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rsa-tools / installing-RSAT

Installation guides for the Regulatory Sequence Analysis Tools (RSAT) software suite
https://rsa-tools.github.io/installing-RSAT/
Apache License 2.0
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Customize RSAT configuration #4

Open jvanheld opened 2 years ago

jvanheld commented 2 years ago

To have a properly working server, we need to define the external URL in RSAT configuration.

The URL of the production server is:

http://rsat.france-bioinformatique.fr/rsat/

Other options would also need to be defined for a full use of the server.

I will run the configuration script and revise the different options, then I will provide a command that automatically sets these options to the appropriate value.

jvanheld commented 2 years ago

Command to configure manually the RSAT options :

perl perl-scripts/configure-rsat.pl

I then revise the options one by one and take note of the choices (below)

For RSAT_config.mk

jvanheld commented 2 years ago

After having revised the configuration, I needed to replace the system-wise bash profile in order for changes to take effect for all users (including Apache user).

rsync -v source RSAT_config.bashrc /etc/profile.d/RSAT.sh
jvanheld commented 2 years ago

Par défaut le script configure-rsat.pl fonctionne en mode interactif (prompt pour chaque paramètre) mais on peut aussi filer une option -autoet ensuite lui fournir en arguments les paramètres qu'on veut modifier.

Pour la liste des paramètres ci-dessus ça donnerait la commande suivante. 

perl perl-scripts/configure_rsat.pl \
   --auto \
   rsat_site=ifb-rsat \
   rsat_server_admin=jacques.van-helden@france-bioinformatique.fr \
   group_specificity=Teaching \
   phylo_tools=1 \
   prokaryote_server=1 \
   compara_tools=1 \
   variations_tools=1 \
   plant_server=1 \
   rsat_www=http://rsat.france-bioinformatique.fr/rsat/ \
   rsat_ws=http://rsat.france-bioinformatique.fr/rsat/ \
   ensembl_release=97 \
   ensemblgenomes_release=44

@FanchTheSystem , serait-il possible d'inclure cela dans la recette ansible ?

FanchTheSystem commented 2 years ago

A priori c'est fixé ici : https://gitlab.com/ifb-elixirfr/ansible-roles/ansible-rsat/-/commit/d929ee2ce583b4e506b9bb57d8f26090bb6453cc