sjn delly fix and java

# + install bamtools
RUN cd /usr/local/pipeline \
&& git clone https://github.com/pezmaster31/bamtools.git \
&& cd /usr/local/pipeline/bamtools/ \
&& mkdir build \
&& cd build/ \
&& cmake .. \
&& make \
&& chown -R pipeman:ngsgroup /usr/local/pipeline/bamtools

# + install seqtk
RUN cd /usr/local/pipeline \
&& git clone https://github.com/lh3/seqtk.git \
&& cd seqtk/ \
&& make \
&& 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 \
&& git clone https://github.com/tobiasrausch/delly.git \
&& cd delly/ \
&& make -B src/delly \
&& chown -R pipeman:ngsgroup /usr/local/pipeline/delly