Difference between revisions of "Gbrowse on 4.0.2CD"
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(link back to gmod) |
m (Reverted edits by 203.158.221.227 (Talk); changed back to last version by Gmodhelp) |
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− | The [http://www.gmod.org/ | + | The [http://www.gmod.org/GBrowse Generic Genome Browser], GBrowse, is a combination of database and interactive web page for manipulating and displaying annotations on genomes. |
+ | __TOC__ | ||
− | = Code to install a basic | + | = Code to install a basic GBrowse environment = |
− | + | Prerequisites: a persistent disk image of about 300 MB. I used 500 MB just to be sure I had enough room for temporary files and the like. | |
<pre><nowiki>#!/bin/bash | <pre><nowiki>#!/bin/bash | ||
Line 14: | Line 15: | ||
apt-get update || die "unable to apt-get" 1 | apt-get update || die "unable to apt-get" 1 | ||
− | apt-get -y install libcgi-perl libgd-gd2-perl libdbi-perl \ | + | apt-get -y install perl-doc libcgi-perl libgd-gd2-perl libdbi-perl \ |
libdbd-mysql-perl libmd5-perl libtext-shellwords-perl bioperl || die "unable to install " 2 | libdbd-mysql-perl libmd5-perl libtext-shellwords-perl bioperl || die "unable to install " 2 | ||
cd /root | cd /root | ||
+ | # wget 'http://umn.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser-1.62.tar.gz' || die "unable to wget" 3 | ||
wget 'http://umn.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser-1.62.tar.gz' || die "unable to wget" 3 | wget 'http://umn.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser-1.62.tar.gz' || die "unable to wget" 3 | ||
tar -xzvf Generic-Genome-Browser-1.62.tar.gz || die "unable to untar" 4 | tar -xzvf Generic-Genome-Browser-1.62.tar.gz || die "unable to untar" 4 | ||
Line 25: | Line 27: | ||
make && | make && | ||
make install || die "unable to install gbrowse" 5 | make install || die "unable to install gbrowse" 5 | ||
− | )</nowiki></pre> | + | ) |
+ | |||
+ | /etc/init.d/apache restart | ||
+ | |||
+ | |||
+ | </nowiki></pre> | ||
+ | Point your browser to http://localhost/gbrowse | ||
+ | |||
+ | To enable gbrowse to start at boot time: | ||
+ | update-rc.d apache start 40 2 3 4 5 . stop 60 0 1 6 . | ||
+ | |||
+ | = Code to install an intermediate gbrowse environment = | ||
+ | Perform a basic install and then run the following code: | ||
+ | <pre><nowiki>#!/bin/bash | ||
+ | set -x | ||
+ | |||
+ | die () { | ||
+ | echo "$1" | ||
+ | exit $2 | ||
+ | } | ||
+ | |||
+ | apt-get update || die "unable to apt-get" 1 | ||
+ | |||
+ | # XML::Parser, XML::Writer, XML::Twig, XML::DOM, LWP, GD::SVG | ||
+ | apt-get install libxml-parser-perl libxml-writer-perl libxml-twig-perl \ | ||
+ | libxml-dom-perl libwww-perl | ||
+ | |||
+ | # don't have this quite down yet | ||
+ | |||
+ | </nowiki></pre> |
Latest revision as of 05:31, 15 July 2008
The Generic Genome Browser, GBrowse, is a combination of database and interactive web page for manipulating and displaying annotations on genomes.
Contents
Code to install a basic GBrowse environment
Prerequisites: a persistent disk image of about 300 MB. I used 500 MB just to be sure I had enough room for temporary files and the like.
#!/bin/bash set -x die () { echo "$1" exit $2 } apt-get update || die "unable to apt-get" 1 apt-get -y install perl-doc libcgi-perl libgd-gd2-perl libdbi-perl \ libdbd-mysql-perl libmd5-perl libtext-shellwords-perl bioperl || die "unable to install " 2 cd /root # wget 'http://umn.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser-1.62.tar.gz' || die "unable to wget" 3 wget 'http://umn.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser-1.62.tar.gz' || die "unable to wget" 3 tar -xzvf Generic-Genome-Browser-1.62.tar.gz || die "unable to untar" 4 ( cd Generic-Genome-Browser-1.62/ && perl Makefile.PL CONF=/etc/apache/ HTDOCS=/var/www/ CGIBIN=/usr/lib/cgi-bin/ && make && make install || die "unable to install gbrowse" 5 ) /etc/init.d/apache restart
Point your browser to http://localhost/gbrowse
To enable gbrowse to start at boot time:
update-rc.d apache start 40 2 3 4 5 . stop 60 0 1 6 .
Code to install an intermediate gbrowse environment
Perform a basic install and then run the following code:
#!/bin/bash set -x die () { echo "$1" exit $2 } apt-get update || die "unable to apt-get" 1 # XML::Parser, XML::Writer, XML::Twig, XML::DOM, LWP, GD::SVG apt-get install libxml-parser-perl libxml-writer-perl libxml-twig-perl \ libxml-dom-perl libwww-perl # don't have this quite down yet