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Merge pull request #9 from adriantich/master
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‎.gitignore

+10
Original file line numberDiff line numberDiff line change
@@ -48,4 +48,14 @@ lib/jquery-autocomplete/
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lib/pandaseq/
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lib/papa/
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lib/swarm/
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lib/swarm2/
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lib/swarm3/
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lib/vsearch/
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lib/dada2/
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lib/lulu/
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lib/msi/
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lib/miniconda/
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lib/DECIPHER/
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lib/ASHURE/
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lib/miniforge3
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‎Dockerfile

+161-28
Original file line numberDiff line numberDiff line change
@@ -7,14 +7,24 @@ RUN mkdir /app
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WORKDIR /app
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COPY jranke.asc /app
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RUN mkdir /app/lib
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# Add the CRAN repos sources for install latest version of R
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RUN apt-get update && apt-get install -y dirmngr gnupg apt-transport-https ca-certificates software-properties-common
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RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
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#RUN sh -c 'echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" >> /etc/apt/sources.list'
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#RUN apt-key add /app/jranke.asc
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#RUN apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
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# ----- install conda ----- #
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# RUN curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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COPY lib/miniforge3 /app/lib/miniforge3
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RUN bash /app/lib/miniforge3/miniforge3.sh -b
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# RUN rm Miniconda3-latest-Linux-x86_64.sh
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ENV PATH="/root/miniforge3/bin:${PATH}"
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# RUN conda update conda
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# Install packages needed for tools
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RUN apt-get update && apt-get install -y \
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libgit2-dev \
@@ -32,8 +42,12 @@ RUN apt-get update && apt-get install -y \
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pigz \
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dos2unix \
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python3-pip python3-dev python3-numpy python3-biopython \
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libc6 \
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r-base-dev r-base-core r-recommended r-base-html r-base
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libc6
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# libcurl4-openssl-dev
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RUN apt-get install -y \
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r-base-core r-recommended r-base-html r-base r-base-dev \
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libfontconfig1-dev
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## solving locales issue for biopython
@@ -42,32 +56,14 @@ ENV LC_ALL=en_US.UTF-8
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ENV LANG=en_US.UTF-8
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ENV LANGUAGE=en_US.UTF-8
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RUN dpkg -l locales
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#RUN python3 -m pip install biopython --upgrade
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RUN mkdir /app/lib
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# ----- R dependancies -----
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###RUN apt-get -y build-dep libcurl4-gnutls-dev
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###RUN apt-get -y install libcurl4-gnutls-dev
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RUN R -e 'install.packages("devtools", repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("dplyr", repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("seqinr", repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'library(devtools);install_github("tobiasgf/lulu")'
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RUN R -e 'install.packages("BiocManager",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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#RUN R -e 'BiocManager::install("DECIPHER")'
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#RUN R -e 'BiocManager::install("dada2")'
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RUN R -e 'library(devtools);devtools::install_github("benjjneb/dada2", ref="v1.16")'
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RUN R -e 'install.packages("https://www.bioconductor.org/packages/3.11/bioc/src/contrib/Archive/DECIPHER/DECIPHER_2.16.0.tar.gz", repos = NULL, type = "source")'#
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ENV CXXFLAGS="-std=c++11"
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# ----- Libraries deployments -----
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# install app dependencies
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RUN apt-get install curl -y
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RUN curl -sL https://deb.nodesource.com/setup_15.x | bash -
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RUN curl -sL https://deb.nodesource.com/setup_18.x | bash -
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RUN apt install nodejs -y
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COPY package.json /app
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RUN npm install
@@ -77,7 +73,9 @@ COPY lib/DTD /app/lib/DTD
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COPY lib/pandaseq /app/lib/pandaseq
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COPY lib/vsearch /app/lib/vsearch
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COPY lib/casper /app/lib/casper
80-
COPY lib/swarm /app/lib/swarm
76+
COPY lib/swarm2 /app/lib/swarm2
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COPY lib/swarm3 /app/lib/swarm3
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# COPY lib/sratoolkit /app/lib/sratoolkit
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# Compile DTD
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RUN cd /app/lib/DTD && make && cd /app
@@ -87,13 +85,142 @@ RUN cd /app/lib/pandaseq && ./autogen.sh && ./configure && make && cd /app
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RUN cd /app/lib/vsearch && ./autogen.sh && ./configure && make && cd /app
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# Compile casper
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RUN cd /app/lib/casper/casper_v0.8.2 && make && cd /app
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# Compile swarm
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RUN cd /app/lib/swarm/src && make && cd /app
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# Compile swarm2
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RUN cd /app/lib/swarm2/src && make && cd /app
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# Compile swarm3
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RUN cd /app/lib/swarm3/src && make && cd /app
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# Copy Python and R scripts
93+
# ----- R dependancies -----
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COPY lib/lulu /app/lib/lulu
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COPY lib/dada2 /app/lib/dada2
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98+
RUN R -e 'install.packages("dplyr", repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("seqinr", repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("/app/lib/lulu",repos=NULL)'
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RUN R -e 'install.packages("BiocManager",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("ggplot2",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("reshape2",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("RcppParallel",dependencies=TRUE)'
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RUN R -e 'install.packages("IRanges",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("XVector",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("BiocGenerics",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'BiocManager::install("Biostrings")'
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RUN R -e 'BiocManager::install("ShortRead")'
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RUN R -e 'install.packages("/app/lib/dada2",repos=NULL, dependencies = TRUE)'
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COPY lib/DECIPHER /app/lib/DECIPHER
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RUN R -e 'install.packages("RSQLite",dependencies=TRUE,repos="https://stat.ethz.ch/CRAN/")'
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RUN R -e 'install.packages("/app/lib/DECIPHER",repos=NULL, dependencies = TRUE)'
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# ----- install conda dependencies ----- #
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RUN apt-get install -y \
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clang
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# for those packages that require conda install create a new environment
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# for each to avoid incompatibilities
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# ----- install chopper ----- #
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RUN conda create -n chopper python=3.9 -y
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# RUN echo "source activate env" >> ~/.bashrc
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RUN /bin/bash -c "source activate chopper && \
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conda install -c conda-forge libgcc-ng -y && \
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conda update -c conda-forge libgcc-ng -y && \
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conda install -c conda-forge libstdcxx-ng -y && \
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conda update -c conda-forge libstdcxx-ng -y && \
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conda install -c conda-forge zlib -y && \
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conda update -c conda-forge zlib -y && \
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conda install -c bioconda chopper=0.8.0 -y "
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# ----- install msi ----- #
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COPY lib/msi /app/lib/msi
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RUN conda create -n msi python=3.9 -y
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RUN /bin/bash -c "source activate msi && \
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apt-get update && \
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apt-get install emboss -y && \
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apt-get install time -y && \
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conda install cmake -y && \
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conda install -c conda-forge git -y && \
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conda install -c conda-forge wget -y && \
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conda install -c bioconda java-jdk -y"
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# Update and install GCC and G++
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RUN apt-get update && apt-get install -y software-properties-common
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RUN add-apt-repository ppa:ubuntu-toolchain-r/test -y
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RUN apt-get update && apt-get install -y \
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gcc-10 \
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g++-10
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# Set GCC and G++ to the new versions
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RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 100 \
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&& update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 100
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# # Install the latest libstdc++6
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RUN apt-get install -y libstdc++6
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# # Verify the installation
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RUN gcc --version && g++ --version
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# # Check the installed versions of libstdc++
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RUN strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
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RUN /bin/bash -c "source activate msi && \
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conda install -c conda-forge r-base=4.1.0 -y"
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# the path used to install BiocManager in metabinkit is not available.
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# this is solved if we install BiocManager in the msi environment and
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# in the specified path
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RUN /bin/bash -c "source activate msi && \
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mkdir -p /app/lib/msi/Rlibs && \
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R -e \"install.packages('BiocManager',dependencies=TRUE,repos='https://stat.ethz.ch/CRAN/',lib='/app/lib/msi/Rlibs')\""
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# RUN /bin/bash -c "source activate msi && \
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# R -e \"!requireNamespace('BiocManager', quietly = TRUE)\""
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RUN /bin/bash -c "source activate msi && \
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/app/lib/msi/scripts/msi_install.sh -i /app/lib/msi"
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# ----- install ASHURE ----- #
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COPY lib/ASHURE /app/lib/ASHURE
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RUN conda create -n ashure python=3.9 -y
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# minimap2 has been installed with msi and its located at /app/lib/msi/bin/minimap2
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# RUN /bin/bash -c "source activate ashure && \
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# /app/lib/msi/bin/minimap2"
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# install cmake and git in ashure environment
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RUN /bin/bash -c "source activate ashure && \
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conda install -c conda-forge cmake git -y"
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# install spoa
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RUN /bin/bash -c "source activate ashure && \
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cd /app/lib/ASHURE/spoa && \
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cmake -B build -DCMAKE_BUILD_TYPE=Release && \
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make -C build && cd /app"
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# install python modules for ASHURE
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# due to a deprecation error, pandas need to be previous to 1.4.0
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RUN /bin/bash -c "source activate ashure && \
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pip install pandas==1.3.3 && \
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pip install scikit-learn && \
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pip install hdbscan &&\
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pip install numpy==1.26.4"
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# install ashure
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RUN /bin/bash -c "source activate ashure && \
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cd /app/lib/ASHURE && \
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chmod +x src/ashure.py && \
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src/ashure.py run -h && cd /app"
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# check if ashure commands are working
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RUN /bin/bash -c "source activate ashure && \
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/app/lib/ASHURE/src/ashure.py prfg -h && \
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/app/lib/ASHURE/src/ashure.py fgs -h && \
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/app/lib/ASHURE/src/ashure.py msa -h && \
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/app/lib/ASHURE/src/ashure.py fpmr -h"
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# ----- copy python_scripts -----
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COPY lib/python_scripts /app/lib/python_scripts
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# ----- copy R_scripts -----
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COPY lib/R_scripts /app/lib/R_scripts
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# ----- copy bash_scripts -----
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COPY lib/bash_scripts /app/lib/bash_scripts
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RUN chmod +x /app/lib/bash_scripts/*
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# ----- correction on msi source code -----
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RUN sed -i 's/\/dev\/stderr/stderr_msi/g' /app/lib/msi/bin/bam_annotate.sh /app/lib/msi/bin/fastq2bam /app/lib/msi/bin/fastq_validator.sh /app/lib/msi/*/msi /app/lib/msi/exe/metabinkit_blastgendb
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# RUN sed -i 's/ nmembers / \$nmembers /g' /app/lib/msi/bin/msi_clustr_add_size.pl /app/lib/msi/scripts/msi_clustr_add_size.pl
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RUN cd /app/lib/msi/seqtk && make && cd /app
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# updates on biopython
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RUN python3 -m pip install biopython --upgrade
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# ----- Webserver -----
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# prepare the web server
@@ -108,9 +235,15 @@ RUN cp node_modules/jquery/dist/jquery.js /app/www/js/jquery.js
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COPY lib/jquery-autocomplete/dist/jquery.autocomplete.js /app/www/js/jquery.autocomplete.js
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COPY lib/papa/papaparse.js /app/www/js/papaparse.js
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# use browserify to create the bundle.js file
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# RUN browserify /app/www/js/upload_SRA.js -o /app/www/js/bundle.js
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# prepare data folder
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RUN mkdir /app/data
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RUN apt update --fix-missing
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RUN apt install vim -y
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# commamd executed to run the server
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CMD ["npm", "start"]
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CMD ["npm", "start"]

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