diff pmlst/Dockerfile @ 0:cfab64885f66 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pmlst/Dockerfile	Mon Sep 06 18:27:45 2021 +0000
@@ -0,0 +1,43 @@
+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==1.3.2;
+
+# Install kma 
+RUN git clone --branch 1.0.1 --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \
+    cd kma && make; \
+    mv kma* /bin/
+
+COPY pmlst.py /usr/src/pmlst.py 
+
+RUN chmod 755 /usr/src/pmlst.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
+
+WORKDIR /workdir
+
+# Execute program when running the container
+ENTRYPOINT ["/usr/src/pmlst.py"]