EMMAWiki/AdministratorDocumentation/SoftwareRequirements: Difference between revisions

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When you install e.g. on a LINUX box you will find all or most of the required software in the
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
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 installed using the [http://www.cpan.org CPAN shell].
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 [http://www.cpan.org CPAN].


== Requirements ==
== Requirements ==


We list only the software and the minimum required version which is needed to run the server here.
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.
Where special setup options are required for a software, it is listed.


'''Operating systems'''
'''Operating systems'''


As a Perl application emma should in principle be platform independent.
As a Perl application EMMA should in principle be platform independent.
It has been tested with these operating systems or distributions:
It has been tested with these operating systems or distributions:


Line 25: Line 25:
* [http://www.freebsd.org FreeBSD > 5.3]
* [http://www.freebsd.org FreeBSD > 5.3]


'''Required libraries'''
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'''
{| border="1" cellpadding="2" cellspacing="0"
{| border="1" cellpadding="2" cellspacing="0"
| ''Library''
| ''Library''
Line 40: Line 50:
| [ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/unpacked/COPYING University of Illinois/NCSA Open Source License]
| [ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/unpacked/COPYING University of Illinois/NCSA Open Source License]
| {configure, make}
| {configure, make}
| (./)
| Available
| Only C-API required
| Only C-API required
|}
'''Applications'''
{| border="1" cellpadding="2" cellspacing="0"
| ''Application''
| ''Version''
| ''Download URL''
| ''License''
| ''Source build''
| ''Binary packages''
| ''Remarks''
|-
|  [[ImageMagick]]
|  6.2.x
|  http://www.imagemagick.org/script/download.php
|  [http://www.imagemagick.org/script/license.php GPL compatible]
|  {configure, make}
|  Available
| <-2>
|}
You also need one of:
{| border="1" cellpadding="2" cellspacing="0"
| ''Application''
| ''Version''
| ''URL''
| ''License''
| ''Source build''
| ''Binary packages''
| ''Remarks''
|-
|  Grid Engine
|  >=5.3, >= 6 recommended
|  http://gridengine.sunsource.net/
| [http://gridengine.sunsource.net/project/gridengine/Gridengine_SISSL_license.html Sun Industry Standards Source License]
| 
|  recommended
| 
|-
|  Sun N1 Grid Engine
|  >= 6
|  http://www.sun.com/software/gridware/
|  commercial
|  not available
| 
| 
|}
|}


'''Programming languages'''
'''Programming languages'''
{| border="1" cellpadding="2" cellspacing="0"
| ''Application''
| ''Version''
| ''Download URL''
| ''License''
| ''Source build''
| ''Binary packages''
| ''Remarks''
|-
|  Perl
|  >= 5.8
|  http://www.perl.org/get.html
|  [http://dev.perl.org/licenses/artistic.html Artistic License] or [http://dev.perl.org/licenses/gpl1.html GPL]
|  {configure, make}
|  Available
|  We recommend to use binary packages from your Distribution
|-
|  R
|  >= 2.0
|  http://www.r-project.org/
|  [http://www.r-project.org/COPYING GPL]
|  {configure, make}
|  Available
|  /!\ Use configure option { --enable-R-shlib } (most binary packages have it)
|}


'''Perl modules'''
'''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.
{| border="1" cellpadding="2" cellspacing="0"
{| border="1" cellpadding="2" cellspacing="0"
| ''Module''
| ''Module''
| ''Version''
| ''Version''
| ''License''
| ''Download''
| ''Download''
| ''Remarks''
| ''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'''
R packages should be installed via the
<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''
| ''Version''
| ''Version''
| ''Download''
| ''Download''
|  ''License''
| ''Remarks''
| ''Remarks''
|-
|  sma
|  >=0.5
| [http://cran.r-project.org/mirrors.html CRAN mirrors]
|  GPL
| 
|-
|  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
| 
|}
|}


Line 68: Line 238:
| ''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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