Update docker setup.

To build and run:
    $ cp example.env.yml env.yml
    # add fb app id and secret to eny.yml
    $ docker build -t afra .
    $ docker run -itp 9292:9292 afra

Signed-off-by: Saurabh Kumar <[email protected]>

.dockerignore

@@ -1,3 +1,11 @@
+.git
+Gemfile.lock
+MYMETA.yml
+MYMETA.json
+Makefile
+.extlib
+node_modules
+www/lib
 node_modules
 data/jbrowse
 data/genevalidator

Dockerfile

@@ -5,11 +5,74 @@
 #
 # VERSION   0.0.1
 
-FROM        bmpvieira/afra-environment
+FROM  debian:sid
 MAINTAINER  Anurag Priyam <[email protected]>
 
-USER root
-ADD . /afra
-WORKDIR /afra
-RUN ./scripts/build.sh
-ENTRYPOINT ["./scripts/run.sh"]
+RUN echo 'APT::Install-Recommends "false";' >> /etc/apt/apt.conf
+RUN echo 'APT::Install-Suggests "false";' >> /etc/apt/apt.conf
+
+RUN apt-get update && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y \
+      apt-utils locales build-essential git curl openssl ca-certificates && \
+    rm -rf /var/lib/apt/lists/*
+
+# FIXME:
+#   Added this line so that Postgres will be UTF-8 by default. However, it
+#   doesn't seem to have any effect - Postgres has the default 'C' locale.
+RUN localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8
+ENV LANG en_US.utf8
+
+## Setup Ruby.
+RUN cd /tmp/ && \
+      curl -o ruby-install-0.5.0.tar.gz -L https://github.com/postmodern/ruby-install/archive/v0.5.0.tar.gz && \
+      tar xvf ruby-install-0.5.0.tar.gz && \
+      cd ruby-install-0.5.0/ && \
+      make install && \
+    cd /tmp/ && \
+      curl -o chruby-0.3.8.tar.gz -L https://github.com/postmodern/chruby/archive/v0.3.8.tar.gz && \
+      tar xvf chruby-0.3.8.tar.gz && \
+      cd chruby-0.3.8/ && \
+      make install && \
+    cd / && rm -rf /tmp/*
+
+RUN apt-get update && \
+    ruby-install ruby 2.1.4 -- --disable-install-rdoc && \
+    rm -rf /var/lib/apt/lists/* && \
+    rm -rf /tmp/*
+
+## Setup NodeJS and npm.
+# FIXME:
+#   This pulls in a lot of packages. Consider using pre-built binaries.
+RUN apt-get update && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y \
+      nodejs nodejs-legacy npm && \
+    rm -rf /var/lib/apt/lists/*
+
+## Setup Postgres.
+RUN apt-get update && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y \
+      postgresql postgresql-contrib postgresql-client libpq-dev \
+      libexpat1-dev libperlio-gzip-perl && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN /etc/init.d/postgresql start &&\
+    su postgres -c "psql --command \"CREATE USER afra WITH SUPERUSER PASSWORD 'afra';\"" \
+    && /etc/init.d/postgresql stop
+
+COPY etc/postgresql/9.4/main/pg_hba.conf /etc/postgresql/9.4/main/
+
+RUN chmod 644 /etc/postgresql/9.4/main/pg_hba.conf
+
+## Setup Afra
+
+RUN groupadd -r afra && useradd -m -g afra afra
+
+COPY . /home/afra/src
+
+RUN chown -R afra /home/afra/src/
+
+WORKDIR /home/afra/src
+
+RUN /etc/init.d/postgresql start && su afra -s /bin/bash -c "source /usr/local/share/chruby/chruby.sh && chruby ruby-2.1.4 && /usr/local/src/ruby-2.1.4/bin/rake" && /etc/init.d/postgresql stop
+
+CMD /etc/init.d/postgresql start && su afra -s /bin/bash -c "source /usr/local/share/chruby/chruby.sh && chruby ruby-2.1.4 && /usr/local/src/ruby-2.1.4/bin/rake serve"

Rakefile

@@ -26,15 +26,6 @@ fi;
   set -e;
   bin/cpanm -v --notest -l $PWD/.extlib/ --installdeps . < /dev/null;
 );
-
-if [ $? == 0 ]; then
-    echo "Done."
-    touch ".rake/pl"
-else
-    echo "Failed."
-    echo "As a first troubleshooting step, make sure development libraries and
-header files for Zlib are installed and try again.";
-fi
 SH
 end
 

etc/postgresql/9.4/main/pg_hba.conf

@@ -0,0 +1,99 @@
+# PostgreSQL Client Authentication Configuration File
+# ===================================================
+#
+# Refer to the "Client Authentication" section in the PostgreSQL
+# documentation for a complete description of this file.  A short
+# synopsis follows.
+#
+# This file controls: which hosts are allowed to connect, how clients
+# are authenticated, which PostgreSQL user names they can use, which
+# databases they can access.  Records take one of these forms:
+#
+# local      DATABASE  USER  METHOD  [OPTIONS]
+# host       DATABASE  USER  ADDRESS  METHOD  [OPTIONS]
+# hostssl    DATABASE  USER  ADDRESS  METHOD  [OPTIONS]
+# hostnossl  DATABASE  USER  ADDRESS  METHOD  [OPTIONS]
+#
+# (The uppercase items must be replaced by actual values.)
+#
+# The first field is the connection type: "local" is a Unix-domain
+# socket, "host" is either a plain or SSL-encrypted TCP/IP socket,
+# "hostssl" is an SSL-encrypted TCP/IP socket, and "hostnossl" is a
+# plain TCP/IP socket.
+#
+# DATABASE can be "all", "sameuser", "samerole", "replication", a
+# database name, or a comma-separated list thereof. The "all"
+# keyword does not match "replication". Access to replication
+# must be enabled in a separate record (see example below).
+#
+# USER can be "all", a user name, a group name prefixed with "+", or a
+# comma-separated list thereof.  In both the DATABASE and USER fields
+# you can also write a file name prefixed with "@" to include names
+# from a separate file.
+#
+# ADDRESS specifies the set of hosts the record matches.  It can be a
+# host name, or it is made up of an IP address and a CIDR mask that is
+# an integer (between 0 and 32 (IPv4) or 128 (IPv6) inclusive) that
+# specifies the number of significant bits in the mask.  A host name
+# that starts with a dot (.) matches a suffix of the actual host name.
+# Alternatively, you can write an IP address and netmask in separate
+# columns to specify the set of hosts.  Instead of a CIDR-address, you
+# can write "samehost" to match any of the server's own IP addresses,
+# or "samenet" to match any address in any subnet that the server is
+# directly connected to.
+#
+# METHOD can be "trust", "reject", "md5", "password", "gss", "sspi",
+# "ident", "peer", "pam", "ldap", "radius" or "cert".  Note that
+# "password" sends passwords in clear text; "md5" is preferred since
+# it sends encrypted passwords.
+#
+# OPTIONS are a set of options for the authentication in the format
+# NAME=VALUE.  The available options depend on the different
+# authentication methods -- refer to the "Client Authentication"
+# section in the documentation for a list of which options are
+# available for which authentication methods.
+#
+# Database and user names containing spaces, commas, quotes and other
+# special characters must be quoted.  Quoting one of the keywords
+# "all", "sameuser", "samerole" or "replication" makes the name lose
+# its special character, and just match a database or username with
+# that name.
+#
+# This file is read on server startup and when the postmaster receives
+# a SIGHUP signal.  If you edit the file on a running system, you have
+# to SIGHUP the postmaster for the changes to take effect.  You can
+# use "pg_ctl reload" to do that.
+
+# Put your actual configuration here
+# ----------------------------------
+#
+# If you want to allow non-local connections, you need to add more
+# "host" records.  In that case you will also need to make PostgreSQL
+# listen on a non-local interface via the listen_addresses
+# configuration parameter, or via the -i or -h command line switches.
+
+
+
+
+# DO NOT DISABLE!
+# If you change this first entry you will need to make sure that the
+# database superuser can access the database using some other method.
+# Noninteractive access to all databases is required during automatic
+# maintenance (custom daily cronjobs, replication, and similar tasks).
+#
+# Database administrative login by Unix domain socket
+local   all             postgres                                peer
+
+# TYPE  DATABASE        USER            ADDRESS                 METHOD
+
+# "local" is for Unix domain socket connections only
+local   all             all                                     trust
+# IPv4 local connections:
+host    all             all             127.0.0.1/32            trust
+# IPv6 local connections:
+host    all             all             ::1/128                 trust
+# Allow replication connections from localhost, by a user with the
+# replication privilege.
+#local   replication     postgres                                peer
+#host    replication     postgres        127.0.0.1/32            md5
+#host    replication     postgres        ::1/128                 md5