User talk:Darek Kedra/sandbox 24: Difference between revisions
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== local MySQL Ensembl DB all the way for mirroring main Ensembl site== | == 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 | |||
Some perl modules versions have changed since first installation. | |||
Debian 5.04 install seemed to be the easiest, but this may be simply due to the fact that I have already documented Fedora/Ubuntu installs. Also Debians was an installation on otherwise unspoiled system. | |||
===Perl=== | |||
http://www.perl.org/get.html | |||
got perl-5.12.0 | |||
<pre> | |||
cd perl-5.12.0 | |||
cd perl-5.12.0/ | |||
CFLAGS='-m64 -mtune=nocona' ./Configure -des -A ccflags=-fPIC -Dprefix=/home/ensembl/local/ | |||
make | |||
make test | |||
make install | |||
</pre> | |||
The "CFLAGS" line is required on 64-bit Linux system to compile mod_perl. For the 32bit Debian | |||
<pre> | |||
./Configure -Dprefix=/home/ensembl/local/ | |||
</pre> | |||
was enough. | |||
===Apache httpd=== | |||
http://httpd.apache.org/download.cgi | |||
got httpd-2.2.15.tar.gz | |||
installation: | |||
<pre> | |||
./configure --enable--deflate --enable--headers --enable--expires --prefix=/home/ensembl/local/apache2 | |||
make | |||
make install | |||
</pre> | |||
checking what is build in: | |||
<pre> | |||
/home/ensembl/local/apache2/bin/apachectl -t -D DUMP_MODULES | |||
</pre> | |||
wget http://perl.apache.org/dist/mod_perl-2.0-current.tar.gz |
Revision as of 10:45, 1 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
Some perl modules versions have changed since first installation.
Debian 5.04 install seemed to be the easiest, but this may be simply due to the fact that I have already documented Fedora/Ubuntu installs. Also Debians was an installation on otherwise unspoiled system.
Perl
http://www.perl.org/get.html got perl-5.12.0
cd perl-5.12.0 cd perl-5.12.0/ 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