Updating requirements to install vsearch and fasttree using apt

docker/Dockerfile

@@ -8,6 +8,7 @@ ADD 99parallel /etc/apt/apt.conf.d/99parallel
 RUN apt-get update -y && \
     apt-get upgrade -y && \
     apt-get install -y \
+    fasttree \
     python3-pip \
     r-cran-ape \
     r-cran-biocmanager \
@@ -22,11 +23,14 @@ RUN apt-get update -y && \
     r-cran-tidyr \
     libcurl4-openssl-dev \
     libxml2 \
-    libxml2-dev
+    libxml2-dev \
+    vsearch
 
-ADD requirements.txt /tmp/
-RUN pip3 install -U pip wheel
-RUN pip3 install -r /tmp/requirements.txt
+ADD requirements.txt 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
@@ -37,7 +41,8 @@ RUN /tmp/install_vsearch.sh 2.21.1
 ADD install_xsv.sh /tmp/
 RUN /tmp/install_xsv.sh
 
-# uses value of $DADA2_REF
-ADD install-dada2.R /tmp/
-RUN Rscript /tmp/install-dada2.R
-RUN mkdir -p /app /fh /mnt /run/shm
+ADD install_pplacer.sh /tmp/
+RUN /tmp/install_pplacer.sh
+
+RUN pip3 install -U pip wheel
+RUN pip3 install -r /tmp/requirements.txt

docker/requirements.txt

@@ -7,4 +7,6 @@ fastalite==0.4.1
 isal==1.1.0
 numpy==1.23.5
 openpyxl==3.0.10
+sqlalchemy
+taxtastic
 xopen==1.7.0