User talk:Darek Kedra/sandbox 24

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".

System(s)

• Fedora 8 64bit as host
• VirtualBox 3.1.8
• Debian 5.04 64bit with LXDE:

http://cdimage.debian.org/debian-cd/5.0.4/amd64/iso-cd/debian-504-amd64-xfce+lxde-CD-1.iso

I installed only Debian inside VirtualBox. For 64bit or multiple cores&procesor use you have to switch VT-x in: VirtualBox > Debian_5.04_64bit > System > Acceleration

On my system VT-x was not set up by default, so I had to enable it (reboot, enter Setup, etc.).

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.bz2

installation:

wget http://apache.securedservers.com/httpd/httpd-2.2.15.tar.bz2
tar xfvj httpd-2.2.15.tar.bz2
cd httpd-2.2.15/

./configure  --enable-deflate --enable-headers --enable-expires --prefix=/home/ensembl/local/apache2
make
make install

checking what is build in *specified modules(:

/home/ensembl/local/apache2/bin/apachectl -t -D DUMP_MODULES | grep deflate
/home/ensembl/local/apache2/bin/apachectl -t -D DUMP_MODULES | grep expires
/home/ensembl/local/apache2/bin/apachectl -t -D DUMP_MODULES | grep headers

mod_per 4 apache2.x

http://perl.apache.org/download/index.html got mod_perl-2.0.4

wget http://perl.apache.org/dist/mod_perl-2.0-current.tar.gz
tar xfvz  mod_perl-2.0-current.tar.gz

export PATH=/home/ensembl/local/bin/:$PATH

cd mod_perl-2.0.4
perl Makefile.PL MP_APXS=/home/ensembl/local/apache2/bin/apxs 
make
make test
make install

• Unsolved:* mod_perl skips some tests due to Perl being compiled without "ithreads enabled". Debian's perl is with threads:

ldd /usr/bin/perl | grep thread
libpthread.so.0