutils-perl libmath-derivative-perl libmath-spline-perl libmldbm-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libnamespace-clean-perl libole-storage-lite-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libparams-classify-perl libparams-util-perl libparse-recdescent-perl libpostscript-perl libset-scalar-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libstaden-read1 libstatistics-descriptive-perl libsub-exporter-perl libsub-identify-perl libsub-install-perl libsvg-graph-perl libsvg-perl libtree-dagnode-perl libtry-tiny-perl libunicode-map-perl libvariable-magic-perl libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-regexp-perl libxml-sax-writer-perl libxml-xpathengine-perl libyaml-syck-perl samtools sim4 wise wwwconfig-common libjson-perl libterm-readkey-perl libcapture-tiny-perl libmodule-build-perl apache2 build-essential

Then you can use the cpan shell to install GBrowse manually:

 cpan
 cpan> install Bio::Graphics::Browser2

This will still install a few perl modules, but it should go smoothly and quickly since most of the prerequisites will have been installed by the above apt-get command.

The information below is deprecated.

GBrowse does not have a .deb package, but many of its prerequisites are distributed in this way. This document describes how to install GBrowse on Ubuntu and other Linux distributions that use the Debian packaging system.

Prerequisites

Install Apache and Apache-modperl
 sudo apt-get install apache2
 sudo apt-get install libapache2-mod-perl2
 sudo apt-get install libapache2-mod-perl2-dev
 sudo apt-get install libapache2-mod-perl2-doc
 sudo apt-get install apache2-doc
Make the missing cgi-bin directory
 sudo mkdir /usr/lib/cgi-bin

This is not necessary for Ubuntu 7.10, as the Apache install creates it. For previous versions of Ubuntu, this did not happen.

Install libgd
 sudo apt-get install libgd2-dev

or

 sudo apt-get install libgd2-xpm-dev

for Ubuntu 7.10.

Install MySQL database (optional, but recommended)
 sudo apt-get install mysql-server
Install installer prereqs
 sudo apt-get install libarchive-zip-perl
 sudo apt-get install libarchive-tar-perl
 sudo apt-get install ncftp

Installing GBrowse with the Net Installer

Get the netinstaller script from SourceForge and save it to disk as "gbrowse_netinstall.pl". Then run:

sudo perl gbrowse_netinstall.pl

Be sure to double-check the paths that GBrowse guesses for the Apache configuration, htdocs, and cgibin directories, as these may have changed.

The script will download and install all the Perl modules on which GBrowse depends. During the installation process, some of these modules will ask you questions. You can almost always accept the defaults. If you change your mind later, you can simply run the script again.

When the installer is finished, you can browse the documentation and example database at http://localhost/gbrowse.

Author

Lincoln Stein 12:36, 17 April 2007 (EDT)