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FROM ubuntu:focal
ARG DEBIAN_FRONTEND=noninteractive
WORKDIR /app
RUN ulimit -d unlimited
RUN apt-get update && apt-get upgrade -yy && apt-get install -yy build-essential software-properties-common \
apt-transport-https libz-dev npm cmake parallel python3-openstackclient jq unzip pandoc \
curl wget git libssl-dev libcurl4-openssl-dev libxml2-dev -y && \
npm i nugget -g && \
wget -P /tmp/ "https://repo.anaconda.com/miniconda/Miniconda3-py38_4.12.0-Linux-x86_64.sh" && \
bash "/tmp/Miniconda3-py38_4.12.0-Linux-x86_64.sh" -b -p /usr/local/miniconda
RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" \
unzip awscliv2.zip \
./aws/install
COPY env.yml /app/env.yml
ADD bin /usr/local/crux_bin
RUN wget https://www.poirrier.ca/ben/ben-2.16.tar.gz && \
tar -xf ben-2.16.tar.gz && \
cd ben && make && mv ben /usr/local/crux_bin
RUN git clone https://github.com/stamatak/standard-RAxML.git && \
cd standard-RAxML && make -f Makefile.gcc && make -f Makefile.AVX2.gcc && \
make -f Makefile.AVX2.PTHREADS.gcc && make -f Makefile.PTHREADS.gcc && \
make -f Makefile.SSE3.PTHREADS.gcc && make -f Makefile.SSE3.gcc && \
mv raxmlHPC* /usr/local/crux_bin
RUN git clone https://github.com/lpipes/AncestralClust.git && \
cd AncestralClust && \
sed -i 's/#define MAXNUMBEROFCLUSTERS 100/#define MAXNUMBEROFCLUSTERS 10000/' global.h && \
sed -i 's/#define MAXNUMINCLUSTER 10000/#define MAXNUMINCLUSTER 1000000/' global.h && \
sed -i 's/#define MAXNUMBEROFKSEQS 10000/#define MAXNUMBEROFKSEQS 1000000/' global.h && \
sed -i 's/#define FASTA_MAXLINE 6000/#define FASTA_MAXLINE 600000/' global.h && \
make && mv ancestralclust /usr/local/crux_bin
RUN git clone https://github.com/refresh-bio/FAMSA && \
cd FAMSA && make && \
mv famsa /usr/local/crux_bin
RUN git clone https://github.com/lpipes/tronko.git && \
cd tronko/tronko-build && \
sed -i 's/#define MAX_NUMBEROFROOTS 10000/#define MAX_NUMBEROFROOTS 100000/' global.h && \
sed -i 's/-T 8/-T 16/' tronko-build.c && \
make && mv tronko-build /usr/local/crux_bin && \
cd ../tronko-assign && make && mv tronko-assign /usr/local/crux_bin
ENV PATH="/usr/local/crux_bin:$PATH"
ENV PATH="/usr/local/miniconda/bin:$PATH"
RUN conda install -n base -c anaconda cython && \
conda env update -f /app/env.yml -n base && \
conda init && \
. /root/.bashrc