Changed files using best practices to reduce number of image layers

Dockerfile

@@ -1,17 +1,16 @@
 #dockerfile for adding usearch9 to base-amptk and downloading databases
 FROM nextgenusfs/base-amptk
-MAINTAINER Jon Palmer <[email protected]>
+
+LABEL maintainer="Jon Palmer <[email protected]>"
 
 WORKDIR /amptk
 
 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

Dockerfile-base

@@ -1,36 +1,43 @@
-#docker config for base-AMPtk installation 
+#docker config for base-AMPtk installation
 FROM continuumio/miniconda
-MAINTAINER Jon Palmer <[email protected]>
 
-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 <[email protected]>"
 
-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
+WORKDIR /work