From 0a3a5bee1f6420ab7f25ceb864e20d55995610db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Mon, 2 Dec 2024 09:28:52 +0100 Subject: [PATCH 01/25] add jupyterlab stuff --- .../tutorials/interactive-tools/tutorial.md | 623 ++++++++++++++++-- 1 file changed, 566 insertions(+), 57 deletions(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 2a1ee90102a73f..ab18cbd323a127 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -38,6 +38,7 @@ contributors: - abretaud # editing - hexylena + - Marie59 --- @@ -110,9 +111,7 @@ visualising data, but if it is possible to provide the same functionality with a regular tool (e.g. by rendering an HTML file as an output), then an Interactive Tool might not be necessary. -If you are sure that a static -output is not sufficient, then it's time to start building your first -Interactive Tool! +If you are sure that a static output is not sufficient, then it's time to start building your first Interactive Tool! > Interactive tool infrastructure > Interactive tools require some rather complex infrastructure in order to work! However, most of the infrastructure requirements are taken care of by Galaxy core. As such, wrapping a new GxIT requires only three components: @@ -158,6 +157,10 @@ cycle. {: .comment} +{% include _includes/cyoa-choices.html option1="Application" option2="Jupyterlab" default="Application" text="Do you want to build a desktop application or a jupyterlab tool ?" %} + +
+ # The application The application that we will wrap in this tutorial is a simple web tool which @@ -204,6 +207,8 @@ These are specific to your container; these are required for an R-Shiny containe ## The Dockerfile +If you need some help to start your Dockerfile you can always some inspiration from the previous interactve tools build in Galaxy. Go check some of the Dockerfiles for instance the one for the application [QGIS](https://github.com/usegalaxy-eu/docker-qgis) or for [ODV](https://github.com/bgruening/docker-odv/tree/main) + > A brief primer on Docker > Docker allows an entire application context to be containerized. A typical web application consists of an operating system, installed dependancies, web server configuration, database configuration and, of course, the codebase of the software itself. A Docker container can encapsulate all of these components in a single "image", which can be run on any machine with Docker installed. > @@ -434,7 +439,7 @@ our new Docker container as a Galaxy tool. > > Writing the GxIT tool XML > > > > * Refer to the [Galaxy tool XML docs](https://docs.galaxyproject.org/en/latest/dev/schema.html). -> > * You can take inspiration from [Askomics](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_askomics.xml), and other [existing Interactive Tools](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive). +> > * You can take inspiration from [Askomics](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_askomics.xml), [QGIS](https://github.com/usegalaxy-eu/galaxy/blob/release_24.1_europe/tools/interactive/interactivetool_qgis3_34.xml), [ODV](https://github.com/usegalaxy-eu/galaxy/blob/release_24.1_europe/tools/interactive/interactivetool_odv.xml), and other [existing Interactive Tools](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive). > > * Check XML syntax with [xmlvalidation.com](https://www.xmlvalidation.com/) or [w3schools XML validator](https://www.w3schools.com/xml/xml_validator.asp), or use a linter in your code editor. > > * [planemo lint](https://planemo.readthedocs.io/en/latest/commands/lint.html) can also be used for XML linting. But be aware that `planemo test` won't work. > > * When it comes to testing and debugging your tool XML, it can be easier to update the XML file directly on your Galaxy server between tests. @@ -525,6 +530,535 @@ our new Docker container as a Galaxy tool. > Don't forget to change the image path (see the `$REMOTE` variable above) and the citation to fit your project settings. {: .hands_on} +# Additional components + +The GxIT that we wrapped in this tutorial was a simple example, and you should now understand what is required to create an Interactive Tool for Galaxy. However, there are a few additional components that can enhance the reliability and user experience of the tool. In addition, more complex applications may require some additional components or workarounds the create the desired experience for the user. + +## Run script +In the case of our `Tabulator` application, the run script is simply the R script that renders our Shiny App. It is quite straightforward to call this from our Galaxy tool XML. However, some web apps might require more elaborate commands to be run. In this situation, there are a number of solutions demonstrated in the `` section of [existing GxITs](https://github.com/galaxyproject/galaxy/tree/dev/tools/interactive): +- [Guacamole Desktop](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_guacamole_desktop.xml): application startup with `startup.sh` +- [HiCBrowser](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_hicbrowser.xml): application startup with `supervisord` +- [AskOmics](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_askomics.xml): configuration with Python and Bash scripts, followed by `start_all.sh` to run the application. + +## Templated config files +Using the `` section in the tool XML, we can enable complex user configuration for the application by templating a run script or configuration file to be read by the application. In this application, for example, we could use a `` section to template user input into the `app.R` script that runs the application within the Docker container. This could enable the user to customize the layout of the app before launch. + +## Reserved environment variables + +There are a few environment variables +that are accessible in the command section of the tool XML - these can be handy when writing your tool script. +[Check the docs](https://docs.galaxyproject.org/en/latest/dev/schema.html#reserved-variables) for a full reference on the tool XML. + +```sh +$__tool_directory__ +$__root_dir__ +$__user_id__ +$__user_email__ +``` + +It can also be useful to create and inject environment variables into the tool context. This can be acheived using the `` tag in the tool XML. The [RStudio GxIT](https://github.com/galaxyproject/galaxy/blob/b180b7909dc3fe2750fbc8b90214e201eb276794/tools/interactive/interactivetool_rstudio.xml#L12) again provides an example of this: + +```xml + + ${__app__.security.encode_id($jupyter_notebook.history_id)} + ${__app__.config.galaxy_infrastructure_url} + 8080 + $__galaxy_url__ + true + true + + +``` + +## Galaxy history interaction +We have demonstrated how to pass an input file to the Docker container. But what if the application needs to interact with the user's Galaxy history? For example, if the user creates a file within the application. That's where the environment variables created in the tool XML become useful. + +> Access histories in R +> From the [R-Studio GxIT](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_rstudio.xml) we can see that there is [an R library](https://github.com/hexylena/rGalaxyConnector) that allows us to interact with Galaxy histories. +> +> "The convenience functions `gx_put()` and `gx_get()` are available to you to interact with your current Galaxy history. You can save your workspace with `gx_save()`" +> +> Under the hood, this library uses [galaxy_ie_helpers](https://github.com/bgruening/galaxy_ie_helpers) - a Python interface to Galaxy histories written with [BioBlend](https://github.com/galaxyproject/bioblend). You could also use BioBlend directly (or even the Galaxy REST API) if your GxIT requires a more flexible interface than these wrappers provide. +> +{: .tip} + + +
+ +
+ +# The jupyterlab + +The jupyterlab environement that we will wrap in this tutorial is a simple jupyterlab tool which +allows the user to upload data in an jupyter environment, manipulate notebooks, and download +outputs. + +Our example jupyterlab can already be found [online](https://github.com/usegalaxy-eu/docker-copernicus-notebooks) +But you can also check an other implementation of [jupyterlabs](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile). +In the following sections, we will study how it can be built into a GxIT. + + +> +> +> First, let's clone the repository to take a quick look at a basic implementation of a jupyterlab. +> +> ```console +> $ git clone https://github.com/bgruening/docker-jupyter-notebook.git +> $ cd docker-jupyter-notebook +> +> $ tree . +> ├── Dockerfile +> ├── LICENSE +> ├── README.md +> ├── . +> ├── . +> ├── . +> └── startup.sh +> ``` +> You'll find a Dockerfile, startup.sh, and a README that will describe how the dockerfile here for an Gxit works. We encourage you to read thi README. +> +{: .hands_on} + +## The Dockerfile + +If you need some help to start your Dockerfile you can always some inspiration from the previous interactve tools build in Galaxy. Go check some of the Dockerfiles for instance the one for the [Copernicus data sapce ecosystem jupyterlab](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) or for a basic [jupyterlab here](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile) + +> A brief primer on Docker +> Docker allows an entire application context to be containerized. A typical web application consists of an operating system, installed dependancies, web server configuration, database configuration and, of course, the codebase of the software itself. A Docker container can encapsulate all of these components in a single "image", which can be run on any machine with Docker installed. +> +> **Essentials of Docker:** +> +> 1. Write an image recipe as a Dockerfile. This single file selects an OS, installs software, pulls code repositories and copies files from the host machine (your computer). +> 2. Build the image from your recipe: +> +> `docker build -t .` +> 3. View existing images with +> +> `docker image list` +> 4. Run a container with a specified command: +> +> `docker run ` +> 5. View running containers: +> +> `docker ps` +> 6. Stop a running container: +> +> `docker stop ` +> 7. Remove a stopped container: +> +> `docker container rm ` +> 8. Remove an image: +> +> `docker image rm ` +{: .tip} + + +Let's check out [the Dockerfile](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) that we'll use to containerize our Jupyterlab. + +This container recipe can be used to build a Docker image which can be pushed to a +container registry in the cloud, ready for consumption by our Galaxy instance: + +```dockerfile +# Jupyter container used for Galaxy copernicus notebooks (+other kernels) Integration + +# from 5th March 2021 +FROM jupyter/datascience-notebook:python-3.10 + +MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com + +ENV DEBIAN_FRONTEND noninteractive +USER root + +RUN apt-get -qq update && \ + apt-get install -y wget unzip net-tools procps && \ + apt-get autoremove -y && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +# Set channels to (defaults) > bioconda > conda-forge +RUN conda config --add channels conda-forge && \ + conda config --add channels bioconda + #conda config --add channels defaults +RUN pip install --upgrade pip +RUN pip install --no-cache-dir bioblend galaxy-ie-helpers + +ENV JUPYTER /opt/conda/bin/jupyter +ENV PYTHON /opt/conda/bin/python +ENV LD_LIBRARY_PATH /opt/conda/lib/ + +# Python packages +RUN conda config --add channels conda-forge && \ + conda config --add channels bioconda && \ + conda install --yes --quiet \ + bash_kernel \ + ansible-kernel \ + bioblend galaxy-ie-helpers \ +``` +With those packages installed you have the bases to have a functionnal environement in your jupyterlab AND be able to link your jupyterlab to the Galaxy history with the pacakage `bioblend galaxy-ie-helpers`. + +Then you can add the package specific to the environement you want to have in you jupyterlab for instance + +``` + # specific sentinel, openeo packages + sentinelhub \ + openeo \ + # other packages for notebooks + geopandas \ + rasterio \ + ipyleaflet \ + netcdf4 \ + h5netcdf \ + # Jupyter widgets + jupytext && \ + conda clean -yt && \ + pip install jupyterlab_hdf \ + fusets + +``` + +Then, you can add some configurations to have some configuration and a welcome notebook by default (this generic to all jupyterlabs gxit) + +``` +ADD ./startup.sh /startup.sh +ADD ./get_notebook.py /get_notebook.py + +# We can get away with just creating this single file and Jupyter will create the rest of the +# profile for us. +RUN mkdir -p /home/$NB_USER/.ipython/profile_default/startup/ && \ + mkdir -p /home/$NB_USER/.jupyter/custom/ + +COPY ./ipython-profile.py /home/$NB_USER/.ipython/profile_default/startup/00-load.py +COPY jupyter_notebook_config.py /home/$NB_USER/.jupyter/ +COPY jupyter_lab_config.py /home/$NB_USER/.jupyter/ + +ADD ./custom.js /home/$NB_USER/.jupyter/custom/custom.js +ADD ./custom.css /home/$NB_USER/.jupyter/custom/custom.css +ADD ./default_notebook.ipynb /home/$NB_USER/notebook.ipynb + +``` + +You can also add your own set of notebooks to guide the user like that : + +``` +# Download notebooks +RUN cd /home/$NB_USER/ && \ + wget -O notebook-samples.zip https://github.com/eu-cdse/notebook-samples/archive/refs/heads/main.zip && \ + unzip notebook-samples.zip && \ + rm /home/$NB_USER/notebook-samples.zip && \ + mv /home/$NB_USER/notebook-samples-main/geo /home/$NB_USER && \ + mv /home/$NB_USER/notebook-samples-main/sentinelhub /home/$NB_USER && \ + mv /home/$NB_USER/notebook-samples-main/openeo /home/$NB_USER && \ + rm -r /home/$NB_USER/notebook-samples-main +``` + +Finally, some general variables of environment : + +``` +# ENV variables to replace conf file +ENV DEBUG=false \ + GALAXY_WEB_PORT=10000 \ + NOTEBOOK_PASSWORD=none \ + CORS_ORIGIN=none \ + DOCKER_PORT=none \ + API_KEY=none \ + HISTORY_ID=none \ + REMOTE_HOST=none \ + GALAXY_URL=none + +# @jupyterlab/google-drive not yet supported + +USER root +WORKDIR /import + +# Start Jupyter Notebook +CMD /startup.sh + +``` + +And with all this your Dockerfile is ready + +You now need to publish this image o a public repository. +Anyone can use this Dockerfile to rebuild the image if necessary. +In any case don't forget to have all the files shown when we cloned this [repository](https://github.com/bgruening/docker-jupyter-notebook/tree/master) next to your Dockerfile. + +> +> +> Let's start working on this Docker container. +> +> 1. Install Docker as described on the [docker website](https://docs.docker.com/engine/install/). Click on your distribution name to get specific information. +> +> 2. Now let's use the recipe to build our Docker image. +> +> ```sh +> # Build a container image from our Dockerfile +> IMAGE_TAG="myimage" +> LOG_PATH=`pwd` # Create log output in current directory +> PORT=8765 +> docker build -t $IMAGE_TAG --build-arg LOG_PATH=$LOG_PATH --build-arg PORT=$PORT . +> ``` +> +> > Automating the build +> > While developing the Docker container you may find yourself tweaking and rebuilding the container image many times. +> > In the GitHub repository linked above, you'll notice that the author has used a `Makefile` to accelerate the build and deploy process. +> > This allows the developer to simply run `make docker` and `make push_hub` to build and push the container, or `make` to rebuild the container after making changes during development. Check out the `Makefile` to see what commands can be run using `make` in this repository. +> > +> {: .tip} +{: .hands_on} + +If you are lucky, you might find an available Docker image for the application you are trying to wrap. However, existing Docker images often require some "tweaking" before they will work as a GxIT. Some example configuration changes are: + +1. Expose the correct port. The application, Docker and tool XML ports must be aligned! +2. Log output to an external file - useful for debugging. +3. Make the application callable from tool `` - this sometimes requires a wrapper script to interface the application inside the container (we'll take a look at this later). + + + +## Test the image + +Before we go pushing our container to the cloud, we should give it a local test run to ensure that it's working correctly on our development machine. Have a play and see how our little web app works! + +> +> ```sh +> # Run our application in the container +> docker run -it -p 127.0.0.1:8765:$PORT $IMAGE_TAG +> +> # Or to save time, take advantage of the Makefile +> make it +> +> # Give it a few moments to start up, and the application should be available +> # in your browser at http://127.0.0.1:8765 +> ``` +{: .hands_on} + +## Push the image + +If you are happy with the image, we are ready to push it to a container registry +to make it accessible to our Galaxy server. + +During development, we suggest making an account on +[Docker Hub](https://hub.docker.com/) +if you don't have one already. This can be used for hosting container images +during development. +[Docker Hub](https://hub.docker.com/) +has great documentation on creating repositories, authenticating with tokens +and pushing images. + +> +> ```sh +> # Set remote tag for your container. This should include your username and +> # repository name for Docker Hub. +> REMOTE=/my-first-gxit +> +> # Tag your image +> docker tag $IMAGE_TAG:latest $REMOTE:latest +> +> # Authenticate your DockerHub account +> docker login # >>> Enter username and token for your account +> +> # Push the image +> docker push $REMOTE:latest +> ``` +> +> > Production container hosting +> > For production deployment, the +> > [Galaxy standard](https://docs.galaxyproject.org/en/latest/admin/special_topics/mulled_containers.html) +> > for container image hosting is +> > [Biocontainers](https://biocontainers.pro). +> > This requires you to +> > [make a pull request](https://biocontainers-edu.readthedocs.io/en/latest/contributing.html) +> > against the Biocontainers GitHub repository, so this should only be done when an +> > image is considered production-ready. You can also push your image to a +> > repository on +> > [hub.docker.com](https://hub.docker.com) or +> > [quay.io](https://quay.io) +> > but please ensure that it links to a public code repository +> > (e.g. GitHub) to enable maintenance of the image by the Galaxy community! +> {: .tip} +{: .hands_on} + +You should now have a container in the cloud, ready for action. +Check out your repo on Docker Hub and you should find the container image there. +Awesome! + +Now we just need to write a tool XML that will enable Galaxy to pull and run +our new Docker container as a Galaxy tool. + +## The tool XML + +> +> +> Create a Galaxy tool XML file named `interactivetool_copernicus.xml`. The file is similar to a regular tool XML, but calls on our remote Docker image as a dependency. The tags that we are most concerned with are: +> - A `` (under the `` tag) +> - A `` which matches our container +> - An `` file +> - The `` section +> +> > Writing the tool command +> > +> > This step can cause a lot of confusion. Here are a few pointer that you will find critical to understanding the process: +> > - The `` will be templated by Galaxy +> > - The templated command will run *inside* the Docker container +> > +> {: .comment} +> +> > Writing the GxIT tool XML +> > +> > * Refer to the [Galaxy tool XML docs](https://docs.galaxyproject.org/en/latest/dev/schema.html). +> > * You can take inspiration from [Copernicus](https://github.com/usegalaxy-eu/galaxy/blob/release_24.1_europe/tools/interactive/interactivetool_copernicus.xml) or for a more advanced [jupyterlab](https://github.com/usegalaxy-eu/galaxy/blob/release_24.1_europe/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml) [existing Interactive Tools](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive). +> > * Check XML syntax with [xmlvalidation.com](https://www.xmlvalidation.com/) or [w3schools XML validator](https://www.w3schools.com/xml/xml_validator.asp), or use a linter in your code editor. +> > * [planemo lint](https://planemo.readthedocs.io/en/latest/commands/lint.html) can also be used for XML linting. But be aware that `planemo test` won't work. +> > * When it comes to testing and debugging your tool XML, it can be easier to update the XML file directly on your Galaxy server between tests. +> {: .tip} +> +> > +> > +> > {% raw %} +> > +> > ```xml +> > +> > sample notebooks to access and discover data +> > +> > 0.0.1 +> > +> > +> > quay.io/galaxy/copernicus-jupyterlab:@VERSION@ +> > +> > +> > +> > 8888 +> > ipython/lab +> > +> > +> > +> > $__history_id__ +> > $__galaxy_url__ +> > 8080 +> > $__galaxy_url__ +> > < environment_variable name="API_KEY" inject="api_key" /> +> > +> > > #import re +> > export GALAXY_WORKING_DIR=`pwd` && +> > mkdir -p ./jupyter/outputs/ && +> > mkdir -p ./jupyter/data && +> > mkdir -p ./jupyter/notebooks && +> > mkdir -p ./jupyter/notebooks/geo && +> > mkdir -p ./jupyter/notebooks/openeo && +> > mkdir -p ./jupyter/notebooks/sentinelhub && +> > +> > #for $count, $file in enumerate($input): +> > #set $cleaned_name = str($count + 1) + '_' + re.sub('[^\w\-\.\s]', '_', str($file.element_identifier)) +> > ln -sf '$file' './jupyter/data/${cleaned_name}' && +> > #end for +> > +> > ## change into the directory where the notebooks are located +> > cd ./jupyter/ && +> > export HOME=/home/jovyan/ && +> > export PATH=/home/jovyan/.local/bin:\$PATH && +> > +> > #if $mode.mode_select == 'scratch' +> > ## copy all notebooks, workflows and data +> > cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb && +> > jupyter trust ./ipython_galaxy_notebook.ipynb && +> >  cp -r /home/\$NB_USER/geo/* ./notebooks/geo/ && +> >  cp -r /home/\$NB_USER/openeo/* ./notebooks/openeo/ && +> >  cp -r /home/\$NB_USER/sentinelhub/* ./notebooks/sentinelhub/ && +> > +> > +> > ## provide all rights to copied files +> > jupyter lab --allow-root --no-browser && +> > cp ./*.ipynb '$jupyter_notebook' && +> > +> > cd outputs/ && +> > sleep 2 && +> > for file in *; do mv "\$file" "\$file.\${file\#\#*.}"; done +> > #else +> > #set $noteboook_name = re.sub('[^\w\-\.\s]', '_', str($mode.ipynb.element_identifier)) +> > cp '$mode.ipynb' './${noteboook_name}.ipynb' && +> > jupyter trust './${noteboook_name}.ipynb' && +> > #if $mode.run_it +> > jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors ./*.ipynb && +> > #set $noteboook_name = 'ipython_galaxy_notebook' +> > #else +> > jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True && +> > #end if +> > cp './${noteboook_name}.ipynb' '$jupyter_notebook' && +> > +> > cd outputs/ && +> > sleep 2 && +> > for file in *; do mv "\$file" "\$file.\${file\#\#*.}"; done +> > #end if +> > ]]> +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > > help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/> +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > +> > This tool contains sample Jupyter notebooks for the Copernicus Data Space Ecosystem. Notebooks are grouped per kernel: sentinelhub, openeo and geo. To know more https:/github.com/eu-cdse/notebook-samples +> > +> > To have more example notebooks produced by th OpenEO community that you can use in this jupyterlab go there https://github.com/Open-EO/openeo-community-examples/tree/main +> > +> > +> > +> > +> > @Manual{, +> > title = {Copernicus Data Space Ecosystem }, +> > author = {The eu-cdse community}, +> > year = {2023}, +> > note = {https://github.com/eu-cdse} +> > +> > +> > +> > ``` +> > {% endraw %} +> {: .solution} +> +> In order to get your data from your galaxy history into your jupyterlab don't forget to have this kind of line in the executable +> ``` +> #for $count, $file in enumerate($input): +> #set $cleaned_name = str($count + 1) + '_' + re.sub('[^\w\-\.\s]', '_', str($file.element_identifier)) +> ln -sf '$file' './jupyter/data/${cleaned_name}' && +> #end for +> ``` +> AND to get your output in your history data +> +> ``` +> +> +> +> ``` +> Don't forget to change the image path and the citation to fit your project settings. +{: .hands_on} + +
+ # Testing locally You would like to check your GxIT integration in Galaxy but don't have a development server or don't want to disturb your sysadmin at this point? @@ -581,6 +1115,7 @@ Let's check this integration on your machine. You can use a VM if you prefer not > ```xml >
> +> >
> ``` > With these lines, Galaxy will create a new section named "Interactive tools" in the tool panel @@ -617,10 +1152,14 @@ Let's check this integration on your machine. You can use a VM if you prefer not > > > ``` -> Finally, copy your GxIT wrapper to the Interactive Tool directory: +> Finally, copy your GxIT wrapper to the Interactive Tool directory (depending on if you followed the Application or Jupyterlab part of the tuto): > ```sh > cp ~/my_filepath/interactivetool_tabulator.xml ~/GxIT/galaxy/tools/interactive/ > ``` +> OR +> ```sh +> cp ~/my_filepath/interactivetool_copernicus.xml ~/GxIT/galaxy/tools/interactive/ +> ``` {: .hands_on} ## Run Galaxy @@ -685,6 +1224,14 @@ the Galaxy core application directory, and adding the tool to our > > > > > > ``` +> > OR +> > ``` +> > +> >
+> > +> >
+> > +> > ``` > {: .solution} > > 5. Now we just need to restart the Galaxy server to refresh the tool registry @@ -734,6 +1281,20 @@ Have a look in the web interface of your Galaxy instance. You should find the ne > ``` > {% endraw %} > +> OR +> +> {% raw %} +> ```xml +> +> +>
+> +>
+> +> ``` +> {% endraw %} +> +> > 3. Create variables in the following sections of `group_vars/galaxyservers.yml` > > {% raw %} @@ -768,58 +1329,6 @@ The most obvious way to test a tool is simply to run it in the Galaxy UI, straig {: .tip} -# Additional components - -The GxIT that we wrapped in this tutorial was a simple example, and you should now understand what is required to create an Interactive Tool for Galaxy. However, there are a few additional components that can enhance the reliability and user experience of the tool. In addition, more complex applications may require some additional components or workarounds the create the desired experience for the user. - -## Run script -In the case of our `Tabulator` application, the run script is simply the R script that renders our Shiny App. It is quite straightforward to call this from our Galaxy tool XML. However, some web apps might require more elaborate commands to be run. In this situation, there are a number of solutions demonstrated in the `` section of [existing GxITs](https://github.com/galaxyproject/galaxy/tree/dev/tools/interactive): -- [Guacamole Desktop](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_guacamole_desktop.xml): application startup with `startup.sh` -- [HiCBrowser](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_hicbrowser.xml): application startup with `supervisord` -- [AskOmics](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_askomics.xml): configuration with Python and Bash scripts, followed by `start_all.sh` to run the application. - -## Templated config files -Using the `` section in the tool XML, we can enable complex user configuration for the application by templating a run script or configuration file to be read by the application. In this application, for example, we could use a `` section to template user input into the `app.R` script that runs the application within the Docker container. This could enable the user to customize the layout of the app before launch. - -## Reserved environment variables - -There are a few environment variables -that are accessible in the command section of the tool XML - these can be handy when writing your tool script. -[Check the docs](https://docs.galaxyproject.org/en/latest/dev/schema.html#reserved-variables) for a full reference on the tool XML. - -```sh -$__tool_directory__ -$__root_dir__ -$__user_id__ -$__user_email__ -``` - -It can also be useful to create and inject environment variables into the tool context. This can be acheived using the `` tag in the tool XML. The [RStudio GxIT](https://github.com/galaxyproject/galaxy/blob/b180b7909dc3fe2750fbc8b90214e201eb276794/tools/interactive/interactivetool_rstudio.xml#L12) again provides an example of this: - -```xml - - ${__app__.security.encode_id($jupyter_notebook.history_id)} - ${__app__.config.galaxy_infrastructure_url} - 8080 - $__galaxy_url__ - true - true - - -``` - -## Galaxy history interaction -We have demonstrated how to pass an input file to the Docker container. But what if the application needs to interact with the user's Galaxy history? For example, if the user creates a file within the application. That's where the environment variables created in the tool XML become useful. - -> Access histories in R -> From the [R-Studio GxIT](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_rstudio.xml) we can see that there is [an R library](https://github.com/hexylena/rGalaxyConnector) that allows us to interact with Galaxy histories. -> -> "The convenience functions `gx_put()` and `gx_get()` are available to you to interact with your current Galaxy history. You can save your workspace with `gx_save()`" -> -> Under the hood, this library uses [galaxy_ie_helpers](https://github.com/bgruening/galaxy_ie_helpers) - a Python interface to Galaxy histories written with [BioBlend](https://github.com/galaxyproject/bioblend). You could also use BioBlend directly (or even the Galaxy REST API) if your GxIT requires a more flexible interface than these wrappers provide. -> -{: .tip} - ## Self-destruct script Unlike regular tools that exit after the execution of the underlying command is complete, web applications will run indefinitely until terminated. With Galaxy's legacy "Interactive Environments", this used to result in "zombie" containers hanging around and clogging up the Galaxy server. You may notice a `terminate.sh` script in some older GxITs as a workaround to this problem, but the new GxIT architecture handles container termination for you. This script is no longer required nor recommended. From ca8562d432af262a823641059fa0791a4270e721 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 10:28:46 +0100 Subject: [PATCH 02/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index ab18cbd323a127..8dfdb5a999a856 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -157,7 +157,7 @@ cycle. {: .comment} -{% include _includes/cyoa-choices.html option1="Application" option2="Jupyterlab" default="Application" text="Do you want to build a desktop application or a jupyterlab tool ?" %} +{% include _includes/cyoa-choices.html option1="Application" option2="JupyterLab" default="Application" text="Do you want to build a desktop application or a JupyterLab tool ?" %}
From 2623f67f1dc68c561820451052fc4c0def8ea18b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:05:40 +0100 Subject: [PATCH 03/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 8dfdb5a999a856..504348f990acb3 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -587,7 +587,7 @@ We have demonstrated how to pass an input file to the Docker container. But what
-# The jupyterlab +# The JupyterLab The jupyterlab environement that we will wrap in this tutorial is a simple jupyterlab tool which allows the user to upload data in an jupyter environment, manipulate notebooks, and download From 07b400f5944891a4fbee9f84af5634e855ca1c44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:08:01 +0100 Subject: [PATCH 04/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 504348f990acb3..871ed83269bc8a 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -535,12 +535,15 @@ our new Docker container as a Galaxy tool. The GxIT that we wrapped in this tutorial was a simple example, and you should now understand what is required to create an Interactive Tool for Galaxy. However, there are a few additional components that can enhance the reliability and user experience of the tool. In addition, more complex applications may require some additional components or workarounds the create the desired experience for the user. ## Run script -In the case of our `Tabulator` application, the run script is simply the R script that renders our Shiny App. It is quite straightforward to call this from our Galaxy tool XML. However, some web apps might require more elaborate commands to be run. In this situation, there are a number of solutions demonstrated in the `` section of [existing GxITs](https://github.com/galaxyproject/galaxy/tree/dev/tools/interactive): + +In the case of our `Tabulator` application, the run script is simply the R script that renders our Shiny App. It is quite straightforward to call this from our Galaxy tool XML. +However, some web apps might require more elaborate commands to be run. In this situation, there are several solutions demonstrated in the `` section of [existing GxITs](https://github.com/galaxyproject/galaxy/tree/dev/tools/interactive): - [Guacamole Desktop](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_guacamole_desktop.xml): application startup with `startup.sh` - [HiCBrowser](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_hicbrowser.xml): application startup with `supervisord` - [AskOmics](https://github.com/galaxyproject/galaxy/blob/dev/tools/interactive/interactivetool_askomics.xml): configuration with Python and Bash scripts, followed by `start_all.sh` to run the application. ## Templated config files + Using the `` section in the tool XML, we can enable complex user configuration for the application by templating a run script or configuration file to be read by the application. In this application, for example, we could use a `` section to template user input into the `app.R` script that runs the application within the Docker container. This could enable the user to customize the layout of the app before launch. ## Reserved environment variables From e1a18a3669b046f88a1eda799eeb055a42af81fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:08:12 +0100 Subject: [PATCH 05/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 871ed83269bc8a..8e7522c4c32080 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -559,7 +559,7 @@ $__user_id__ $__user_email__ ``` -It can also be useful to create and inject environment variables into the tool context. This can be acheived using the `` tag in the tool XML. The [RStudio GxIT](https://github.com/galaxyproject/galaxy/blob/b180b7909dc3fe2750fbc8b90214e201eb276794/tools/interactive/interactivetool_rstudio.xml#L12) again provides an example of this: +It can also be useful to create and inject environment variables into the tool context. This can be achieved using the `` tag in the tool XML. The [RStudio GxIT](https://github.com/galaxyproject/galaxy/blob/b180b7909dc3fe2750fbc8b90214e201eb276794/tools/interactive/interactivetool_rstudio.xml#L12) again provides an example of this: ```xml From 860c662b6538eb475e0125faa9ab16563b69a4fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:08:30 +0100 Subject: [PATCH 06/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 1 + 1 file changed, 1 insertion(+) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 8e7522c4c32080..730545f1d3219f 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -574,6 +574,7 @@ It can also be useful to create and inject environment variables into the tool c ``` ## Galaxy history interaction + We have demonstrated how to pass an input file to the Docker container. But what if the application needs to interact with the user's Galaxy history? For example, if the user creates a file within the application. That's where the environment variables created in the tool XML become useful. > Access histories in R From 9aebcce092fc613e4022ef20035fdadafd6cc044 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:08:51 +0100 Subject: [PATCH 07/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 730545f1d3219f..7899e8cc30c268 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -589,7 +589,7 @@ We have demonstrated how to pass an input file to the Docker container. But what
-
+
# The JupyterLab From c4fd194d285b50baff6f484acb0daa2452b2760d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:09:14 +0100 Subject: [PATCH 08/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 7899e8cc30c268..149be5dd1edb07 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -593,12 +593,12 @@ We have demonstrated how to pass an input file to the Docker container. But what # The JupyterLab -The jupyterlab environement that we will wrap in this tutorial is a simple jupyterlab tool which -allows the user to upload data in an jupyter environment, manipulate notebooks, and download +The JupyterLab environment that we will wrap in this tutorial is a simple JupyterLab tool which +allows the user to upload data in a Jupyter environment, manipulate notebooks, and download outputs. -Our example jupyterlab can already be found [online](https://github.com/usegalaxy-eu/docker-copernicus-notebooks) -But you can also check an other implementation of [jupyterlabs](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile). +Our example JupyterLab can already be found [online](https://github.com/usegalaxy-eu/docker-copernicus-notebooks) +But you can also check another implementation of [JupyterLabs](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile). In the following sections, we will study how it can be built into a GxIT. From 01f36dbb01482213efac111092cb919b8bb47f4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:09:27 +0100 Subject: [PATCH 09/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 149be5dd1edb07..81494669e17f34 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -604,7 +604,7 @@ In the following sections, we will study how it can be built into a GxIT. > > -> First, let's clone the repository to take a quick look at a basic implementation of a jupyterlab. +> First, let's clone the repository to take a quick look at a basic implementation of a JupyterLab. > > ```console > $ git clone https://github.com/bgruening/docker-jupyter-notebook.git From 735a00414d65ae8dd35ac7dc36f92f12bfa2f6e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:09:44 +0100 Subject: [PATCH 10/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 81494669e17f34..49ce98639c470c 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -619,7 +619,7 @@ In the following sections, we will study how it can be built into a GxIT. > ├── . > └── startup.sh > ``` -> You'll find a Dockerfile, startup.sh, and a README that will describe how the dockerfile here for an Gxit works. We encourage you to read thi README. +> You'll find a Dockerfile, startup.sh, and a README that will describe how the Dockerfile here for a GxIT works. We encourage you to read this README. > {: .hands_on} From 1212094e7c48b3bf6a8399623bc4c91906359c61 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:10:04 +0100 Subject: [PATCH 11/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 49ce98639c470c..4917422fa68cd3 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -625,7 +625,7 @@ In the following sections, we will study how it can be built into a GxIT. ## The Dockerfile -If you need some help to start your Dockerfile you can always some inspiration from the previous interactve tools build in Galaxy. Go check some of the Dockerfiles for instance the one for the [Copernicus data sapce ecosystem jupyterlab](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) or for a basic [jupyterlab here](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile) +If you need some help to start your Dockerfile you can always some inspiration from the previous interactive tools built in Galaxy. Go check some of the Dockerfiles, for instance, the one for the [Copernicus data space ecosystem JupyterLab](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) or for a basic [JupyterLab here](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile) > A brief primer on Docker > Docker allows an entire application context to be containerized. A typical web application consists of an operating system, installed dependancies, web server configuration, database configuration and, of course, the codebase of the software itself. A Docker container can encapsulate all of these components in a single "image", which can be run on any machine with Docker installed. From 1c53ca6769d6b6614b4c192602fa8f6596e09900 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:10:19 +0100 Subject: [PATCH 12/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 4917422fa68cd3..32ef48be69d2a9 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -657,7 +657,7 @@ If you need some help to start your Dockerfile you can always some inspiration f {: .tip} -Let's check out [the Dockerfile](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) that we'll use to containerize our Jupyterlab. +Let's check out [the Dockerfile](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) that we'll use to containerize our JupyterLab. This container recipe can be used to build a Docker image which can be pushed to a container registry in the cloud, ready for consumption by our Galaxy instance: From 782d5f60a05fa0772d73393e4561f206b8413606 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:10:47 +0100 Subject: [PATCH 13/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 32ef48be69d2a9..3ca372cf007d7f 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -698,7 +698,7 @@ RUN conda config --add channels conda-forge && \ ansible-kernel \ bioblend galaxy-ie-helpers \ ``` -With those packages installed you have the bases to have a functionnal environement in your jupyterlab AND be able to link your jupyterlab to the Galaxy history with the pacakage `bioblend galaxy-ie-helpers`. +With those packages installed, you have the bases to have a functional environment in your JupyterLab AND be able to link your JupyterLab to the Galaxy history with the package `bioblend galaxy-ie-helpers`. Then you can add the package specific to the environement you want to have in you jupyterlab for instance From 7336110e71c1857b224500de1f2c5a2199575af7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:11:03 +0100 Subject: [PATCH 14/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 3ca372cf007d7f..05a99f88cfc6d9 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -720,7 +720,7 @@ Then you can add the package specific to the environement you want to have in yo ``` -Then, you can add some configurations to have some configuration and a welcome notebook by default (this generic to all jupyterlabs gxit) +Then, you can add some configurations to have some configuration and a welcome notebook by default (this is generic to all JupyterLab GxITs) ``` ADD ./startup.sh /startup.sh From 994d46116ec4879732883586101cb9e794a7154e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:11:12 +0100 Subject: [PATCH 15/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 05a99f88cfc6d9..0f52e7fb1e8a91 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -741,7 +741,7 @@ ADD ./default_notebook.ipynb /home/$NB_USER/notebook.ipynb ``` -You can also add your own set of notebooks to guide the user like that : +You can also add your own set of notebooks to guide the user like that: ``` # Download notebooks From e276f94bd6ded85b806b7230fff9086a295eba05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:12:46 +0100 Subject: [PATCH 16/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 0f52e7fb1e8a91..4895b2c08f24e7 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -755,7 +755,7 @@ RUN cd /home/$NB_USER/ && \ rm -r /home/$NB_USER/notebook-samples-main ``` -Finally, some general variables of environment : +Finally, some general variables of environment: ``` # ENV variables to replace conf file From d493c4c9474226cfddd695d877131d0145f9e04b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:13:19 +0100 Subject: [PATCH 17/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 4895b2c08f24e7..83583c2a55025e 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -700,7 +700,7 @@ RUN conda config --add channels conda-forge && \ ``` With those packages installed, you have the bases to have a functional environment in your JupyterLab AND be able to link your JupyterLab to the Galaxy history with the package `bioblend galaxy-ie-helpers`. -Then you can add the package specific to the environement you want to have in you jupyterlab for instance +Then you can add the package specific to the environment you want to have in your JupyterLab for instance ``` # specific sentinel, openeo packages From 234efab2e36a9da141e97503c7818f824f85b3c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:26:50 +0100 Subject: [PATCH 18/25] Update topics/dev/tutorials/interactive-tools/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 83583c2a55025e..f3258100d8f05d 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -819,7 +819,7 @@ If you are lucky, you might find an available Docker image for the application y ## Test the image -Before we go pushing our container to the cloud, we should give it a local test run to ensure that it's working correctly on our development machine. Have a play and see how our little web app works! +Before we push our container to the cloud, we should give it a local test run to ensure that it's working correctly on our development machine. Have a play and see how our little web app `works!` > > ```sh From 3bd14bf9a64544e18f1617f8b4572ac1dc05c53e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 11:50:12 +0100 Subject: [PATCH 19/25] change sentencen tweaking --- topics/dev/tutorials/interactive-tools/tutorial.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index f3258100d8f05d..c9228e6ff47628 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -340,7 +340,7 @@ next to your Dockerfile. > {: .tip} {: .hands_on} -If you are lucky, you might find an available Docker image for the application you are trying to wrap. However, existing Docker images often require some "tweaking" before they will work as a GxIT. Some example configuration changes are: +If you are lucky, you might find an available Docker image for the application you are trying to wrap. Some configuration changes can be needed such as: 1. Expose the correct port. The application, Docker and tool XML ports must be aligned! 2. Log output to an external file - useful for debugging. @@ -809,7 +809,8 @@ In any case don't forget to have all the files shown when we cloned this [reposi > {: .tip} {: .hands_on} -If you are lucky, you might find an available Docker image for the application you are trying to wrap. However, existing Docker images often require some "tweaking" before they will work as a GxIT. Some example configuration changes are: +If you are lucky, you might find an available Docker image for the application you are trying to wrap. Some configuration changes can be needed such as: + 1. Expose the correct port. The application, Docker and tool XML ports must be aligned! 2. Log output to an external file - useful for debugging. From 76ae7623a5447e7dc8c2a5455da31f16d281abaa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 16:04:14 +0100 Subject: [PATCH 20/25] Update topics/dev/tutorials/interactive-tools/tutorial.md Co-authored-by: Anthony Bretaudeau --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index c9228e6ff47628..9c9982b4ccb632 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -207,7 +207,7 @@ These are specific to your container; these are required for an R-Shiny containe ## The Dockerfile -If you need some help to start your Dockerfile you can always some inspiration from the previous interactve tools build in Galaxy. Go check some of the Dockerfiles for instance the one for the application [QGIS](https://github.com/usegalaxy-eu/docker-qgis) or for [ODV](https://github.com/bgruening/docker-odv/tree/main) +If you need some help to start your Dockerfile you can always get some inspiration from the previous interactive tools built in Galaxy. Go check some of the Dockerfiles, for instance the one for the [QGIS](https://github.com/usegalaxy-eu/docker-qgis) application or for [ODV](https://github.com/bgruening/docker-odv/tree/main). > A brief primer on Docker > Docker allows an entire application context to be containerized. A typical web application consists of an operating system, installed dependancies, web server configuration, database configuration and, of course, the codebase of the software itself. A Docker container can encapsulate all of these components in a single "image", which can be run on any machine with Docker installed. From 0a4b0bf7b48e406234114d545de0b848443bd420 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 16:04:37 +0100 Subject: [PATCH 21/25] Update topics/dev/tutorials/interactive-tools/tutorial.md Co-authored-by: Anthony Bretaudeau --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 9c9982b4ccb632..f5eedd965da7d9 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -597,7 +597,7 @@ The JupyterLab environment that we will wrap in this tutorial is a simple Jupyte allows the user to upload data in a Jupyter environment, manipulate notebooks, and download outputs. -Our example JupyterLab can already be found [online](https://github.com/usegalaxy-eu/docker-copernicus-notebooks) +Our example JupyterLab can already be found [online](https://github.com/usegalaxy-eu/docker-copernicus-notebooks) . But you can also check another implementation of [JupyterLabs](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile). In the following sections, we will study how it can be built into a GxIT. From efbd9acd39b799d1d77b0e7f90e02211985918b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 16:04:51 +0100 Subject: [PATCH 22/25] Update topics/dev/tutorials/interactive-tools/tutorial.md Co-authored-by: Anthony Bretaudeau --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index f5eedd965da7d9..656a76ce14e33c 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -625,7 +625,7 @@ In the following sections, we will study how it can be built into a GxIT. ## The Dockerfile -If you need some help to start your Dockerfile you can always some inspiration from the previous interactive tools built in Galaxy. Go check some of the Dockerfiles, for instance, the one for the [Copernicus data space ecosystem JupyterLab](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) or for a basic [JupyterLab here](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile) +If you need some help to start your Dockerfile you can always get some inspiration from the previous interactive tools built in Galaxy. Go check some of the Dockerfiles, for instance, the one for the [Copernicus data space ecosystem JupyterLab](https://github.com/usegalaxy-eu/docker-copernicus-notebooks/blob/main/Dockerfile) or for a basic [JupyterLab here](https://github.com/bgruening/docker-jupyter-notebook/blob/master/Dockerfile). > A brief primer on Docker > Docker allows an entire application context to be containerized. A typical web application consists of an operating system, installed dependancies, web server configuration, database configuration and, of course, the codebase of the software itself. A Docker container can encapsulate all of these components in a single "image", which can be run on any machine with Docker installed. From 6c0981c1bb34f924122a535d63e36aa8ebef304e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 16:10:30 +0100 Subject: [PATCH 23/25] Update topics/dev/tutorials/interactive-tools/tutorial.md Co-authored-by: Anthony Bretaudeau --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 656a76ce14e33c..6605c30f17ebc0 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -720,7 +720,7 @@ Then you can add the package specific to the environment you want to have in you ``` -Then, you can add some configurations to have some configuration and a welcome notebook by default (this is generic to all JupyterLab GxITs) +Then, you can add some configurations to have some configuration and a welcome notebook by default (this is generic to all JupyterLab GxITs). ``` ADD ./startup.sh /startup.sh From 9f0e042af4d5aa8ed1d3318026afb3e56e0a5fc9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 16:10:41 +0100 Subject: [PATCH 24/25] Update topics/dev/tutorials/interactive-tools/tutorial.md Co-authored-by: Anthony Bretaudeau --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 6605c30f17ebc0..4f860518f282fe 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -779,7 +779,7 @@ CMD /startup.sh ``` -And with all this your Dockerfile is ready +And with all this your Dockerfile is ready. You now need to publish this image o a public repository. Anyone can use this Dockerfile to rebuild the image if necessary. From 05cfe43b1f05accc817e739a7224f08c56748c8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Tue, 3 Dec 2024 16:10:57 +0100 Subject: [PATCH 25/25] Update topics/dev/tutorials/interactive-tools/tutorial.md Co-authored-by: Anthony Bretaudeau --- topics/dev/tutorials/interactive-tools/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/dev/tutorials/interactive-tools/tutorial.md b/topics/dev/tutorials/interactive-tools/tutorial.md index 4f860518f282fe..3b8776ac541a92 100644 --- a/topics/dev/tutorials/interactive-tools/tutorial.md +++ b/topics/dev/tutorials/interactive-tools/tutorial.md @@ -781,7 +781,7 @@ CMD /startup.sh And with all this your Dockerfile is ready. -You now need to publish this image o a public repository. +You now need to publish this image on a public repository. Anyone can use this Dockerfile to rebuild the image if necessary. In any case don't forget to have all the files shown when we cloned this [repository](https://github.com/bgruening/docker-jupyter-notebook/tree/master) next to your Dockerfile.