Vector CNV pipeline version 1.0.0

.dockstore.yml

@@ -18,3 +18,6 @@ workflows:
   - name: MalariaVector_StatisticalPhasing
     subclass: WDL
     primaryDescriptorPath: /pipelines/phasing-vector/gcp/StatisticalPhasing.wdl
+  - name: MalariaVector_CNV
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/copy-number-variation-vector/gcp/CNV.wdl

dockerfiles/CNV/Dockerfile

@@ -0,0 +1,34 @@
+FROM --platform=linux/amd64 continuumio/miniconda3
+
+# Update the package lists and install necessary packages
+RUN apt-get update && \
+    apt-get install -y curl bzip2 ca-certificates gnupg && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+#TODO: Determine if R is really required here
+# # Add the R repository and install the latest R
+# RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu hirsute-cran40/" >> /etc/apt/sources.list && \
+#     apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
+#     apt-get update && \
+#     apt-get install -y r-base && \
+#     apt-get clean && \
+#     rm -rf /var/lib/apt/lists/*
+
+# Copy the environment file to the container
+COPY requirements_conda.yml requirements_conda.yml
+
+# Create a conda environment and activate it
+RUN mkdir -p /cnv/output && \
+    mkdir -p /cnv/input && \
+    conda env create -f requirements_conda.yml && \
+    echo "conda activate $(head -1 /opt/conda/envs/*/etc/environment.yml | cut -d'/' -f6)" >> ~/.bashrc
+
+# Set the working directory
+WORKDIR /cnv
+
+# Copy the source code to the container
+COPY . .
+
+# Set the default command to run when the container starts
+# CMD ["python", ""]

dockerfiles/CNV/R3.6.1/Dockerfile

@@ -0,0 +1,41 @@
+## Platform tag ensures that images built on ARM-based machines (ex. M-series macs) are portable
+FROM --platform="linux/amd64" ubuntu:18.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Set parameteres
+ARG R_VERSION="3.6.1"
+
+WORKDIR /usr/local/
+
+# Update and install dependencies and wet
+RUN sed -Ei 's/^# deb-src /deb-src /' /etc/apt/sources.list && apt-get update \
+    && apt-get install -y \
+    build-essential \
+    wget
+
+# Install R and addtional dependencies
+RUN apt-get build-dep -y r-base \
+    && wget https://cloud.r-project.org/src/base/R-3/R-${R_VERSION}.tar.gz \
+    && tar xzf R-${R_VERSION}.tar.gz \
+    && cd "R-${R_VERSION}" \
+    && ./configure --prefix=/opt/R/${R_VERSION}/ --enable-R-shlib --with-blas --with-lapack \
+    && make \
+    && make install
+
+RUN rm -r R-${R_VERSION} \
+    && rm R-${R_VERSION}.tar.gz
+
+# Run an R script to install several libraries
+COPY installRDeps.R /usr/local/
+RUN /opt/R/${R_VERSION}/bin/Rscript /usr/local/installRDeps.R \
+    && rm installRDeps.R
+
+# Add R installation directory to path
+ENV PATH="/opt/R/${R_VERSION}/bin/:$PATH"
+
+# Copy source code
+COPY . .
+
+
+