diff --git a/bamliquidator_internal/Dockerfile b/bamliquidator_internal/Dockerfile index fdf6082..50a9495 100644 --- a/bamliquidator_internal/Dockerfile +++ b/bamliquidator_internal/Dockerfile @@ -11,10 +11,12 @@ RUN make -j6 FROM ubuntu:bionic as runner -RUN apt-get -y update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends python3 \ - python3-tables python3-scipy \ +RUN apt-get -y update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends python \ + python-setuptools python-pip python-tables python-scipy \ && rm -rf /var/lib/apt/lists/* +RUN pip install bokeh==0.9.3 "openpyxl>=1.6.1,<2.0.0" + WORKDIR /opt/liquidator COPY --from=builder /usr/lib/x86_64-linux-gnu/libtcmalloc_minimal.so.4 \ /usr/lib/x86_64-linux-gnu/libtbb.so.2 \ @@ -55,9 +57,10 @@ COPY --from=builder /opt/liquidator/bamliquidatorbatch /opt/liquidator/bamliquid ENV PATH="$PATH:/opt/liquidator" -RUN python3 bamliquidatorbatch/test.py +RUN python bamliquidatorbatch/test.py +RUN chmod +rx /opt/liquidator/bamliquidatorbatch/*.py ARG GIT_COMMIT LABEL git_commit=$GIT_COMMIT -ENTRYPOINT ["/usr/bin/python3","/opt/liquidator/bamliquidatorbatch/bamliquidator_batch.py"] +ENTRYPOINT ["/usr/bin/python","/opt/liquidator/bamliquidatorbatch/bamliquidator_batch.py"] diff --git a/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py b/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py index 297f26b..2fe9794 100755 --- a/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py +++ b/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py @@ -19,7 +19,7 @@ from os.path import basename from os.path import dirname -__version__ = '1.5.1' +__version__ = '1.5.3' default_black_list = ["chrUn", "_random", "Zv9_", "_hap"]