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FROM python:2.7.14
RUN apt-get update && apt-get install -y --no-install-recommends \
r-base \
zlib1g-dev \
time
RUN wget -qO- https://github.com/lomereiter/sambamba/releases/download/v0.6.7/sambamba_v0.6.7_linux.tar.bz2 \
| tar xj -C /usr/local/bin
RUN wget -qO- https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.24/samblaster-v.0.1.24.tar.gz \
| tar xz -C /tmp \
&& cd /tmp/samblaster-v.0.1.24/ && make && mv samblaster /usr/local/bin && rm -rf /tmp/samblaster-v-0.1.24
WORKDIR /ref
ADD hg38_GENCODE_v23_basic.bed.gz /ref/hg38_GENCODE_v23_basic.bed.gz
RUN gunzip -c /ref/hg38_GENCODE_v23_basic.bed.gz > /ref/hg38_GENCODE_v23_basic.bed
WORKDIR /app
ADD ./requirements.txt /app/requirements.txt
RUN pip install --no-cache-dir -r /app/requirements.txt
RUN wget -q https://cran.microsoft.com/snapshot/2015-07-29/src/contrib/rjson_0.2.15.tar.gz
RUN R -e 'install.packages("./rjson_0.2.15.tar.gz", repos=NULL)'
WORKDIR /app
ADD . /app
ENTRYPOINT ["/bin/bash", "run.sh"]