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Commit 6f563761 authored by Bryan BRANCOTTE's avatar Bryan BRANCOTTE
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update dockerfile doc to follow the examples

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1 merge request!31update dockerfile doc to follow the examples
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source/user_guide/configure_image.rst
+ 48
− 36
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......@@ -14,16 +14,18 @@ Here, you can see the content of the ``Dockerfile``:
# Build image from the base image, previously configured for you
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye--1.5.22.1017
# Add workdir information
WORKDIR /srv/shiny-server/
# install additional dependencies, comment the block if you don't have one
RUN apt-get update \
&& apt-get install -y \
wget \
&& rm -rf /var/lib/apt/lists/*
# Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
# RUN apt-get update \
# && apt-get install -y \
# your-system-dependency \
# && rm -rf /var/lib/apt/lists/*
# Copy your dependencies, destination filename must be "packages_to_install.csv"
COPY ./requirements.txt /opt/scripts/requirements.txt
......@@ -48,16 +50,18 @@ Here, you can see the content of the ``Dockerfile``:
# Build image from the base image, previously configured for you
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1--1.5.22.1017
# Add workdir information
WORKDIR /srv/shiny-server/
# install additional dependencies, comment the block if you don't have one
RUN apt-get update \
&& apt-get install -y \
wget \
&& rm -rf /var/lib/apt/lists/*
# Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
# RUN apt-get update \
# && apt-get install -y \
# your-system-dependency \
# && rm -rf /var/lib/apt/lists/*
# Copy your dependencies, destination filename must be "packages_to_install.csv"
COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv
......@@ -88,7 +92,9 @@ Line 1: The base image, with the right version
# Build image from the base image, previously configured for you
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye--1.5.22.1017
.. code-tab:: Dockerfile
:caption: R
......@@ -96,7 +102,9 @@ Line 1: The base image, with the right version
# Build image from the base image, previously configured for you
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1--1.5.22.1017
The ``FROM ...`` indicate which base image should be used, the image contains:
......@@ -129,7 +137,7 @@ Line 5: Working Directory
:caption: Python & R
:linenos:
:selected:
:lineno-start: 4
:lineno-start: 6
# Add workdir information
WORKDIR /srv/shiny-server/
......@@ -137,7 +145,7 @@ Line 5: Working Directory
We set the **current working directory** to ``/srv/shiny-server/`` .
Lines 8-11: The system dependencies
Lines 10-13: The system dependencies
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. tabs::
......@@ -146,26 +154,30 @@ Lines 8-11: The system dependencies
:caption: Python & R
:linenos:
:selected:
:lineno-start: 7
:lineno-start: 9
# install additional dependencies, comment the block if you don't have one
RUN apt-get update \
&& apt-get install -y \
wget \
&& rm -rf /var/lib/apt/lists/*
# Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
# RUN apt-get update \
# && apt-get install -y \
# your-system-dependency \
# && rm -rf /var/lib/apt/lists/*
Some of your package dependencies require system dependencies (such as
`graphviz-dev <https://packages.ubuntu.com/graphviz-dev>`_ for
`pygraphviz <https://pypi.org/project/pygraphviz/>`_).
To add such dependencies, duplicate line 10, and replace **wget** with your
dependencies.
To add such dependencies,
uncomment the bloc 10-13,
adapte/duplicate line 12,
and replace **your-system-dependency** with your actual dependency.
We recommend you to specify one dependency per line, its helps later investigation
when searching for why a dependency have been added.
If you have **no additional system dependencies** you can remove this block.
If you have **no additional system dependencies** you can keep this block commented.
Lines 14-17: The package dependencies
Lines 16-19: The package dependencies
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. tabs::
......@@ -173,7 +185,7 @@ Lines 14-17: The package dependencies
.. code-tab:: Dockerfile
:caption: Python
:linenos:
:lineno-start: 13
:lineno-start: 15
:selected:
# Copy your dependencies, destination filename must be "packages_to_install.csv"
......@@ -186,7 +198,7 @@ Lines 14-17: The package dependencies
.. code-tab:: Dockerfile
:caption: R
:linenos:
:lineno-start: 13
:lineno-start: 15
# Copy your dependencies, destination filename must be "packages_to_install.csv"
COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv
......@@ -195,8 +207,8 @@ Lines 14-17: The package dependencies
RUN Rscript /opt/scripts/install_r_packages.R
The package dependencies are copied into the images line 14,
and installed line 17. The format of the file listing the dependencies depends
The package dependencies are copied into the images line 16,
and installed line 19. The format of the file listing the dependencies depends
on the language you use:
......@@ -243,7 +255,7 @@ If can be from cran, from bioconductor, or even a github package.
tidyverse/tibble; github package
Line 20: Grant shiny to create bookmark state
Line 22: Grant shiny to create bookmark state
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. tabs::
......@@ -252,7 +264,7 @@ Line 20: Grant shiny to create bookmark state
:caption: Python & R
:linenos:
:selected:
:lineno-start: 19
:lineno-start: 21
# grant shiny to created bookmark state directory in this directory
RUN chown shiny:shiny /var/lib/shiny-server
......@@ -260,7 +272,7 @@ Line 20: Grant shiny to create bookmark state
In order to run your application, the user ``shiny`` must be allow to write file in
``/var/lib/shiny-server`` directory .
Line 23: Copy your app into the image
Line 25: Copy your app into the image
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. tabs::
......@@ -269,7 +281,7 @@ Line 23: Copy your app into the image
:caption: Python & R
:linenos:
:selected:
:lineno-start: 22
:lineno-start: 24
# Copy you shiny app
COPY ./my_project /srv/shiny-server
......@@ -279,7 +291,7 @@ Line 23: Copy your app into the image
At that moment you copy you app in the image.
Keep in mind that this folder name :ref:`can be adapted <Custom source dir name>`.
Line 26: Grant shiny to write output data
Line 28: Grant shiny to write output data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. tabs::
......@@ -288,7 +300,7 @@ Line 26: Grant shiny to write output data
:caption: Python & R
:linenos:
:selected:
:lineno-start: 25
:lineno-start: 27
# grant shiny to use www folder
RUN chown shiny:shiny /srv/shiny-server/www
......
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