fix packages for arm and add tutorial for docker desktop

Dockerfile

@@ -23,6 +23,12 @@ RUN apt-get install -y cmake
 RUN apt-get install -y python3-dev
 RUN	pip3 install cython
 
+# install ecoPCR
+RUN apt-get install -y ecopcr
+#WORKDIR /app/ecopcr/src/
+#RUN make
+#RUN echo "export PATH=$PATH:/app/ecopcr/src/" >> /home/rstudio/.bashrc
+
 RUN /rocker_scripts/install_rstudio.sh
 RUN /rocker_scripts/install_pandoc.sh
 
@@ -73,10 +79,15 @@ RUN apt-get install -y ecopcr
 WORKDIR /app
 RUN git clone https://git.metabarcoding.org/obitools/obitools3.git
 WORKDIR /app/obitools3
-RUN if [ $TARGETPLATFORM == linux/arm64 ]; then sed -e "s/'-msse2',//" -i setup.py 
+ARG TARGETPLATFORM
+RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then sed -e "s/'-msse2',//" -i setup.py; fi
 RUN python3 setup.py install
-RUN	source obi_completion_script.bash
-#ENV PATH=:$PATH
+RUN	/bin/bash obi_completion_script.bash
+
+# install dependencies for mkbdr
+RUN apt-get update -y
+RUN apt-get install -y python3-pyqt5.qtsvg
+RUN apt-get install -y python3-pyqt5.qtopengl 
 
 # cleanup
 WORKDIR /app

README.md

@@ -30,9 +30,24 @@ sudo dockerd
 
 In another terminal, download the image from [dockerhub](https://hub.docker.com/r/thesanc/edna_tools) and run it with this single command:
 ```bash
-docker run -v path/to/your/local/file:path/inside/the/container -p 8787:8787 thesanc/edna_tools
+docker run -v /path/to/your/local/file:/path/inside/the/container -p 8787:8787 thesanc/edna_tools
 ```
 
-You should now be able to have access to the **Rstudio** instance by typing `localhost:8787` in your browser. You can log in with `rstudio` as username and as password.
+You should now be able to have access to the **Rstudio** instance by typing `localhost:8787` in your browser. You can log in with `rstudio` username and as password.
 
 ### Docker desktop
+
+Once you have installed the **docker desktop** UI, you can search for the `thesanc/edna_tools` image in the research toolbar:
+
+![](tutorial_images/docker_desktop_containers.png)
+
+Once you have found the image, you can download it and click on the "▷ " button. A pop-up windows should open to set up the settings of the container:
+
+![](tutorial_images/docker_desktop_run.png)
+
+Fill the **Host port** field with `8787` (you can set up another port if this one is already used). 
+
+Fill the **Host path** with the file path to your files and fill the **Container path** with the path where these fill should appear in the container (it is recommended to use the host path as container path to avoid path related issues when you are running your code inside and outside the container).
+
+Now you should now be able to have access to the **Rstudio** instance by typing `localhost:8787` (if you have set up the **Host port** to `8787`) in your browser. You can log in with `rstudio` as username and password.
+