librairies nécessaires

emerge -qv MailTools
emerge -qv dev-perl/CGI

wEMBOSS utilise apache pour fonctionner, il est nécessaire de l'installer et de l'activer avant l'installation de wEMBOSS :

  /etc/init.d/apache2 start
ou systemd :
  systemctl enable apache2
  systemctl start apache2

cd /opt
git clone https://github.com/ugadal/wemboss.git
cd wemboss
cd wEMBOSSinstall

lisez INSTALL lancez: perl install.pl

et répondez aux questions comme suit: (valeurs par défaut adaptées à Gentoo)

/usr/local/share/EMBOSS
/usr/local/bin
apache
/var/www/localhost/htdocs
localhost
80
/opt/wemboss_site
"moi"@localhost

Modifications à effectuer dans le fichier /etc/apache2/vhosts.d/default_vhost.include

première modif dans /etc/apache2/httpd.conf

Ajoutez Trois lignes un peu avant la fin

  LoadModule usertrack_module modules/mod_usertrack.so
  LoadModule vhost_alias_module modules/mod_vhost_alias.so
  <AuthnProviderAlias file shadfile>
       AuthUserFile "/etc/shadow"
  </AuthnProviderAlias>
  # If you wish httpd to run as a different user or group, you must run
  # httpd as root initially and it will switch.
  #

La modification dans le default_vhost.include se simplifie elle devient :

fichier: /etc/apache2/vhosts.d/default_vhost.include qqpart ou il y a déjà une ligne ScriptAlias

ScriptAlias /wEMBOSS_cgi/ "/opt/wemboss_site/wEMBOSS_cgi/"
qqpart là où il y a déjà des balises <Directory>

<Directory "/opt/wemboss_site/wEMBOSS_cgi">
      AuthBasicProvider shadfile
      AuthType basic
      Authname "EMBOSS user"
      Require valid-user
</Directory>

pour finir

/etc/init.d/apache2 reload
groupadd shadow
usermod -a -G shadow apache
chgrp shadow /etc/shadow
chmod 640 /etc/shadow
/etc/init.d/apache2 reload

#Créer un compte : useradd -m 'Nom' passwd 'Nom'

wEMBOSS, a web interface for EMBOSS

wEMBOSS is an interface to the EMBOSS bioinformatics tools (http://emboss.sourceforge.net). wEMBOSS can be downloaded from http://wemboss.sourceforge.net.

wEMBOSS reference

wEMBOSS: a web interface for EMBOSS Sarachu M. and Colet M. Bioinformatics 2005 21(4):540-541

About the included applets

All applets are included with permission of the authors.

Zmasek C.M. and Eddy S.R. (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics, 17: 383-384.

ATV web site http://www.phylosoft.org/archaeopteryx

M. Clamp, J. Cuff, S.M. Searle and G.J. Barton (2004) The Jalview Java alignment editor. Bioinformatics, 20: 426-427.
A.M. Waterhouse, J.B. Procter, D.M.A. Martin, M. Clamp and G.J. Barton (2009) Jalview version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.

Jalview web site http://www.jalview.org

Warning

The Jalview applet does not run under MacOS X with the Firefox browser. It does however work properly with Safari and Opera.

wEMBOSS-2

wEMBOSS-2 is completely reorganized from the developer and manager point-of-vue. wEMBOSS-2 has the same functionality as wEMBOSS-1.8.1 for the users. wEMBOSSDEV-2 for the developer is now a project in Eclipse using the Epic plug-in. wEMBOSSDIST-2.x is the corresponding distribution package. It is distributed as successive releases with version numbers. We are starting the distribution at version 2.1.

What is different, in a few words : wEMBOSS does not install anymore its modules in the Perl system libraries. This is completely justified because the wEMBOSS Perl code is used first at installation time and later at wEMBOSS run time but never as reusable code for other applications.

Thus after installation you can find wEMBOSS-2 files only at 3 places : - where you put the distribution package (of course) - where you did install it (wEMBOSS home) - under the document root of your Web server, where are all the files needed to create the Web pages (html, images, css, js, ...). - a fourth place could be the one where you have put all your personal stuff that successive installations could otherwise have erased !

The wEMBOSS.pm module has been split into 8 modules each one corresponding to one of the 8 possible actions (project management, menu of programs, program page, run ...) Part of the code is rewritten for clarity, the others parts will be rewritten later.

My idea is to facilitate my succession for a new wEMBOSS developer.

I am now retired so its more easy to spend time on it!

Marc