update tutorial, remove obitools3 and add other packages

Dockerfile

@@ -8,47 +8,49 @@ ENV DEFAULT_USER=rstudio
 ENV PANDOC_VERSION=default
 ENV PATH=/usr/lib/rstudio-server/bin:$PATH
 
-# install dependencies
+# install base packages
 RUN apt-get update -y
-RUN apt-get install -y wget
+RUN apt-get install -y build-essential
+RUN apt-get install -y wget htop vim nano man cmake git
+
+# install python 
 RUN apt-get install -y python2
 RUN apt-get install -y python3
 RUN apt-get install -y python3-pip
 RUN wget https://bootstrap.pypa.io/pip/2.7/get-pip.py
 RUN python2 get-pip.py
-RUN apt-get install -y autoconf
-RUN apt-get install -y python3-pyqt5
-RUN apt-get install -y git
-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
+# dependencies
+RUN apt-get update -y
+RUN apt-get install -y mc zlib1g zlib1g-dev libghc-bzlib-dev liblzma-dev libxml2 libxml2-dev libigraph-dev autoconf
 
-RUN /rocker_scripts/install_rstudio.sh
-RUN /rocker_scripts/install_pandoc.sh
 
 # install R packages
+RUN /rocker_scripts/install_rstudio.sh
+RUN /rocker_scripts/install_pandoc.sh
 RUN R -e "install.packages('tidyverse')"
-
-# install dada2
 RUN R -e "install.packages('BiocManager')"
-RUN R -e "BiocManager::install('dada2', version = '3.16')"
+RUN R -e "BiocManager::install('ShortRead')"
+RUN R -e "BiocManager::install('Biostrings')"
+RUN R -e "BiocManager::install('phyloseq')"
+RUN R -e "BiocManager::install('dada2')"
+RUN R -e "install.packages('devtools')"
+RUN R -e "devtools::install_url(https://cran.r-project.org/src/contrib/Archive/PhyloMeasures/PhyloMeasures_2.1.tar.gz)"
+RUN R -e "install.packages('ape')"
+RUN R -e "install.packages('mFD')"
+RUN R -e "install.packages('worrms')"
+RUN R -e "install.packages('patchwork')"
+RUN R -e "install.packages('hillR')"
+RUN R -e "install.packages('betapart')"
 
 # download sources
 WORKDIR /app
+
 RUN wget https://gitlab.mbb.cnrs.fr/edna/custom_reference_database/-/archive/v1.1/custom_reference_database-v1.1.tar.gz
 RUN tar -zxvf custom_reference_database-v1.1.tar.gz
+
 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
@@ -64,35 +66,15 @@ RUN ./configure CFLAGS="-O3" CXXFLAGS="-O3"
 RUN make
 RUN make install 
 
-# install ecoPrimers
-#WORKDIR /app/ecoprimers/src/
-#RUN make
-#RUN echo "export PATH=$PATH:/app/ecopcr/src/" >> /home/rstudio/.bashrc
-
 # install ecoPCR
-RUN apt-get install -y ecopcr
-#WORKDIR /app/ecopcr/src/
-#RUN make
-#RUN echo "export PATH=$PATH:/app/ecopcr/src/" >> /home/rstudio/.bashrc
-
-# install obitools
-WORKDIR /app
-RUN git clone https://git.metabarcoding.org/obitools/obitools3.git
-WORKDIR /app/obitools3
-ARG TARGETPLATFORM
-RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then sed -e "s/'-msse2',//" -i setup.py; fi
-RUN python3 setup.py install
-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 
+RUN apt-get install -y ecopcr
 
 # cleanup
 WORKDIR /app
 RUN rm *.tar.gz* 
 RUN rm -rf /var/lib/apt/lists/* 
+RUN apt-get clean
 WORKDIR /home/rstudio
 
 EXPOSE 8787

README.md

 # eDNA docker
 
-This repository contains a `Dockerfile` used to build the `edna_tools` docker image including **Rstudio** web interface and the following packages:
-
-- [`tidyverse`](https://www.tidyverse.org/) (`ggplot2`, `dplyr` ...)
-- [`dada2`](https://benjjneb.github.io/dada2/index.html)
-- [`OBITools`](https://pythonhosted.org/OBITools/welcome.html)
-- [`cutadapt`](https://cutadapt.readthedocs.io/en/stable/)
-- [`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 usefull softwares for eDNA analysis. Independently from your operating system, the container is launched with all the softwares pre-installed in a self-contained linux environment. 
-
-Keep in mind that any modifications made inside the container (e.g. packages newly installed or files modified) will be lost after stopping it. Therefore, you need to use the `-v` argument (or use the dedicated field in docker desktop) to mount the local files inside the container as explained in the tutorial bellow. Modification made to the mounted files will not be lost and you can even create new files from inside the container in the mounted path.
-
-The **Rstudio** web interface provides an **R** IDE (Integrated Development Environment) in addition to a terminal to execute any bash command you may need. 
+This repository contains a `Dockerfile` used to build the `edna_tools` docker image including **Rstudio** web interface
+and the following packages:
+
+-   [`tidyverse`](https://www.tidyverse.org/) (`ggplot2`, `dplyr` ...)
+-   [`dada2`](https://benjjneb.github.io/dada2/index.html)
+-   [`OBITools`](https://pythonhosted.org/OBITools/welcome.html)
+-   [`cutadapt`](https://cutadapt.readthedocs.io/en/stable/)
+-   [`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 usefull softwares for eDNA analysis. Independently from your operating system, the container is
+launched with all the softwares pre-installed in a self-contained linux environment.
+
+Keep in mind that any modifications made inside the container (e.g. packages newly installed or files modified) will be
+lost after stopping it. Therefore, you need to use the `-v` argument (or use the dedicated field in docker desktop) to
+mount the local files inside the container as explained in the tutorial bellow. Modification made to the mounted files
+will not be lost and you can even create new files from inside the container in the mounted path.
+
+The **Rstudio** web interface provides an **R** IDE (Integrated Development Environment) in addition to a terminal to
+execute any bash command you may need.
 
 ## Docker tutorial
 
-Docker images can be either used with the **command line interface** (CLI) after installing docker from your favorite linux package manager or by using the **docker desktop** UI available on [Mac](https://docs.docker.com/desktop/install/mac-install/), [Windows](https://docs.docker.com/desktop/install/windows-install/) and [Linux](https://docs.docker.com/desktop/install/linux-install/). 
+Docker images can be either used with the **command line interface** (CLI) after installing docker from your favorite
+linux package manager or by using the **docker desktop** UI available on
+[Mac](https://docs.docker.com/desktop/install/mac-install/),
+[Windows](https://docs.docker.com/desktop/install/windows-install/) and
+[Linux](https://docs.docker.com/desktop/install/linux-install/).
 
 ### Command line interface
 
 Start the docker daemon by running:
+
 ```bash
 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:
+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
 ```
 
-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` both as username and 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` both as username and password.
 
 ### Docker desktop
 
-Once you have installed the **docker desktop** UI, you can search for the `thesanc/edna_tools` image in the research toolbar:
+After unstalling the **docker desktop** UI, you can search for the `thesanc/edna_tools` image in the research toolbar:
 
-![](tutorial_images/docker_desktop_containers.png)
+![](tutorial_images/docker_desktop_home.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 container:
+Once you have found the image, download it and run it by clicking on "run".
 
-<img src="tutorial_images/docker_desktop_run.png" width="400"/>
+![](tutorial_images/docker_desktop_search.png)
 
-Fill the **Host port** field with `8787` (you can set up another port if this one is already used). 
+A pop-up windows should open to set up the container:
+
+<img src="tutorial_images/docker_desktop_run.png" width="400"/>
 
-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. If you are using linux or macos, I recommend to use the host path as container path to avoid path related issues when you are running your code inside and outside the container. On windows, you can type in the desired **Host path** in windows style and type in `/home/rstudio` for the **Container path**, since the path should be in unix style.
+Fill the **Host port** field with `8787` (you can set up another port if this one is already used).
 
-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` both as username and password.
+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. If you are using linux or macos, I recommend to use the host path as container path to
+avoid path related issues when you are running your code inside and outside the container. On windows, you can type in
+the desired **Host path** in windows style and type in `/home/rstudio` for the **Container path**, since the path should
+be in unix style.
 
+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` both as username and password.