added dockerfile for the storage container and fixed up the pipeine container a bit
rm uneccessary comments
fix ENTRYPOINT and CMD
sjn begin delly additions

added # delly requirements 
RUN apt-get install -y build-essential cmake zlib1g-dev libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev
sjn added delly install/build

Taken from https://github.com/tobiasrausch/delly/blob/master/docker/Dockerfile
and adapted: NOT TESTED
#---------------------------------- DELLY ---------------------------------------

# + install bamtools
RUN cd /usr/local/pipeline
RUN git clone https://github.com/pezmaster31/bamtools.git
RUN cd bamtools/ ; mkdir build ; cd build/ ; cmake .. ; make
RUN chown -R pipeman:ngsgroup /usr/local/pipeline/bamtools

# + install seqtk
RUN cd /usr/local/pipeline
RUN git clone https://github.com/lh3/seqtk.git
RUN cd seqtk/ ; make
RUN chown -R pipeman:ngsgroup /usr/local/pipeline/seqtk

# + set environment
ENV BOOST_ROOT /usr
ENV BAMTOOLS_ROOT /bamtools
ENV SEQTK_ROOT /seqtk
ENV LD_LIBRARY_PATH /bamtools/lib

# + install delly
RUN cd /usr/local/pipeline
RUN git clone https://github.com/tobiasrausch/delly.git
RUN cd delly/ ; make -B src/delly
RUN chown -R pipeman:ngsgroup /usr/local/pipeline/delly
sjn added some bioconductor ngs stuff

# GenomicRanges
RUN /usr/bin/Rscript --no-save --no-restore -e 'source("http://www.bioconductor.org/biocLite.R"); biocLite("GenomicRanges",dependencies=TRUE)'
# IRanges
RUN /usr/bin/Rscript --no-save --no-restore -e 'source("http://www.bioconductor.org/biocLite.R"); biocLite("IRanges",dependencies=TRUE)'
# Biostrings
RUN /usr/bin/Rscript --no-save --no-restore -e 'source("http://www.bioconductor.org/biocLite.R"); biocLite("Biostrings",dependencies=TRUE)'
# genomeIntervals
RUN /usr/bin/Rscript --no-save --no-restore -e 'source("http://www.bioconductor.org/biocLite.R"); biocLite("genomeIntervals",dependencies=TRUE)'
# rtracklayer
RUN /usr/bin/Rscript --no-save --no-restore -e 'source("http://www.bioconductor.org/biocLite.R"); biocLite("rtracklayer",dependencies=TRUE)'
sjn R 

added dependencies=TRUE
sjn bioconductor workflows.R: variants

# workflows.R: variants
RUN /usr/bin/Rscript --no-save --no-restore -e 'source("http://bioconductor.org/workflows.R");workflowInstall("variants")'
sjn added SnpEff

# + snpEff
# NEEDS TESTING
RUN wget -O /tmp/snpEff_latest_core.zip http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip \
    && unzip /tmp/snpEff_latest_core.zip -d /usr/local/pipeline/ \
    && chown -R pipeman:ngsgroup /usr/local/pipeline/snpEff_latest_core \
    && sed -i '$aCLASSPATH=.:${CLASSPATH}:/usr/local/pipeline/snpEff_latest_core/snpEff/snpEff.jar' /home/pipeman/.bashrc \
    && sed  -i '$aPATH=${PATH}:/usr/local/pipeline/snpEff_latest_core/snpEff' /home/pipeman/.bashrc
sjn added SnpEff edit
sjn added BEAGLE

# + BEAGLE
RUN wget -O /usr/local/pipeline/beagle/beagle.jar http://faculty.washington.edu/browning/beagle/beagle.jar \
    && chown -R pipeman:ngsgroup /usr/local/pipeline/beagle/ \
    && sed -i '$aCLASSPATH=.:${CLASSPATH}:/usr/local/pipeline/beagle/beagle.jar' /home/pipeman/.bashrc \
    && sed  -i '$aPATH=${PATH}:/usr/local/pipeline/beagle' /home/pipeman/.bashrc
sjn added R plotting packages

RUN /usr/bin/Rscript --no-save --no-restore -e 'install.packages("gdata",dependencies=TRUE ,repos="http://cran.r-project.org")'
RUN /usr/bin/Rscript --no-save --no-restore -e 'install.packages("gplots",dependencies=TRUE ,repos="http://cran.r-project.org")'
RUN /usr/bin/Rscript --no-save --no-restore -e 'install.packages("ggplot2",dependencies=TRUE ,repos="http://cran.r-project.org")'
RUN /usr/bin/Rscript --no-save --no-restore -e 'install.packages("RColorBrewer",dependencies=TRUE ,repos="http://cran.r-project.org")'
sjn FASTQ_STAGGING and reference_data dirs
sjn added R packages
minor edit snpEff
sjn minor fix
Merge pull request #1 from KHP-Informatics/master

update