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myGenomeBrowser

myGenomeBrowser

myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers.

Citation: https://doi.org/10.1093/bioinformatics/btw800

BBRIC::myGenomeBrowser

ABOUT

Build your own genome browser (based on JBrowse) to visualize structural and funtionnal annotation files, mapping results (coverage and variants), blast alignments, quantitative results. Search through keywords or sequence (blast+) and share with your collaborators.

Extract sequences and features.

You will find a full example of the available features here.

COMPLIANT FILE FORMATS

  • GFF3
  • BAM
  • BigWig
  • VCF
  • BED
  • Tabulatted blast results (m8 / outfmt 6)
  • Tabulatted InterProScan results

QUICKSTART (Docker install)

PREREQUISITES

You need to install :

docker-engine (see: https://docs.docker.com/engine/installation/)
git

OPTIONNAL: If you want to create users from host server (not from Docker image), you will need Perl and this perl module

Apache::Htpasswd perl

BUILD

sudo bash
git clone https://framagit.org/BBRIC/myGenomeBrowser.git
cd myGenomeBrowser
export MGB=$PWD
$MGB/build.sh

CONFIGURE

Persistence directory

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

Admin email adress

export MGB_ADMIN=john.doe@somwhere.org

App hostname and port

export MGB_HOSTNAME=myWebServer.org
export MGB_PORT=3232

SMTP Config

export MGB_SMTP=smtp.server.org:port
export MGB_SMTP_SECURITY=STARTTLS|TLS

optionnal

export MGB_SMTP_LOGIN=requiredlogin
export MGB_SMTP_PASSWD=requiredpasswd

:information_source: Exemple for GMAIL configuration (you will need to allow "Less secure apps" on your Gmail account (https://support.google.com/a/answer/6260879?hl=en):

export MGB_SMTP=smtp.gmail.com:587
export MGB_SMTP_SECURITY=STARTTLS
export MGB_SMTP_LOGIN=YourGmailLogin
export MGB_SMTP_PASSWD=YourGmailPassword

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

$MGB/configure.sh

OPTIONNAL : CREATE ADMIN USER

:information_source: If you do not create admin user during installation process, these information will be asked at first web connexion

From the host server (need Apache::Htpasswd module):

$MGB/bin/int/admin_addUser.pl --email=$MGB_ADMIN --password=<azekaze-aze> --common_name='Jon Doe' --outdir=$MGB_DIR/etc

RUN APP

$MGB/run.sh

:information_source: To start Docker image in interactive mode run:

$MGB/run.sh --login

STOP APP

$MGB/stop.sh


ADMINISTRATION TOOLS

ACCOUNT CREATION

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

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

ACCOUNT MIGRATION

:information_source: 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

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

USAGE REPORT

:information_source: This tools is run once a day (cron) and results are available on the administrator account Stats webpage; Nevertheless you can execute the following command to get an up to date JSON stat file

$MGB/bin/int/admin_stats.pl

produces a JSON file with the following structure:

{
   "users" : {
      %USER_EMAIL% : {
         %PORTALNAME% : {
            "shared" : boolean,
            "rawdata" : {
               %TRACKTYPE_A% : "TRACK OF TYPE A DISK USAGE",
               %TRACKTYPE_B% : "TRACK OF TYPE B DISK USAGE"
            },
            "tracks" : {
               %TRACKTYPE_A% : "NUMBER OF TRACK OF TYPE A",
               %TRACKTYPE_B% : "NUMBER OF TRACK OF TYPE B"
            },
            "blastdbsize" : "BLAST INDEX TOTAL DISK USAGE",
            "browsersize" : "JBROWSE DATA TOTAL DISK USAGE"
         },
         "totalsize" : "TOTAL DISK USAGE"
      }
   },
   "summary" : {
      "users" : "TOTAL NUMBER OF USERS",
      "tracks" : {
         %TRACKTYPE_A% : "NUMBER OF TRACK OF TYPE A",
         %TRACKTYPE_B% : "NUMBER OF TRACK OF TYPE B"
      },
      "size" : "TOTAL DISK USAGE",
      "portals" : "TOTAL NUMBER OF BROWSERS"
   }
}


EXPERT INSTALL

:information_source: 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/myGenomeBrowser.git
cd myGenomeBrowser
sudo bash
export MGB=$PWD

CONFIGURATION

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

cp $MGB/site/cfg/site.cfg.template $MGB/site/cfg/site.cfg

PATHS

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

portal_install_dir=/file/system/root/access/to/myGenomeBrowser (should be == to `$MGB`)
portal_http_root=/apache/root/access/to/myGenomeBrowser
portal_web_server=http://localhost

AUTHENTICATION

Choose your authentication protocol by setting authentication_mode parameter in the configuration file $MGB/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 myGenomeBrowser

For each authentication mode, you have to set a list of parameters in $MGB/site/cfg/authentication.cfg (use $MGB/site/cfg/authentication.cfg as a template) 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`)

:information_source: %I is a mask for $MGB

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

:information_source: 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

APACHE

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

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

Restart Apache

service apache2 reload

SMTP

Configure SMTP server using $MGB/site/cfg/ssmtp.cfg.template

mkdir -p $MGB/data/cfg/
cp $MGB/site/cfg/ssmtp.conf.template $MGB/data/cfg/ssmtp.conf 
vi $MGB/data/cfg/ssmtp.conf 

INSTALL

Run install

$MGB/bin/int/admin_install.pl

RUN

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

SCREENCASTS

Video tutorials are available on our Youtube Channel

AUTHORS

  • sebastien.carrere@inra.fr
  • jerome.gouzy@inra.fr

CITATION

Sébastien Carrere and Jérôme Gouzy
myGenomeBrowser: Building and sharing your own genome browser
Bioinformatics, December 23, 2016 doi:10.1093/bioinformatics/btw800

CONTACT