sjn update delly install

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