diff --git a/Dockerfile b/Dockerfile
index 4da515c..eb3f62d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,169 +1,167 @@
 # DOWNLOAD BASE IMAGE OF CENTOS7
 FROM centos:centos7
 
 MAINTAINER alexis rapin
 
 # CREATE APP USER
 RUN adduser -m genocrunch_user
 WORKDIR /home/genocrunch_user
 
 # MISC
 RUN yum -y install nano
 
 # INSTALL RUBY WITH RBENV
 
 # Install dependencies
 RUN yum -y update && yum clean all
 RUN yum install -y git-core \
     zlib \
     zlib-devel \
     gcc \
     gcc-c++ \
     patch \
     readline \
     readline-devel \
     libyaml-devel \
     libffi-devel \
     openssl-devel \
     make \
     bzip2 \
     bzip2-devel \
     autoconf \
     automake \
     libtool \
     bison \
     curl \
     sqlite-devel \
     epel-release \
     nodejs && yum clean all
 
 # Install rbenv from github
 USER genocrunch_user
 RUN git clone https://github.com/rbenv/rbenv.git ~/.rbenv
 RUN echo 'export PATH="~/.rbenv/bin:$PATH"' >> ~/.bashrc \
     && echo 'eval "$(~/.rbenv/bin/rbenv init -)"' >> ~/.bashrc
 RUN git clone https://github.com/rbenv/ruby-build.git ~/.rbenv/plugins/ruby-build
 USER root
 RUN cd /home/genocrunch_user/.rbenv/plugins/ruby-build && ./install.sh
 
 # Install ruby
 USER genocrunch_user
 RUN source ~/.bashrc \
   && rbenv install 2.3.1 \
   && rbenv global 2.3.1
 
 # Install rails
 RUN echo "gem: --no-document" > ~/.gemrc
 RUN source ~/.bashrc \
     && gem install bundler \
     && gem install rails -v 5.0.1 \
     && rbenv rehash
 RUN echo 'export PATH="~/.rbenv/versions/2.3.1/bin:$PATH"' >> .bashrc
 
 # INSTALL POSTGRESQL
 USER root
 RUN yum -y install postgresql \
     postgresql-contrib \
     postgresql-devel \
     postgresql-libs
 #RUN postgresql-setup initdb
 #RUN sed -i 's/^\(host.*\)ident$/\1md5/g;' /var/lib/pgsql/data/pg_hba.conf
 #RUN systemctl start postgresql
 #RUN systemctl enable postgresql
 
 # INSTALL PYTHON2.7
 #RUN yum install -y python-pip
 #RUN pip install numpy
 #RUN yum -y groupinstall 'Development Tools'
 
 # INSTALL R
 RUN yum install -y R-core \
     R-base \
     R-devel \
     libcurl-devel
 
 # Install R packages
 RUN yum install -y libxml2-devel
 RUN echo "options(repos=structure(c(CRAN='https://cran.uib.no')))" >> .Rprofile
 RUN echo ".libPaths('/usr/share/R/library')" >> .Rprofile
 RUN Rscript -e "install.packages('ineq')"
 RUN Rscript -e "install.packages('rjson')"
 RUN Rscript -e "install.packages('fpc')"
 RUN Rscript -e "install.packages('multcomp')"
 RUN Rscript -e "install.packages('FactoMineR')"
 RUN Rscript -e "install.packages('colorspace')"
 RUN Rscript -e "install.packages('vegan')"
 RUN Rscript -e "install.packages('optparse')"
 RUN Rscript -e "install.packages('gplots')"
 RUN Rscript -e "install.packages('fossil')"
 RUN Rscript -e "install.packages('coin')"
 RUN Rscript -e "install.packages('SNFtool')"
 RUN Rscript -e "install.packages('devtools')"
 RUN Rscript -e "library(devtools); install_github('igraph/rigraph')"
 RUN Rscript -e "source('https://bioconductor.org/biocLite.R'); biocLite('sva')"
 
 # INSTALL THE APP
 USER genocrunch_user
 
 # Create a new Rails project
 WORKDIR /home/genocrunch_user
 RUN source ~/.bashrc \
     && rails new genocrunch -d postgresql -B
 RUN GIT_CURL_VERBOSE=1 git clone https://git@c4science.ch/source/genocrunch-2.1.git /tmp/genocrunch
 WORKDIR /home/genocrunch_user/genocrunch
 RUN rsync -r /tmp/genocrunch/ ./
 RUN rm -r /tmp/genocrunch
 
 # Install R/python scripts
-#USER root
 #RUN chmod 755 install.sh && ./install.sh
-#USER genocrunch_user
 
 # Install gems
 RUN source ~/.bashrc \
-    && ~/.rbenv/versions/2.3.1/bin/bundle install
+    && bundle install
 RUN table_fp=$(cd ~/.rbenv/versions/*/lib/ruby/gems/*/gems/jquery-datatables-rails-*/app/assets/javascripts/dataTables/ && pwd) \
     && cp "${table_fp}"/jquery.dataTables.js "${table_fp}"/jquery.dataTables.js.bkp \
     && sed -i -e 's/No data available in table/This table is empty/g' "${table_fp}"/jquery.dataTables.js
 
 # Get versions (print a json file with versions of R packages)
 RUN lib/genocrunch_console/bin/get_version.py
 
 # Configure the app
 USER root
 EXPOSE 3000
 USER genocrunch_user
 
 # config/config.yml
 RUN cp config/config.yml.keep config/config.yml
 RUN sed -i 's/data_dir:.*$/data_dir: \/home\/genocrunch_user\/genocrunch/g' config/config.yml
 RUN sed -i 's/info_links:.*$/info_links: []/g' config/config.yml
 RUN sed -i 's/user_confirmable:.*$/user_confirmable: false/g' config/config.yml
 
 # config/initializers/devise.rb
 RUN cp config/initializers/devise.rb.keep config/initializers/devise.rb
 RUN sed -i 's/config.mailer_sender =.*$/config.mailer_sender = "noreply.genocrunch@gmail.com"/g' config/initializers/devise.rb
 
 # config/environments/development.rb
 RUN cp config/environments/development.rb.keep config/environments/development.rb
 RUN sed -i 's/config.action_mailer.default_url_options =.*$/config.action_mailer.default_url_options = {:host => "localhost:3000"}/g' config/environments/development.rb
 RUN sed -i 's/:address =>.*$/:address => "smtp.gmail.com",/g' config/environments/development.rb
 RUN sed -i 's/:port =>.*$/:port => 587,/g' config/environments/development.rb
 RUN sed -i 's/:domain =>.*$/:domain => "mail.google.com",/g' config/environments/development.rb
 RUN sed -i 's/:user_name =>.*$/:user_name => "noreply.genocrunch@gmail.com",/g' config/environments/development.rb
 RUN sed -i 's/:password =>.*$/:password => "email_password",/g' config/environments/development.rb
 RUN sed -i 's/:authentication =>.*$/:authentication => :plain,/g' config/environments/development.rb
 RUN sed -i 's/:enable_starttls_auto =>.*$/:enable_starttls_auto => true/g' config/environments/development.rb
 
 # config/database.yml
 RUN cp config/database.yml.keep config/database.yml
 RUN sed -i 's/^.*username:.*$/  username: genocrunch_user/g' config/database.yml
 RUN sed -i 's/database:.*$/database: genocrunch/g' config/database.yml
 RUN sed -i 's/^.*password:.*$/  password: genocrunch_db_password/g' config/database.yml
 RUN sed -i 's/^.*host:.*$/  host: hostaddress/g' config/database.yml
 
 RUN cp db/seeds.rb.keep db/seeds.rb
 
 # Run Genocrunch
 CMD source ~/.bashrc \
     && RAILS_ENV=development ruby bin/delayed_job -n 2 start; /home/genocrunch_user/genocrunch/bin/rails server
diff --git a/README.md b/README.md
index 8b10224..2067bed 100644
--- a/README.md
+++ b/README.md
@@ -1,173 +1,175 @@
 Genocrunch in Docker
 ====================
 
 A Dockerfile to run Genocrunch web application on Docker.
 
 ## Resources
 
 - **Git clone URL:** <https://c4science.ch/source/genocrunch_docker.git>
 - **Documentation:** <https://c4science.ch/source/genocrunch_docker>
 - **Genocrunch documentation:** <https://c4science.ch/source/genocrunch-2.1>
 - **Genocrunch official web server:** <https://genocrunch.epfl.ch>
 
 ## Rights
 
 - **Copyright:** All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, Laboratory of Intestinal Immunology, 2018
 - **License:** MIT (See LICENSE.txt for details)
 - **Author:** A Rapin
 
 ## Requirements
 
 - **Docker version 17.12.0-ce**
 
 ## Installation (on Debian linux)
 
 Note: you may have to use `sudo` with docker commands if docker is not configured to be used as a non-root user.
 
 ### Set the Docker container external resources
 
 The Genocrunch web application will need to store some data files and to use a database. To avoid data loses when updating a container, you can set both data storage location and database on the host (as opposed to on the docker container itself).
 
 First, create a new data storage directory on the host side. This directory will be used by the Genocrunch web app running on the docker container:
 
 ```
 $ mkdir /path/to/genocrunch/storage
 ```
 
 Also create a PostgreSQL database on the host side. This database will be used by the Genocrunch web app running on the docker container:
 
 ```
 $ sudo apt-get install postgresql postgresql-contrib
 $ sudo su postgres
 $ psql
 postgres=# create role genocrunch_user with login password 'genocrunch_db_password';
 postgres=# create database genocrunch owner genocrunch_user;
 postgres=# \q
 $ exit
 ```
 
 Then, allow the docker container to be listened from the database by modifying the `/etc/postgresql/9.?/main/postgresql.conf` file as following:
 
 ```
 #/etc/postgresql/9.?/main/postgresql.conf 
 ...
 listen_addresses = '*'
 ...
 ```
 
 Also add the following line to `/etc/postgresql/9.?/main/pg_hba.conf`:
 
 ```
 #/etc/postgresql/9.?/main/pg_hba.conf 
 ...
 host    all             all             0.0.0.0/0               md5 
 ...
 ```
 
 Finally, restart the PostgreSQL service:
 
 ```
 $ sudo /etc/init.d/postgresql restart
 ```
 
 ### Build the docker image
 
 First, download the Dockerfile from its git repository:
 
 ```
 $ git clone https://c4science.ch/source/genocrunch_docker.git
 ```
 
 Before building a docker image using the Dockerfile, you may want to edit the Dockerfile in order to customize the installation of the Genocrunch web app.
 For this, open `genocrunch_docker/Dockerfile` with your favorite editor and follow the following instructions:
 
 Edit this line to define any custom link to be included in the info menu of the Genocrunch web app topbar:
 
 ```
 #Dockerfile
 
 ...
 # config/config.yml
 ...
 RUN sed -i 's/info_links:.*$/info_links: [{name: "link_name", href: "link_url", target: "_blank"}]/g' config/config.yml
 ```
 
 Edit this line to define whether new users will be asked to confirm their email address via a confirmation link or not:
 
 ```
 #Dockerfile
 
 ...
 # config/config.yml
 ...
 RUN sed -i 's/user_confirmable:.*$/user_confirmable: false/g' config/config.yml
 ```
 
 Edit these lines to set the email address to be used by the web app:
 
 ```
 #Dockerfile
 
 ...
 # config/initializers/devise.rb
 ...
 RUN sed -i 's/config.mailer_sender =.*$/config.mailer_sender = "app_email@gmail.com"/g' config/initializers/devise.rb
 
 # config/environments/development.rb
 ...
 RUN sed -i 's/config.action_mailer.default_url_options =.*$/config.action_mailer.default_url_options = {:host => "localhost:3000"}/g' config/environments/development.rb
 RUN sed -i 's/:address =>.*$/:address => "smtp.gmail.com",/g' config/environments/development.rb
 RUN sed -i 's/:port =>.*$/:port => 587,/g' config/environments/development.rb
 RUN sed -i 's/:domain =>.*$/:domain => "mail.google.com",/g' config/environments/development.rb
 RUN sed -i 's/:user_name =>.*$/:user_name => "app_email@gmail.com",/g' config/environments/development.rb
 RUN sed -i 's/:password =>.*$/:password => "app_email_password",/g' config/environments/development.rb
 RUN sed -i 's/:authentication =>.*$/:authentication => :plain,/g' config/environments/development.rb
 RUN sed -i 's/:enable_starttls_auto =>.*$/:enable_starttls_auto => true/g' config/environments/development.rb
 ...
 ```
 
 Edit these lines to fit the database name, user and password set previously:
 
 ```
 #Dockerfile
 
 ...
 # config/database.yml
 ...
 RUN sed -i 's/^.*username:.*$/  username: genocrunch_user/g' config/database.yml
 RUN sed -i 's/database:.*$/database: genocrunch/g' config/database.yml
 RUN sed -i 's/^.*password:.*$/  password: genocrunch_db_password/g' config/database.yml
 ...
 ```
 
 Finally, build the docker image:
 
 ```
 $ docker build --rm -t genocrunch .
 ```
 
 ### Database initialization
 
 Complete the installation of the Genocrunch web app by initializing its database from within a docker container using rails schema (`db/schema.rb`) and seeds (`db/seeds.rb`).
 Caution: this will overwrite the database and should be applied only for initialization/re-initialization, not updates. For updates, use migrations or SQL queries.
 
 ```
 $ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch bash
 $ rails db:schema:load
 
 # To change default guest and admin passwords and emails, edit the `User.create` query in the db/seeds.rb file with nano:
 $ nano db/seeds.rb
 
 # Finally, seed the database:
 $ rails db:seed
 $ exit
 ```
 
 ### Run a docker container
 
 Run a docker container using the command below. Make sure to replace `/path/to/genocrunch/storage` with the appropriate path (see the `Set the Docker container external resources` section above) and replace `host.ip.address` by the host ip address.
 This will automatically start the Genocrunch web server which will be accessible in a web browser at <http://localhost:3000> on the host and `host.ip.address:3000` on your network.
 
 ```
 $ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch
 ```
+
+Note: Avoid using the same data storage directory and database for apps running on docker containers and apps running directly on the host (especially if the usernames and main directory paths are not matching).