diff --git a/R-minimal/Dockerfile b/R-minimal/Dockerfile index 7f15d32..8c6dd81 100644 --- a/R-minimal/Dockerfile +++ b/R-minimal/Dockerfile @@ -1,51 +1,51 @@ # For finding latest versions of the base image see # https://github.com/SwissDataScienceCenter/renkulab-docker -ARG RENKU_BASE_IMAGE=renku/renkulab-r:4.0.5-0.10.1 +ARG RENKU_BASE_IMAGE=renku/renkulab-r:4.1.2-0.11.0 FROM ${RENKU_BASE_IMAGE} # Uncomment and adapt if code is to be included in the image # COPY src /code/src # Uncomment and adapt if your R or python packages require extra linux (ubuntu) software # e.g. the following installs apt-utils and vim; each pkg on its own line, all lines # except for the last end with backslash '\' to continue the RUN line # # USER root # RUN apt-get update && \ # apt-get install -y --no-install-recommends \ # apt-utils \ # vim # USER ${NB_USER} # install the R dependencies COPY install.R /tmp/ RUN R -f /tmp/install.R # install the python dependencies COPY requirements.txt /tmp/ RUN pip3 install -r /tmp/requirements.txt # RENKU_VERSION determines the version of the renku CLI # that will be used in this image. To find the latest version, # visit https://pypi.org/project/renku/#history. -ARG RENKU_VERSION={{ __renku_version__ | default("0.16.2") }} +ARG RENKU_VERSION={{ __renku_version__ | default("1.0.5") }} ######################################################## # Do not edit this section and do not add anything below # Install renku from pypi or from github if it's a dev version RUN if [ -n "$RENKU_VERSION" ] ; then \ source .renku/venv/bin/activate ; \ currentversion=$(renku --version) ; \ if [ "$RENKU_VERSION" != "$currentversion" ] ; then \ pip uninstall renku -y ; \ gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \ if [ -n "$gitversion" ] ; then \ pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\ else \ pip install --force renku==${RENKU_VERSION} ;\ fi \ fi \ fi ######################################################## diff --git a/bioc-minimal/Dockerfile b/bioc-minimal/Dockerfile index 52d2ac0..4aa1153 100644 --- a/bioc-minimal/Dockerfile +++ b/bioc-minimal/Dockerfile @@ -1,50 +1,50 @@ # see https://github.com/SwissDataScienceCenter/renkulab-docker # to swap this image for the latest version available -FROM renku/renkulab-bioc:RELEASE_3_12-0.10.1 +FROM renku/renkulab-bioc:RELEASE_3_14-0.11.0 # Uncomment and adapt if code is to be included in the image # COPY src /code/src # Uncomment and adapt if your R or python packages require extra linux (ubuntu) software # e.g. the following installs apt-utils and vim; each pkg on its own line, all lines # except for the last end with backslash '\' to continue the RUN line # # USER root # RUN apt-get update && \ # apt-get install -y --no-install-recommends \ # apt-utils \ # vim # USER ${NB_USER} # install the R dependencies COPY install.R /tmp/ RUN R -f /tmp/install.R # install the python dependencies COPY requirements.txt /tmp/ RUN pip3 install -r /tmp/requirements.txt # RENKU_VERSION determines the version of the renku CLI # that will be used in this image. To find the latest version, # visit https://pypi.org/project/renku/#history. -ARG RENKU_VERSION={{ __renku_version__ | default("0.16.2") }} +ARG RENKU_VERSION={{ __renku_version__ | default("1.0.5") }} ######################################################## # Do not edit this section and do not add anything below # Install renku from pypi or from github if it's a dev version RUN if [ -n "$RENKU_VERSION" ] ; then \ source .renku/venv/bin/activate ; \ currentversion=$(renku --version) ; \ if [ "$RENKU_VERSION" != "$currentversion" ] ; then \ pip uninstall renku -y ; \ gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \ if [ -n "$gitversion" ] ; then \ pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\ else \ pip install --force renku==${RENKU_VERSION} ;\ fi \ fi \ fi ######################################################## diff --git a/julia-minimal/Dockerfile b/julia-minimal/Dockerfile index 0c91efa..9ab74c3 100644 --- a/julia-minimal/Dockerfile +++ b/julia-minimal/Dockerfile @@ -1,56 +1,56 @@ # For finding latest versions of the base image see # https://github.com/SwissDataScienceCenter/renkulab-docker -ARG RENKU_BASE_IMAGE=renku/renkulab-julia:1.6.1-0.10.1 +ARG RENKU_BASE_IMAGE=renku/renkulab-julia:1.7.1-0.11.0 FROM ${RENKU_BASE_IMAGE} # Uncomment and adapt if code is to be included in the image # COPY src /code/src # Uncomment and adapt if your python, R, or Julia packages require extra linux (ubuntu) software # e.g. the following installs apt-utils and vim; each pkg on its own line, all lines # except for the last end with backslash '\' to continue the RUN line # # USER root # RUN apt-get update && \ # apt-get install -y --no-install-recommends \ # apt-utils \ # vim # USER ${NB_USER} # install the python dependencies COPY requirements.txt environment.yml /tmp/ RUN conda env update -q -f /tmp/environment.yml && \ /opt/conda/bin/pip install -r /tmp/requirements.txt && \ conda clean -y --all && \ conda env export -n "root" # download and precompile any libaries to speed up startup time COPY Project.toml Manifest.toml /tmp/ RUN mkdir /tmp/julia-pkg && \ cp /tmp/Project.toml /tmp/Manifest.toml /tmp/julia-pkg/ && \ julia -e'using Pkg; Pkg.activate("/tmp/julia-pkg/"); Pkg.instantiate(); Pkg.precompile()' # RENKU_VERSION determines the version of the renku CLI # that will be used in this image. To find the latest version, # visit https://pypi.org/project/renku/#history. -ARG RENKU_VERSION={{ __renku_version__ | default("0.16.2") }} +ARG RENKU_VERSION={{ __renku_version__ | default("1.0.5") }} ######################################################## # Do not edit this section and do not add anything below # Install renku from pypi or from github if it's a dev version RUN if [ -n "$RENKU_VERSION" ] ; then \ source .renku/venv/bin/activate ; \ currentversion=$(renku --version) ; \ if [ "$RENKU_VERSION" != "$currentversion" ] ; then \ pip uninstall renku -y ; \ gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \ if [ -n "$gitversion" ] ; then \ pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\ else \ pip install --force renku==${RENKU_VERSION} ;\ fi \ fi \ fi ######################################################## diff --git a/minimal/Dockerfile b/minimal/Dockerfile index 23496ad..f76fe0f 100644 --- a/minimal/Dockerfile +++ b/minimal/Dockerfile @@ -1,55 +1,55 @@ # For finding latest versions of the base image see # https://github.com/SwissDataScienceCenter/renkulab-docker -ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.9-0.10.1 +ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.9-0.11.0 FROM ${RENKU_BASE_IMAGE} # Uncomment and adapt if code is to be included in the image # COPY src /code/src # Uncomment and adapt if your R or python packages require extra linux (ubuntu) software # e.g. the following installs apt-utils and vim; each pkg on its own line, all lines # except for the last end with backslash '\' to continue the RUN line # # USER root # RUN apt-get update && \ # apt-get install -y --no-install-recommends \ # apt-utils \ # vim # USER ${NB_USER} # Uncomment and adapt if you want to automatically install # python dependencies when the Docker image builds (pip or conda) # Note: you will need to add a (pip) requirements.txt file # AND a (conda) environment.yml file for the below code to run, # but you can remove one or the other. # # COPY requirements.txt environment.yml /tmp/ # RUN conda env update -q -f /tmp/environment.yml && \ # /opt/conda/bin/pip install -r /tmp/requirements.txt && \ # conda clean -y --all && \ # conda env export -n "root" # RENKU_VERSION determines the version of the renku CLI # that will be used in this image. To find the latest version, # visit https://pypi.org/project/renku/#history. -ARG RENKU_VERSION={{ __renku_version__ | default("0.16.2") }} +ARG RENKU_VERSION={{ __renku_version__ | default("1.0.5") }} ######################################################## # Do not edit this section and do not add anything below # Install renku from pypi or from github if it's a dev version RUN if [ -n "$RENKU_VERSION" ] ; then \ source .renku/venv/bin/activate ; \ currentversion=$(renku --version) ; \ if [ "$RENKU_VERSION" != "$currentversion" ] ; then \ pip uninstall renku -y ; \ gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \ if [ -n "$gitversion" ] ; then \ pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\ else \ pip install --force renku==${RENKU_VERSION} ;\ fi \ fi \ fi ######################################################## diff --git a/python-minimal/Dockerfile b/python-minimal/Dockerfile index 644636a..8a364a5 100644 --- a/python-minimal/Dockerfile +++ b/python-minimal/Dockerfile @@ -1,50 +1,50 @@ # For finding latest versions of the base image see # https://github.com/SwissDataScienceCenter/renkulab-docker -ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.9-0.10.1 +ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.9-0.11.0 FROM ${RENKU_BASE_IMAGE} # Uncomment and adapt if code is to be included in the image # COPY src /code/src # Uncomment and adapt if your R or python packages require extra linux (ubuntu) software # e.g. the following installs apt-utils and vim; each pkg on its own line, all lines # except for the last end with backslash '\' to continue the RUN line # # USER root # RUN apt-get update && \ # apt-get install -y --no-install-recommends \ # apt-utils \ # vim # USER ${NB_USER} # install the python dependencies COPY requirements.txt environment.yml /tmp/ RUN conda env update -q -f /tmp/environment.yml && \ /opt/conda/bin/pip install -r /tmp/requirements.txt && \ conda clean -y --all && \ conda env export -n "root" # RENKU_VERSION determines the version of the renku CLI # that will be used in this image. To find the latest version, # visit https://pypi.org/project/renku/#history. -ARG RENKU_VERSION={{ __renku_version__ | default("0.16.2") }} +ARG RENKU_VERSION={{ __renku_version__ | default("1.0.5") }} ######################################################## # Do not edit this section and do not add anything below # Install renku from pypi or from github if it's a dev version RUN if [ -n "$RENKU_VERSION" ] ; then \ source .renku/venv/bin/activate ; \ currentversion=$(renku --version) ; \ if [ "$RENKU_VERSION" != "$currentversion" ] ; then \ pip uninstall renku -y ; \ gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \ if [ -n "$gitversion" ] ; then \ pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\ else \ pip install --force renku==${RENKU_VERSION} ;\ fi \ fi \ fi ########################################################