diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 88c12cd3248208c41a7a68eaaa8ff80f92500fde..25cacb389dc10489c2f61aa8377fd385b4c334ae 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -28,11 +28,13 @@ fetch_fragments:
- image_list.rst
-pages:
+
+# as not named pages, the gitlab pages will not be updated
+check_pages_build:
stage: build
needs: ["fetch_fragments"]
rules:
- - if: $CI_COMMIT_BRANCH == "docs"
+ - if: $CI_COMMIT_BRANCH != "docs"
image: python:3.10
script:
- mv image_list.rst source/user_guide/
@@ -43,4 +45,11 @@ pages:
- mv build/html/ ./public
artifacts:
paths:
- - public
\ No newline at end of file
+ - public
+
+
+
+pages:
+ extends: check_pages_build
+ rules:
+ - if: $CI_COMMIT_BRANCH == "docs"
\ No newline at end of file
diff --git a/source/user_guide/configure_image.rst b/source/user_guide/configure_image.rst
index 8d7ba514ea7aea81ff4650981f4cdc56fab9504d..d7bcc3fa6356b24ed4128dd2d63e62b06b1d2c35 100644
--- a/source/user_guide/configure_image.rst
+++ b/source/user_guide/configure_image.rst
@@ -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
@@ -89,7 +93,9 @@ 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
@@ -97,7 +103,9 @@ 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:
@@ -130,7 +138,7 @@ Line 5: Working Directory
:caption: Python & R
:linenos:
:selected:
- :lineno-start: 4
+ :lineno-start: 6
# Add workdir information
WORKDIR /srv/shiny-server/
@@ -138,7 +146,7 @@ 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::
@@ -147,26 +155,30 @@ 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::
@@ -174,7 +186,7 @@ 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"
@@ -187,7 +199,7 @@ 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
@@ -196,8 +208,8 @@ 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:
@@ -244,7 +256,7 @@ 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::
@@ -253,7 +265,7 @@ 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
@@ -261,7 +273,7 @@ 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::
@@ -270,7 +282,7 @@ 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
@@ -280,7 +292,7 @@ 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::
@@ -289,7 +301,7 @@ 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