diff --git a/Dockerfile b/Dockerfile index 6942113..780288a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,7 @@ #dockerfile for adding usearch9 to base-amptk and downloading databases FROM nextgenusfs/base-amptk -MAINTAINER Jon Palmer + +LABEL maintainer="Jon Palmer " WORKDIR /amptk @@ -8,10 +9,8 @@ COPY usearch9.2.64_i86linux32 /amptk/usearch9 COPY usearch10.0.240_i86linux32 /amptk/usearch10 -RUN chmod +x /amptk/usearch9 - -RUN chmod +x /amptk/usearch10 - -RUN amptk install -i ITS LSU 16S COI --force +RUN chmod +x /amptk/usearch9 && \ + chmod +x /amptk/usearch10 && \ + amptk install -i ITS LSU 16S COI --force WORKDIR /work diff --git a/Dockerfile-base b/Dockerfile-base index 85f6297..13b6004 100644 --- a/Dockerfile-base +++ b/Dockerfile-base @@ -1,36 +1,43 @@ -#docker config for base-AMPtk installation +#docker config for base-AMPtk installation FROM continuumio/miniconda -MAINTAINER Jon Palmer -USER root - -RUN apt-get update && apt-get install -y zlib1g-dev libssl-dev libbz2-dev libgl1-mesa-glx \ - libcurl4-gnutls-dev libxml2-dev libxslt1-dev build-essential pigz wget autoconf +LABEL maintainer="Jon Palmer " -RUN conda config --add channels r && \ - conda config --add channels bioconda && \ - conda install --yes cython biopython natsort pandas psutil matplotlib seaborn \ - biom-format sra-tools r-base htslib samtools bioconductor-dada2 bioconductor-phyloseq - -RUN wget https://github.com/torognes/vsearch/archive/v2.4.4.tar.gz && \ - tar xzf v2.4.4.tar.gz && \ - mv vsearch-2.4.4 vsearch && \ - cd vsearch && \ - ./autogen.sh && \ - ./configure && \ - make && \ - make install && \ - cd .. +USER root -RUN wget https://github.com/nextgenusfs/amptk/archive/1.0.0.tar.gz && \ - tar xzf 1.0.0.tar.gz && \ - mv amptk-1.0.0 amptk - -RUN pip install -U srapy edlib +RUN apt-get update -qq && apt-get install -y \ + zlib1g-dev \ + libssl-dev \ + libbz2-dev \ + libgl1-mesa-glx \ + libcurl4-gnutls-dev \ + libxml2-dev \ + libxslt1-dev \ + build-essential \ + pigz \ + wget \ + autoconf && \ + conda config --add channels r && \ + conda config --add channels bioconda && \ + conda install --yes cython biopython natsort pandas psutil matplotlib seaborn \ + biom-format sra-tools r-base htslib samtools bioconductor-dada2 bioconductor-phyloseq && \ + wget https://github.com/torognes/vsearch/archive/v2.4.4.tar.gz && \ + tar xzf v2.4.4.tar.gz && \ + mv vsearch-2.4.4 vsearch && \ + cd vsearch && \ + ./autogen.sh && \ + ./configure && \ + make && \ + make install && \ + cd .. && \ + wget https://github.com/nextgenusfs/amptk/archive/1.0.0.tar.gz && \ + tar xzf 1.0.0.tar.gz && \ + mv amptk-1.0.0 amptk && \ + pip install -U srapy edlib ENV PATH=/work:/amptk:$PATH \ SHELL=/bin/bash RUN mkdir /work -WORKDIR /work \ No newline at end of file +WORKDIR /work