EMMAWiki/AdministratorDocumentation/SoftwareRequirements: Difference between revisions

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It is not installable under Windows systems, as there is no RSPerl module for Windows.
It is not installable under Windows systems, as there is no RSPerl module for Windows.


'''Required libraries'''
'''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'''
{| border="1" cellpadding="2" cellspacing="0"
{| border="1" cellpadding="2" cellspacing="0"
| ''Library''
| ''Library''
Line 186: Line 194:


R packages should be installed via the
R packages should be installed via the
<code><nowiki> R CMD INSTALL</nowiki></code> method.Consult the [http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages Administration and Installation Guide for R] for more details on how to install R-packages.
<code><nowiki> R CMD INSTALL</nowiki></code> method. Or alternatively from inside a running R using <code><nowiki> install.packages('foo') </nowiki></code>.
Consult the [http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages Administration and Installation Guide for R] for more details on how to install R-packages.
{| border="1" cellpadding="2" cellspacing="0"
{| border="1" cellpadding="2" cellspacing="0"
| ''Package''
| ''Package''
Line 201: Line 210:
|-
|-
|  amap  
|  amap  
|  >= 0.5
| [http://cran.r-project.org/mirrors.html CRAN mirrors]
|  GPL
|   
|   
|-
|  limma
|   
|   
| [http://cran.r-project.org/mirrors.html CRAN mirrors]
|  GPL
| 
|-
|  siggenes
| [http://cran.r-project.org/mirrors.html CRAN mirrors]
|  GPL
| 
|-
|  affy
| [http://cran.r-project.org/mirrors.html CRAN mirrors]
|  GPL
|   
|   
|}
|}
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| ''Download''
| ''Download''
| ''Remarks''
| ''Remarks''
|}
|-
 
| RSPerl
'''Web-server software'''
|  >=0.9-1
 
|  http://www.omegahat.org/RSPerl/index.html
'''Database software'''
|  see HowToInstallRSPerl

Latest revision as of 07:15, 26 October 2011

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:

It is not installable under Windows systems, as there is no RSPerl module for Windows.

Web-server software

Database software

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
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