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version 20240828 resulting from development over IBIS2024 (#576)
* added version 20240828 resulting from development over IBISI2024 * fix branch tag
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| ## <---- Create a clone of Ubuntu image | ||
| FROM ubuntu:focal | ||
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| ## <----- 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="20240828" | ||
| 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="[email protected]" | ||
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| ## <----- maintainers | ||
| MAINTAINER "[email protected]" | ||
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| ## <---- Prevent to open interactive dialogs during the installation process | ||
| ENV DEBIAN_FRONTEND=noninteractive | ||
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| ## <---- 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 | ||
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| ENV LANG en_US.UTF-8 | ||
| ENV LANGUAGE en_US.UTF-8 | ||
| ENV LC_ALL en_US.UTF-8 | ||
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| ## <---- 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/* | ||
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| ## <---- Add the CRAN repository to your system sources list, 4.0 for focal | ||
| 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 - | ||
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| ## <---- 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 \ | ||
| && 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/* | ||
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| ## <---- 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 | ||
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| RUN apt-get update \ | ||
| && apt-get install -y --no-install-recommends \ | ||
| git \ | ||
| git-lfs \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| ## <---- Create INSTALL_ROOT directory and set as working directory: | ||
| ENV INSTALL_ROOT=/packages | ||
| RUN echo $INSTALL_ROOT \ | ||
| && mkdir -p ${INSTALL_ROOT}/ | ||
| WORKDIR /packages | ||
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| ## <---- Actually clone RSAT repository into your working dir and rename to rsat | ||
| RUN git clone https://github.com/rsa-tools/rsat-code.git --branch 2024-08-28c --single-branch | ||
| RUN mv rsat-code rsat | ||
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| # 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 | ||
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| ## <---- 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/ | ||
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| ## <---- 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 | ||
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| ## <---- Declare the environment path and set the new working directory | ||
| ENV RSAT /packages/rsat | ||
| RUN echo $RSAT | ||
| WORKDIR $RSAT | ||
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| ## <---- define your IP, this step is needed to have access to web interface | ||
| ENV MY_IP "localhost" | ||
| RUN echo "MY_IP ${MY_IP}" | ||
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| ## <----Choose your RSAT site name | ||
| ENV RSAT_SITE=my_rsat | ||
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| ## <---- Configure RSAT to be used internally and in web server, this step is needed to generate the RSAT_config.bashrc | ||
| RUN perl perl-scripts/configure_rsat.pl -auto rsat=${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 | ||
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| ## <---- 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 | ||
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| ######################################################## 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" | ||
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| ## <---- switch to bash | ||
| SHELL ["/bin/bash", "-c"] | ||
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| ## <---- make sure you are in your working dir | ||
| RUN cd ${RSAT} | ||
| WORKDIR ${RSAT} | ||
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| ## <---- 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 | ||
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| ######################################################## 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 | ||
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| 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 | ||
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| RUN echo "source ${RSAT}/RSAT_config.bashrc" >> /etc/bash.bashrc \ | ||
| && echo "service apache2 start" >> /etc/bash.bashrc | ||
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| ## <---- 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 | ||
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| ## <---- 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="${RSATUSERHOME}/test_data" | ||
| ENV EXTMOTIFPATH="${RSATUSERHOME}/ext_motifs" | ||
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| 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 ${RSATUSERHOME} | ||
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| ## <---- Set env variables | ||
| ENV R_LIBS_SITE="${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" | ||
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| ## <---- 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" | ||
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| RUN wget ${TESTRSATFILEREMOTE} -O ${TESTRSATFILELOCAL} | ||
| RUN wget ${TESTMAKEURL} -O ${TESTMAKEFILELOCAL} | ||
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| # 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 | ||
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| ## <---- set default user and path | ||
| USER ${RSATUSER} | ||
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| WORKDIR "/home/${RSATUSER}" | ||
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| ################################# 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 |