BioContainers · mboudet · Mar 27, 2025 · Mar 26, 2025
diff --git a/rsat/2025-03-26/Dockerfile b/rsat/2025-03-26/Dockerfile
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+## <---- Create a clone of Ubuntu image
+FROM ubuntu:focal
+
+## <----- METADATA 
+LABEL base_image="ubuntu:focal"
+LABEL version="1"
+LABEL about.summary="Tools to analyse cis elements in genomes: motif discovery, TF factor binding analysis, comparative genomics, regulatory variations"
+LABEL software="rsat"
+LABEL software.version="2025-03-26"
+LABEL about.tags="implemented-in::perl,R,python,C"
+LABEL about.home="http://rsat.eu"
+LABEL extra.identifiers.biotools="rsat"
+LABEL about.software="https://github.com/rsa-tools/rsat-code"
+LABEL about.documentation="https://github.com/rsa-tools"
+LABEL about.license="AGPL-3.0-only"
+LABEL about.license_file="see also licenses at $RSAT/public_html/motif_databasess"
+LABEL maintainer="rsat-developers@list01.bio.ens.psl.eu"
+
+## <----- maintainers 
+MAINTAINER "rsat-developers@list01.bio.ens.psl.eu" 
+
+##  <---- Prevent to open interactive dialogs during the installation process
+ENV DEBIAN_FRONTEND=noninteractive
+
+##  <----  Set the language environment in the docker container: should be included before installing any other package
+RUN apt-get update \
+	&& apt-get install -y locales \
+	&& locale-gen en_US.UTF-8 \
+	&& update-locale LANG=en_US.UTF-8 \
+   	&& apt-get autoremove
+
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+ENV LC_ALL en_US.UTF-8
+
+##  <----  Install required packages, including git
+RUN apt-get install -y --no-install-recommends \
+	apt-transport-https \
+	git \
+	wget \
+	less \
+	vim-tiny \
+	vim \
+	time \
+	lsb-release \
+# gnupg2 needed for gpg command and FOR R key installation
+	gnupg2 \  
+	dirmngr \    
+	ca-certificates\
+	software-properties-common \
+# optimize the space in your docker
+	&& rm -rf /var/lib/apt/lists/*
+
+
+##  <----  Add the CRAN repository to your system sources list
+# commented out, use Ubuntu's instead, r-color-brewer complained
+##RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" > /etc/apt/sources.list.d/cran.list
+##RUN gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
+##	&& gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9| apt-key add -
+
+
+## <---- Now install R and littler, and create a link for littler in /usr/local/bin
+## <---- Also set a default CRAN repo, and make sure littler knows about it too
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends \
+		littler \
+        	r-cran-littler \
+		r-base \
+		r-base-dev \
+		r-recommended \
+		r-cran-rcolorbrewer \
+        && echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site \
+        && echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
+	&& ln -s /usr/share/doc/littler/examples/install.r /usr/local/bin/install.r \
+	&& ln -s /usr/share/doc/littler/examples/install2.r /usr/local/bin/install2.r \
+	&& ln -s /usr/share/doc/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
+	&& ln -s /usr/share/doc/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
+	&& install.r docopt \
+	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
+	&& rm -rf /var/lib/apt/lists/*
+
+
+## <---- Now we will install RSAT from the GitHub repository; requires git see,
+#        https://rsa-tools.github.io/installing-RSAT/unix-install-rsat/installing_RSAT_procedure.html#5_Configuring_RSAT
+#RUN apt-get update \
+#	&& apt-get install -y --no-install-recommends \
+#		git \	
+#		git-lfs \
+#	&& rm -rf /var/lib/apt/lists/*
+
+
+## <---- Create INSTALL_ROOT directory and set as working directory: 
+ENV INSTALL_ROOT=/packages
+RUN echo $INSTALL_ROOT \
+	&& mkdir -p ${INSTALL_ROOT}/
+WORKDIR /packages
+
+
+## <----  Actually clone RSAT repository into your working dir and rename to rsat
+RUN git clone https://github.com/rsa-tools/rsat-code.git --branch 2025-03-26 --single-branch
+RUN mv rsat-code rsat
+
+# Repositories 'demo_files' and 'sample_ouput' are skipped to save space
+# git clone https://github.com/rsa-tools/demo_files.git
+# git clone https://github.com/rsa-tools/sample_outputs.git
+
+## <---- Download licensed motif_databases, move to /packages/motif_databases and symb link
+RUN wget --no-parent -r --reject "index.html*" https://rsat.eead.csic.es/plants/motif_databases/ \
+        && mv /packages/rsat.eead.csic.es/plants/motif_databases/ /packages \
+        && rm -rf /packages/rsat.eead.csic.es
+RUN cd rsat/public_html/ \
+        && ln -s ../../motif_databases/
+
+
+## <---- Remove bulky motif_databases
+RUN rm -rf /packages/motif_databases/cisBP2
+RUN grep -v cisBP2 /packages/motif_databases/db_matrix_files.tab > /packages/motif_databases/db_matrix_files.filt.tab
+RUN mv /packages/motif_databases/db_matrix_files.filt.tab /packages/motif_databases/db_matrix_files.tab
+
+
+## <---- Declare the environment path and set the new working directory
+ENV RSAT /packages/rsat
+RUN echo $RSAT
+WORKDIR $RSAT
+
+## <---- define your IP, this step is needed to have access to web interface
+ENV MY_IP "localhost" 
+RUN echo "MY_IP ${MY_IP}"
+
+## <----Choose your RSAT site name
+ENV RSAT_SITE=my_rsat
+
+## <---- Configure RSAT to be used internally and in web server, this step is needed to generate the RSAT_config.bashrc
+RUN perl perl-scripts/configure_rsat.pl -auto  rsat=${RSAT} rsat_site=${RSAT_SITE} rsat_www=http://${MY_IP}/rsat/ \
+  	rsat_ws=http://${MY_IP}/rsat/ package_manager="apt-get" ucsc_tools=1 ensembl_tools=1
+
+
+
+## <---- Read config and run bash installation scripts: requires sudo and apt-utils
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends \
+	sudo \
+	apt-utils
+
+########################################################       Notes       ########################################################
+# To run the bash installation scripts, we need sudo access 
+# To run source RSAT_config.bashrc we need a bash shell; however, the default shell for RUN instructions is ["/bin/sh", "-c"]. 
+# Using SHELL instruction SHELL ["/bin/bash", "-c"], we can change default shell for subsequent RUN instructions in Dockerfile 
+# then RUN "source file"    # now translates to: RUN /bin/bash -c "source file"
+
+
+## <---- switch to bash
+SHELL ["/bin/bash", "-c"]
+
+
+## <---- make sure you are in your working dir
+RUN cd ${RSAT}
+WORKDIR ${RSAT}
+
+
+## <---- Read config and run bash installation scripts
+RUN  source /packages/rsat/RSAT_config.bashrc \
+	&& bash installer/01_ubuntu_packages.bash \
+	&& bash installer/02_python_packages.bash
+
+########################################################       Notes       ########################################################
+# When installinng python dependencies you might error with rpy2-3.5.12.tar.gz or PySimpleSOAP-1.16.2.tar.gz
+# "note: This error originates from a subprocess, and is likely not a problem with pip"
+# To fix this, we need to pgrade versions of pip, setuptools and wheel -> see installer/02_python_packages.bash
+# end https://bobbyhadz.com/blog/python-note-this-error-originates-from-subprocess
+
+RUN bash installer/03_install_rsat.bash \
+        && bash installer/04_perl_packages.bash \
+#       && bash installer/06_install_organisms.bash \ skipped to save 243MB
+        && bash installer/07_R-and-packages.bash \
+        && bash installer/08_apache_config.bash \
+        && bash installer/10_clean_unnecessary_files.bash
+
+
+RUN echo "source ${RSAT}/RSAT_config.bashrc" >> /etc/bash.bashrc \
+	&& echo "service apache2 start" >>  /etc/bash.bashrc 
+
+
+
+## <---- remove some uneeded folders to save space 
+RUN rm -rf ${RSAT}/ext_lib/ensemblgenomes*/ensembl-*/modules/t \
+        ${RSAT}/ext_lib/ensemblgenomes*/ensembl-*/.git \
+        ${RSAT}/ext_lib/bioperl*/bioperl-live/t \
+        ${RSAT}/ext_lib/bioperl*/bioperl-live/.git \
+        ${RSAT}/.git
+
+
+## <---- add new user called rsat_user and give it permission to $RSAT
+ENV RSATUSER="rsat_user"
+ENV RSATPASS="rsat_2020"
+ENV RSATUSERHOME="/home/${RSATUSER}"
+ENV TESTPATH="${RSATUSERHOME}/test_data"
+ENV MOTIFPATH="/packages/motif_databases"
+ENV EXTMOTIFPATH="/packages/motif_databases/ext_motifs"
+
+RUN useradd ${RSATUSER} \
+	&& echo "${RSATUSER}:${RSATPASS}" | chpasswd \
+	&& adduser ${RSATUSER} sudo \
+	&& chown -R "${RSATUSER}:${RSATUSER}" ${RSAT} \
+	&& chmod 755 ${RSAT} \
+	&& mkdir -p ${TESTPATH} \
+	&& mkdir -p ${EXTMOTIFPATH} \
+	&& chmod -R a+w ${RSATUSERHOME}
+
+## <---- Set env variables
+ENV R_LIBS_SITE="${RSAT}/R-scripts/Rpackages/"
+ENV PATH="${PATH}:${RSAT}/ext_lib/ensemblgenomes-44-97/ensembl-git-tools/bin:${RSAT}/python-scripts:${RSAT}/perl-scripts/parsers:${RSAT}/perl-scripts:${RSAT}/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+
+## <---- Create new folder with test _data 
+ENV TESTMAKEURL="https://raw.githubusercontent.com/eead-csic-compbio/coexpression_motif_discovery/master/makefile/peak-motifs.mk"
+ENV TESTRSATURL="https://raw.githubusercontent.com/eead-csic-compbio/coexpression_motif_discovery/master/peach/Modules/M11"
+ENV TESTRSATFILEREMOTE="${TESTRSATURL}/genesM11.txt"
+ENV TESTRSATFILELOCAL="${TESTPATH}/M11.txt"
+ENV TESTMAKEFILELOCAL="${TESTPATH}/peak-motifs.mk"
+
+RUN wget ${TESTRSATFILEREMOTE} -O ${TESTRSATFILELOCAL}
+RUN wget ${TESTMAKEURL} -O ${TESTMAKEFILELOCAL}
+
+# not needed unless installer/06_install_organisms.bash is run above
+## <---- Rename the container's folder for installing genomes, local volume to be used instead,
+#        this also allows to use preinstalled genomes elsewhere in the file system.
+#
+#        Note that ${RSAT}/public_html/data_container takes 243MB including
+#        Escherichia_coli_GCF_000005845.2_ASM584v2  
+#        Escherichia_coli_K_12_substr__MG1655_uid57779  
+#        Saccharomyces_cerevisiae
+# 
+#        This is a a result of installer/06_install_organisms.bash
+#RUN mv ${RSAT}/public_html/data ${RSAT}/public_html/data_container
+
+## <---- set default user and path
+USER ${RSATUSER}
+
+WORKDIR "/home/${RSATUSER}"
+
+
+
+#################################  Useful command lines  ################################# 
+#
+#
+## 1) Build RSAT Docker container
+#
+# export RSATDOCKERVERSION=`date '+%Y%m%d'` 
+# docker build --tag rsat:$RSATDOCKERVERSION --tag rsat:latest --force-rm --compress .
+# 
+#
+## 2) Create local folders for input data and results, outside the container, as these might be large
+#
+# mkdir -p ~/rsat_data/genomes ~/rsat_results
+# chmod -R a+w ~/rsat_data/genomes ~/rsat_results
+# 
+#  
+## 3) Launch Docker RSAT container:
+#
+# docker run --rm -v ~/rsat_data:/packages/rsat/public_html/data/ -v ~/rsat_results:/home/rsat_user/rsat_results -it rsat:latest
+#
+#
+## 4) Download organism from public RSAT server, such as the Plants server.
+##    Other available servers: http://fungi.rsat.eu, http://metazoa.rsat.eu, http://protists.rsat.eu
+# 
+# download-organism -v 2 -org Prunus_persica.Prunus_persica_NCBIv2.38 -server https://rsat.eead.csic.es/plants
+#
+#
+## 5) Test container
+#
+# cd rsat_results 
+# make -f ../test_data/peak-motifs.mk RNDSAMPLES=2 all
+#
+#
+## 6) Install any organism, please follow 
+##    https://rsa-tools.github.io/managing-RSAT/genome_installation/install_organisms_FASTA_GTF.html
+#
+# 
+## 7) To connect to RSAT Web server running from Docker
+#
+# If you run Docker as a normal user Apache will not start properly and you will see these messages:
+#
+#   * Starting Apache httpd web server apache2
+#   (13)Permission denied: AH00091: apache2: could not open error log file /var/log/apache2/error.log.
+#   AH00015: Unable to open logs
+#   Action 'start' failed.
+#   The Apache error log may have more information
+#
+# If you really want lo launch the Docker Web server launch tge container and do (see RSATPASS above):
+# 
+# sudo service apache2 restart
+# hostname -I
+#
+# open the following URL in your browser, using the obtained the IP address: http://172.17.0.2/rsat