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family-companion

family-companion

owadays, comparative genomics is a classical tool for biologists to address various scientific questions such as pathogeny determinism, bacteria host specificity, duplication and gene family expansion in a species. The large number of available finis

BBRIC::Family-Companion

ABOUT

Perform protein family analyses (OrthoMCL), browse, visualise and share the results!

Nowadays, comparative genomics is a classical tool for biologists to address various scientific questions such as pathogeny determinism, bacteria host specificity, duplication and gene family expansion in a species. The large number of available finished or draft genome sequences associated with the full automatisation of structural annotation pipelines leads to an era of high throughput comparative genomics. Tools like OrthoMCL provide an easy way to compare tens of species at a time and build homologous gene families. However, output results, classically a matrix with groups as lines and genes as columns, remains too raw to be interpreted by an end user without programming skills. In order to help users in the post process of these data, we developed a web user interface that automatically extract frequently asked datasets such as core and pan proteomes, specific proteins, abundance and presence/absence matrix (aka. phylogenetic profiles). Providing optional InterPro annotation will also lead to build tables and charts representing terms (eg : PFAM, GO) count in each previously described datasets. Our tool uses standard formats as input and outputs to ease post-process analyses.

QUICKSTART DOCKER

PREREQUISITES

Install :

docker-engine (see: https://docs.docker.com/engine/installation/)
git
perl
bash
Apache::Htpasswd perl module

BUILD

sudo bash
git clone https://framagit.org/BBRIC/family-companion.git
cd family-companion
export FC=$PWD
$FC/build.sh

CONFIGURE

Persistence directory

export FC_DIR=/local/path/to/persistant/directory

Admin email adress

export FC_ADMIN=john.doe@somwhere.org

App hostname and port

export FC_HOSTNAME=myWebServer.org
export FC_PORT=3232

SMTP Config

export FC_SMTP=smtp.server.org:port

optionnal

export FC_SMTP_LOGIN=requiredlogin
export FC_SMTP_PASSWD=requiredpasswd

Run configuration shell script (will create dir/config files)

$FC/configure.sh

CREATE ADMIN USER

$FC/bin/int/admin_addUser.pl --email=$FC_ADMIN --password=<azekaze-aze> --common_name='Jon Doe' --outdir=$FC_DIR/etc

RUN APP

$FC/run.sh

STOP APP

$FC/stop.sh




EXPERT INSTALL

Tested on Debian / Ubuntu > 14.04

PREREQUISITES

You nee to install :

Perl
Apache 2.4
git
Apache::Htpasswd perl module

Then:

cd /path/to/install/directory/
git clone https://framagit.org/BBRIC/family-companion.git
cd family-companion
sudo bash
export FC=$PWD

CONFIGURATION

Configuration template file : $FC/site/cfg/site.cfg.template

cp $FC/site/cfg/site.cfg.template $FC/site/cfg/site.cfg

PATHS

Set the following parameters in $FC/site/cfg/site.cfg configuration file:

portal_install_dir=/file/system/root/access/to/family-companion (should be == to `$FC`)
portal_http_root=/apache/root/access/to/family-companion
portal_web_server=http://localhost

ADMIN CONTACT

Set the following parameter in $FC/site/cfg/site.cfg configuration file:

admin_mail=contact@mail.org

AUTHENTICATION

Choose your authentication protocol by setting authentication_mode parameter in the configuration file $FC/site/cfg/site.cfg to one of these values:

  • file
  • ldap
  • shibboleth

file is the default authentication mode used with Docker install script; it uses htaccess file authentication : simpliest way to use family-companion

Authentication template file : $FC/site/cfg/authentication.cfg.template

cp $FC/site/cfg/authentication.cfg.template $FC/site/cfg/authentication.cfg

For each authentication mode, you have to set a list of parameters in $FC/site/cfg/authentication.cfg described below :

FILE
authentic_file=PATH/TO/ETC/PASSWD/LIKE/FILE (default is `%I/etc/local.passwd`)
authentic_htpasswd_file=PATH/TO/HTPASSWD/FILE (default is `%I/etc/local.htpasswd`)

%I is a mask for $FC

LDAP
authentic_ldap_host=LDAP DIRECTORY HOST NAME
authentic_ldap_base=BASE DN
authentic_ldap_port=LDAP DIRECTORY PORT
SHIBBOLETH
authentic_sibboleth_login=LOGIN_URL/TO/Shibboleth.sso/Login
authentic_sibboleth_logout=LOGOUT_URL/TO/Shibboleth.sso/Logout

If you use a LDAP directory in complement to manage authorizations you have to set the following parameters

authentic_ldap_host=LDAP DIRECTORY HOST NAME
authentic_ldap_base=BASE DN
authentic_ldap_port=LDAP DIRECTORY PORT

SMTP

Configure SMTP server using $FC/site/cfg/ssmtp.conf.template

mkdir -p $FC/data/cfg/
chown -R www-data.www-data $FC/data
cp $FC/site/cfg/ssmtp.conf.template $FC/data/cfg/ssmtp.conf 
vi $FC/data/cfg/ssmtp.conf 

INSTALL

Run install

$FC/bin/int/admin_install.pl

APACHE

Edit your Apache config file using $FC/site/cfg/apache.conf as a template to set correct rewrite directives

vi /etc/apache2/sites-available/000-default.conf
a2ensite 000-default

Restart Apache

service apache2 reload

RUN

Open a web browser to the right URL : http://$portal_web_server/$portal_http_root

ADMINISTRATION TOOLS

ACCOUNT CREATION

This tool only works for file authentication mode (the one used with Docker install)

$FC/bin/int/admin_addUser.pl --email=$USER_EMAIL --password=$USER_PASSWD --common_name='$USER_NAME' --outdir=$FC/etc

ACCOUNT MIGRATION

This tool can be used when one of your user change his mail address or when a PI wants to retrieve student analysis in his workspace

$FC/bin/int/admin_migrate.pl --former_email=<Current.Case.Sensitive@email.address> --new_email=<New.Case.Sensitive@email.address> 

USAGE REPORT

sudo -u www-data $FC/bin/int/admin_stats.pl

produces a tabullated file with the following structure:

key email date error dir_size proteomes iprscan local_orthomcl file
User hash User email analysis run date erroneous (boolean) complete analysis disk usage number of proteomes InterPro data uploaded local execution of orthomcl analysis configuration file

SCREENCASTS

Youtube Channel

API

Run in Postman

AUTHORS

  • sebastien.carrere@toulouse.inra.fr
  • ludovic.cottret@toulouse.inra.fr
  • martial.briand@angers.inra.fr
  • corinne.rancurel@sophia.inra.fr
  • bbric.contact@toulouse.inra.fr - [ BBRIC Network ]