uncomment

docker/Dockerfile

@@ -10,38 +10,38 @@ RUN apt-get update -y && \
     apt-get install -y \
     fasttree \
     python3-pip
-#     r-cran-ape \
-#     r-cran-biocmanager \
-#     r-cran-devtools \
-#     r-cran-dplyr \
-#     r-cran-lattice \
-#     r-cran-latticeextra \
-#     r-cran-gridextra \
-#     r-cran-r.utils \
-#     r-cran-readr \
-#     r-cran-rmarkdown \
-#     r-cran-tidyr \
-#     libcurl4-openssl-dev \
-#     libxml2 \
-#     libxml2-dev \
-#     vsearch
-# 
-# ADD install-dada2.R /tmp/
-# # uses value of $DADA2_REF
-# RUN Rscript /tmp/install-dada2.R
-# RUN mkdir -p /app /fh /mnt /run/shm
-# 
-# ADD install_infernal_and_easel.sh /tmp/
-# RUN /tmp/install_infernal_and_easel.sh
-# 
-# ADD install_vsearch.sh /tmp/
-# RUN /tmp/install_vsearch.sh 2.21.1
-# 
-# ADD install_xsv.sh /tmp/
-# RUN /tmp/install_xsv.sh
-# 
-# ADD install_pplacer.sh /tmp/
-# RUN /tmp/install_pplacer.sh
+    r-cran-ape \
+    r-cran-biocmanager \
+    r-cran-devtools \
+    r-cran-dplyr \
+    r-cran-lattice \
+    r-cran-latticeextra \
+    r-cran-gridextra \
+    r-cran-r.utils \
+    r-cran-readr \
+    r-cran-rmarkdown \
+    r-cran-tidyr \
+    libcurl4-openssl-dev \
+    libxml2 \
+    libxml2-dev \
+    vsearch
+
+ADD install-dada2.R /tmp/
+# uses value of $DADA2_REF
+RUN Rscript /tmp/install-dada2.R
+RUN mkdir -p /app /fh /mnt /run/shm
+
+ADD install_infernal_and_easel.sh /tmp/
+RUN /tmp/install_infernal_and_easel.sh
+
+ADD install_vsearch.sh /tmp/
+RUN /tmp/install_vsearch.sh 2.21.1
+
+ADD install_xsv.sh /tmp/
+RUN /tmp/install_xsv.sh
+
+ADD install_pplacer.sh /tmp/
+RUN /tmp/install_pplacer.sh
 
 ADD requirements.txt /tmp/
 RUN pip3 install -U pip wheel