Dockerfile.3

# Lappsgrid Galaxy Flavour
#
# Version 0.1

#FROM ksuderman/galaxy-stable:osx
#FROM bgruening/galaxy-stable
FROM lappsgrid/ubuntu:postgres

MAINTAINER Keith Suderman, suderman@cs.vassar.edu

ENV GALAXY_CONFIG_BRAND LAPPS

RUN apt-get update && apt-get install -y bash emacs24-nox git

#ADD ./lsd-2.2.1-SNAPSHOT.jar /usr/bin/lsd.jar
#ADD ./lsd /usr/bin/lsd
ADD ./packages/lsd.tgz /usr/bin
RUN chmod a+x /usr/bin/lsd

RUN groupadd -r galaxy -g 1450 && \
	adduser --system --home /home/galaxy --shell /bin/bash --disabled-login --gecos "" --uid 1450 --gid 1450 galaxy
	
#RUN mkdir /galaxy-central && \
#	chown galaxy:galaxy /galaxy-central
	
#ADD ./welcome.html /galaxy-central/static/welcome.html
#ADD ./welcome.html /galaxy-central/web/welcome.html
#ADD ./tool_conf.xml /galaxy-central/config/tool_conf.xml
#COPY ./tools /galaxy-central/tools
ADD ./startup.sh /usr/bin/startup


RUN service postgresql start && \
	until pg_isready ; do echo "Waiting..." ; sleep 2; done && \
    sudo -u postgres createuser -S -D -R galaxy && \
    sudo -u postgres psql --command "ALTER USER galaxy WITH PASSWORD 'galaxy'" && \
    sudo -u postgres createdb galaxy -O galaxy 

#    createdb galaxy -O galaxy -E "UTF-8" && \
 
USER galaxy
RUN git clone https://github.com/lappsgrid-incubator/Galaxy.git /home/galaxy && \
	cd /home/galaxy && \
	git checkout lappsnew

USER root
WORKDIR /home/galaxy

#RUN add-tool-shed --url 'https://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed'
#RUN install-repository \
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o ksuderman --name lapps_gate_2_0_0 --panel-section-name Gate" \
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o ksuderman --name masc_2_0_0 --panel-section-name Masc" \
#    "--url https://testtoolshed.g2.bx.psu.edu/ -o ksuderman --name lapps_stanford_2_0_0 --panel-section-name Stanford" 

# Mark folders as imported from the host.
VOLUME ["/export/", "/data/", "/var/lib/docker"]

# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy)
EXPOSE :80
EXPOSE :21
EXPOSE :22
EXPOSE :8000
EXPOSE :8800
EXPOSE :9002

# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]