diff resfinder/dockerfile @ 0:55051a9bc58d draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/dockerfile	Mon Jan 10 20:06:07 2022 +0000
@@ -0,0 +1,53 @@
+FROM debian:stretch
+
+ENV DEBIAN_FRONTEND noninteractive
+
+### RUN set -ex; \
+
+RUN apt-get update -qq; \
+    apt-get install -y -qq git \
+    apt-utils \
+    wget \
+    python3-pip \
+    ncbi-blast+ \
+    libz-dev \
+    ; \
+    rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
+
+ENV DEBIAN_FRONTEND Teletype
+
+# Install python dependencies
+RUN pip3 install -U biopython==1.73 tabulate cgecore gitpython python-dateutil;
+
+# RESFINDER setup
+COPY run_resfinder.py /usr/src/run_resfinder.py
+
+ADD cge /usr/src/cge
+ADD tests /usr/src/tests
+
+# Install kma
+RUN cd /usr/src/cge; \
+    git clone --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \
+    cd kma && make; \
+    mv kma* /bin/
+
+
+RUN chmod 755 /usr/src/run_resfinder.py
+RUN chmod 755 /usr/src/tests/functional_tests.py
+
+
+ENV PATH $PATH:/usr/src
+# Setup .bashrc file for convenience during debugging
+RUN echo "alias ls='ls -h --color=tty'\n"\
+"alias ll='ls -lrt'\n"\
+"alias l='less'\n"\
+"alias du='du -hP --max-depth=1'\n"\
+"alias cwd='readlink -f .'\n"\
+"PATH=$PATH\n">> ~/.bashrc
+
+
+# Change working directory
+WORKDIR "/usr/src/"
+
+# Execute program when running the container
+ENTRYPOINT ["python3", "/usr/src/run_resfinder.py"]
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