User talk:Darek Kedra/sandbox 24: Difference between revisions
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===CPAN Shell=== | ===CPAN Shell=== | ||
Easy things first: | <!--- it does not show progress?? | ||
One can also use CPANPLUS with few more options. Start with | |||
<pre> | |||
export PATH=/home/ensembl/local/bin/:$PATH | |||
perl -MCPANPLUS -e shell | |||
install Term::ReadLine::Perl | |||
q | |||
</pre> | |||
This will let you *bash/like( invoke previous commands, jump along the line, delete words etc. | |||
(using CPAN, but you can use CPANPLUS instead | |||
---> | |||
Easy things first : | |||
<pre> | <pre> | ||
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# ~/local/bin/perl | # ~/local/bin/perl | ||
perl -MCPAN -e shell | perl -MCPAN -e shell | ||
install Cache::Memcached | |||
# Cache-Memcached-1.28.tar.gz | |||
install CGI | |||
# CGI.pm-3.49.tar.gz | |||
install CGI::Ajax | |||
# CGI-Ajax-0.707.tar.gz | |||
install CGI::Session | |||
# CGI-Session-4.42.tar.gz | |||
install Class::Accessor | |||
# Class::Accessor is up to date (0.34). // checked after installation of all modules | |||
install Class::Data::Inheritable | |||
# Class::Data::Inheritable is up to date (0.08). // checked after inst. of all modules | |||
install Class::Std | |||
# Class-Std-0.011.tar.gz | |||
install Class::Std::Utils | |||
# Class-Std-Utils-v0.0.3.tar.gz | |||
install Compress::Zlib | |||
# Compress::Zlib is up to date (2.027). | |||
install Compress::Raw::Zlib | |||
# Compress-Raw-Zlib-2.027.tar.gz | |||
install SHLOMIF/Config-IniFiles-2.58.tar.gz | |||
#// i /Config::Inifiles/ lists 3 modules, this one is the only one which version is close to the one listed on 1000genomes.org web page (see above) |
Revision as of 13:23, 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".
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 #optional apt-get instal memcached
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/ -Dusethreads 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
Perl modules required by ENSEMBL
Assumes that you installed Perl in /home/ensembl/local/ and got perl binary in /home/ensembl/local/bin/
Check the list of modules here i.e: http://browser.1000genomes.org/info/docs/webcode/install/non-ensembl-code.html
There are several versions of this list of modules, but ultimately you may be missing several not listed modules, and you will get their names (one by one) after trying to start your ENSEMBL site.
Despite the advise of installing always the newest module versions there is one important exception: LWP. LWP version 5.812 is required by latest (2.57) ParallelUserAgent. This will be covered in a separate section of this page.
Also some modules do not install (at least on my machine) from perls CPAN shell. These may require installation by hand from sources (described later).
CPAN Shell
Easy things first :
export PATH=/home/ensembl/local/bin/:$PATH which perl # ~/local/bin/perl perl -MCPAN -e shell install Cache::Memcached # Cache-Memcached-1.28.tar.gz install CGI # CGI.pm-3.49.tar.gz install CGI::Ajax # CGI-Ajax-0.707.tar.gz install CGI::Session # CGI-Session-4.42.tar.gz install Class::Accessor # Class::Accessor is up to date (0.34). // checked after installation of all modules install Class::Data::Inheritable # Class::Data::Inheritable is up to date (0.08). // checked after inst. of all modules install Class::Std # Class-Std-0.011.tar.gz install Class::Std::Utils # Class-Std-Utils-v0.0.3.tar.gz install Compress::Zlib # Compress::Zlib is up to date (2.027). install Compress::Raw::Zlib # Compress-Raw-Zlib-2.027.tar.gz install SHLOMIF/Config-IniFiles-2.58.tar.gz #// i /Config::Inifiles/ lists 3 modules, this one is the only one which version is close to the one listed on 1000genomes.org web page (see above)