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Dockerfile

@@ -4,6 +4,8 @@ FROM --platform=linux/x86_64 mambaorg/micromamba:0.24.0 as app
 ARG LIFTOFF_VER="1.6.3"
 ARG MINIMAP2_VER="2.24"
 ARG SAMTOOLS_VER="1.20"
+ARG HTSLIBVER="1.12"
+ARG IVARVER="1.4.2"
 
 USER root
 WORKDIR /
@@ -13,29 +15,87 @@ WORKDIR /
 LABEL base.image="mambaorg/micromamba:0.24.0"
 LABEL dockerfile.version="1"
 LABEL software="liftoff"
-LABEL software.version=$LIFTOFF_VER
-LABEL description="A tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species."
-LABEL website="https://github.com/agshumate/Liftoff"
-LABEL license="https://github.com/agshumate/Liftoff/blob/master/LICENSE.md"
-LABEL maintainer="John Arnn"
-LABEL maintainer.email="[email protected]"
+LABEL maintainer="Will Gardner"
+LABEL maintainer.email="[email protected]"
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     wget \
+    build-essential \
+    ca-certificates \
+    procps \
+    autoconf \
+    autotools-dev \
+    automake \
+    python3 \
+    bedtools \
+    python3-pip \
+    bwa \
+    minimap2 \
+    vim \
+    openjdk-11-jdk \
+    libncurses5-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-gnutls-dev \
+    zlib1g-dev \
+    libssl-dev \
+    gcc \
+    make \
     ca-certificates \
     perl \
     zlib1g \
-    libncurses5 \
     bzip2 \
-    liblzma-dev \
-    libcurl4-gnutls-dev \
     gnuplot \
     procps && \
     apt-get autoclean && rm -rf /var/lib/apt/lists/*
 
 RUN micromamba install --yes --name base --channel conda-forge --channel bioconda  \
     minimap2=${MINIMAP2_VER} \
     python=3.9.1 \
-    samtools=${SAMTOOLS_VER} \
     Liftoff=${LIFTOFF_VER} && \
     micromamba clean --all --yes
+
+# Install BBTools
+RUN wget https://sourceforge.net/projects/bbmap/files/BBMap_38.90.tar.gz --no-check-certificate \
+    && tar -xvzf BBMap_38.90.tar.gz \
+    && rm BBMap_38.90.tar.gz \
+    && mv bbmap /opt/
+# Update PATH for BBTools
+ENV PATH="/opt/bbmap:${PATH}"
+
+ENV PATH=/opt/conda/bin:$PATH
+
+# download, compile, and install samtools
+RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    tar -xjf samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    cd samtools-${SAMTOOLS_VER} && \
+    ./configure && \
+    make && \
+    make install && \
+    make test
+
+# installing htslib
+RUN wget -q https://github.com/samtools/htslib/releases/download/${HTSLIBVER}/htslib-${HTSLIBVER}.tar.bz2 && \
+    tar xvf htslib-${HTSLIBVER}.tar.bz2 && \
+    rm htslib-${HTSLIBVER}.tar.bz2 && \
+    cd htslib-${HTSLIBVER}/ && \
+    ./configure && \
+    make && \
+    make install
+
+RUN wget -q https://github.com/andersen-lab/ivar/archive/v${IVARVER}.tar.gz && \
+    tar -xf v${IVARVER}.tar.gz && \
+    rm -rf v${IVARVER}.tar.gz && \
+    cd ivar-${IVARVER} && \
+    ./autogen.sh && \
+    ./configure && \
+    make && \
+    make install && \
+    ldconfig
+
+RUN wget -qO- https://get.nextflow.io | bash && \
+    mv nextflow /usr/local/bin/ && \
+    chmod +x /usr/local/bin/nextflow
+
+# make sure shells are bash
+CMD ["/bin/bash"]