EMMAWiki/AdministratorDocumentation/SoftwareRequirements
Software Requirements
Synopsis
This page is intended for system administrators who intend to install the EMMA-server on a vanilla system. When you install e.g. on a LINUX box you will find all or most of the required software in the distribution. Then you can use the package-management of that system (commands like: rpm, emerge, package_add,...) to install the software. Please consult the documentation provided by your operating system vendor on how to install software. Perl modules can be downloaded from the CPAN.
Requirements
We list only the software and the minimum required version which is needed to run the server here. Where special setup options are required for a software, it is listed.
Operating systems
As a Perl application EMMA should in principle be platform independent. It has been tested with these operating systems or distributions:
- Solaris 9
- SuSE-Linux >= 9
- Gentoo-Linux
- FreeBSD > 5.3
It is not installable under Windows systems, as there is no RSPerl module for Windows.
Web-server software
- The Apache web-server (>= 2.x http://httpd.apache.org/)
- Mod_perl 2 (http://perl.apache.org/)
Database software
- MySQL-Database Server (http://www.mysql.com)
- MySQL-Client
Required system libraries
| Library | Version | Download URL | License | Source build | Binary packages | Remarks |
| HDF5 | 1.6.x | http://hdf.ncsa.uiuc.edu/HDF5/release/obtain5.html | University of Illinois/NCSA Open Source License | {configure, make} | Available | Only C-API required |
Applications
| Application | Version | Download URL | License | Source build | Binary packages | Remarks |
| ImageMagick | 6.2.x | http://www.imagemagick.org/script/download.php | GPL compatible | {configure, make} | Available | <-2> |
You also need one of:
| Application | Version | URL | License | Source build | Binary packages | Remarks |
| Grid Engine | >=5.3, >= 6 recommended | http://gridengine.sunsource.net/ | Sun Industry Standards Source License | recommended | ||
| Sun N1 Grid Engine | >= 6 | http://www.sun.com/software/gridware/ | commercial | not available |
Programming languages
| Application | Version | Download URL | License | Source build | Binary packages | Remarks |
| Perl | >= 5.8 | http://www.perl.org/get.html | Artistic License or GPL | {configure, make} | Available | We recommend to use binary packages from your Distribution |
| R | >= 2.0 | http://www.r-project.org/ | GPL | {configure, make} | Available | /!\ Use configure option { --enable-R-shlib } (most binary packages have it) |
Perl modules We highly ecommend to use binary packages of your operating system Distribution or CPAN-shell install for the Perl modules, except where stated otherwise.
| Module | Version | License | Download | Remarks |
| CGI | 3.x | http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.11.tar.gz | ||
| HTML::Template | > 2.6 | Artistic | http://search.cpan.org/CPAN/authors/id/S/SA/SAMTREGAR/HTML-Template-2.7.tar.gz | |
| Config::IniFiles | 2.x | http://search.cpan.org/CPAN/authors/id/G/GC/GCARLS/Config-IniFiles-2.39.tar.gz | ||
| GD | >= 2.12 | http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GD-2.30.tar.gz | Requires GD system library | |
| MailTools | >= 1.67 | http://search.cpan.org/CPAN/authors/id/M/MA/MARKOV/MailTools-1.67.tar.gz | ||
| Digest::MD5 | >=2.33 | http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Digest-MD5-2.33.tar.gz | ||
| HTML::Table | 2.x | http://search.cpan.org/CPAN/authors/id/A/AJ/AJPEACOCK/HTML-Table-2.02.tar.gz | ||
| PDL | >= 2.4.2 | http://search.cpan.org/CPAN/authors/id/C/CS/CSOE/PDL-2.4.2.tar.gz | /!\ Do not use CPAN shell or packaged install, see HowToInstallPdl | |
| PDL::IO::HDF5 | >= 0.3 | http://search.cpan.org/CPAN/authors/id/C/CE/CERNEY/PDL-IO-HDF5-0.3.tar.gz |
R-packages
R packages should be installed via the
R CMD INSTALL method. Or alternatively from inside a running R using install.packages('foo') .
Consult the Administration and Installation Guide for R for more details on how to install R-packages.
| Package | Version | Download | License | Remarks |
| sma | >=0.5 | CRAN mirrors | GPL | |
| amap | >= 0.5 | CRAN mirrors | GPL | |
| limma | CRAN mirrors | GPL | ||
| siggenes | CRAN mirrors | GPL | ||
| affy | CRAN mirrors | GPL |
Language interfaces
| Package | Version | Download | Remarks |
| RSPerl | >=0.9-1 | http://www.omegahat.org/RSPerl/index.html | see HowToInstallRSPerl |