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===Debian modules=== | ===Debian modules=== | ||
Divided into groups for clarity. Few of these may not be needed, but this was untested. | |||
<pre> | <pre> | ||
apt-get install ssh bzip2 unzip | |||
apt-get install gcc g++ make | apt-get install gcc g++ make | ||
apt-get install | apt-get install cvs subversion git-core | ||
apt-get install expat libxmltok1 libxmltok1-dev zlib1g-dev | |||
apt-get install mysql-server libmysqlclient15-dev | |||
#installs by default also libnet-daemon-perl libdbi-perl libdbd-mysql-perl libhtml-template-perl | |||
apt-get install libgd2-xpm fontconfig libgd-tools | |||
</pre> | </pre> | ||
===Perl=== | ===Perl=== | ||
Revision as of 04:31, 2 June 2010
Local Ensembl install
There are several possible main configurations for installing Ensembl locally with increasing level of complexity.
Running virtual image from Eagle Genomics
The current version (v57) of EagleBrowser are here: http://www.eaglegenomics.com/downloads/eaglebrowser/
It is a system image to be run inside VMware Virtual Machine. It connects to public Ensembl MySQL database, but stores local user data locally.
Pros: simplest to install, gives a chance to look at a working ENSEMBL setup (not tested yet: ssh connection).
remote MySQL Ensembl DB + local SQLite for ensembl_web_user_db
So far not successfully tested. Potentially useful for testing all the components required by Ensembl except connection to local MySQL. There is a special Ensembl plugin (./public-plugins/sqlite/) but no information how to make it work.
remote MySQL Ensembl DB + local MySQL for ensembl_web_user_db
Tested on Ununtu 9.10. Useful for testing all the components required by Ensembl plus finding discrepancies between local and remote MySQL DB.
local MySQL Ensembl DB all the way for mirroring main Ensembl site
Probably the most common setup allowing a possible speedup of Ensembl connections
local MySQL Ensembl DB all the way for custom species
Default setup for groups annotating novel genomes.
any of the above (except EagleBrowser) inside a virtual machine
Greater flexibility, clean de novo installations of an OS, easy migration between machines. Cons: some CPU/networking(?) overhead, greater overal complexity.
Installation
Save for EagleBrowser which comes as a setup system, all other kind of installations require multiple programs / perl modules / at least some configuration. Following procedures were executed so far on three different systems (all versions for workstation):
- Fedora 8 64bit (workstation)
- Ubuntu 9.10 64bit
- Debian 5.04 32bit run inside VirtualBox 3.1
- Debian 5.04 64bit run inside VirtualBox 3.1
Some perl modules versions have changed since first installation.
Debian 5.04 installs seemed to be the easiest, but this may be simply due to the fact that I have already documented Fedora/Ubuntu installs. Also Debians were an installation on otherwise unspoiled systems.
Folowing precedures are records for "Debian 5.04 64bit run inside VirtualBox 3.1".
Debian modules
Divided into groups for clarity. Few of these may not be needed, but this was untested.
apt-get install ssh bzip2 unzip apt-get install gcc g++ make apt-get install cvs subversion git-core apt-get install expat libxmltok1 libxmltok1-dev zlib1g-dev apt-get install mysql-server libmysqlclient15-dev #installs by default also libnet-daemon-perl libdbi-perl libdbd-mysql-perl libhtml-template-perl apt-get install libgd2-xpm fontconfig libgd-tools
Perl
http://www.perl.org/get.html got perl-5.12.1
wget http://www.cpan.org/src/5.0/perl-5.12.1.tar.gz tar xfvz perl-5.12.1.tar.gz cd perl-5.12.1/ CFLAGS='-m64 -mtune=nocona' ./Configure -des -A ccflags=-fPIC -Dprefix=/home/ensembl/local/ make make test make install
The "CFLAGS" line is required on 64-bit Linux system to compile mod_perl. For the 32bit Debian
./Configure -Dprefix=/home/ensembl/local/
was enough.
Apache httpd
http://httpd.apache.org/download.cgi got httpd-2.2.15.tar.gz
installation:
./configure --enable--deflate --enable--headers --enable--expires --prefix=/home/ensembl/local/apache2 make make install
checking what is build in:
/home/ensembl/local/apache2/bin/apachectl -t -D DUMP_MODULES
wget http://perl.apache.org/dist/mod_perl-2.0-current.tar.gz