add ecoPCR and cleanup step

Dockerfile

@@ -35,6 +35,9 @@ RUN wget https://github.com/torognes/vsearch/archive/v2.22.1.tar.gz
 RUN tar -zxvf v2.22.1.tar.gz
 RUN wget https://git.metabarcoding.org/obitools/ecoprimers/uploads/40f0fe1896a15ca9ad29835f93893464/ecoPrimers.tar.gz
 RUN tar -zxvf ecoPrimers.tar.gz
+RUN wget https://git.metabarcoding.org/obitools/ecopcr/uploads/aa3828c196570ea156ce6d4baac22b10/ecopcr-1.0.1.tar.gz
+RUN tar -zxvf ecopcr-*.tar.gz 
+
 
 # install cutadapt
 RUN python3 -m pip install --upgrade cutadapt
@@ -54,4 +57,12 @@ RUN make install
 WORKDIR /app/ecoprimers/src/
 RUN make
 
+# install ecoPCR
+WORKDIR /app/ecopcr/src/
+RUN make
+RUN echo "export PATH=$PATH:/app/ecopcr/src/" >> /home/rstudio/.bashrc
+
+WORKDIR /app
+RUN rm *.tar.gz* 
 RUN rm -rf /var/lib/apt/lists/* 
+WORKDIR /home/rstudio

README.md

@@ -9,6 +9,7 @@ This repository contains a `Dockerfile` used to build the `edna_tools` docker im
 - [`MKBRD`](https://gitlab.mbb.univ-montp2.fr/edna/custom_reference_database)
 - [`vsearch`](https://github.com/torognes/vsearch)
 - [`ecoprimers`](https://git.metabarcoding.org/obitools/ecoprimers/-/wikis/home)
+- [`ecoPCR`](https://pythonhosted.org/OBITools/scripts/ecoPCR.html)
 
 The docker image itself is hosted on [dockerhub](https://hub.docker.com/repository/docker/thesanc/edna_tools). It allows to run a container with all the software needed for eDNA analysis. Independently from your operating system, ubuntu is launched with all the software pre-installed in a self-contained environment.