WIP: docs(guides): Add new admin guides

.gitignore

@@ -1,2 +1,3 @@
 site/
 _site/
+.venv

Makefile

@@ -40,11 +40,17 @@ i: install
 .PHONY: venv
 venv:
 	@echo "\nCreating a virtual environment ++++++++++++++++++++++++++++++++++++++++++++++++\n"
-	@python -m venv .venv
+	@if command -v python3 >/dev/null 2>&1; then \
+		python3 -m venv .venv; \
+	elif command -v python >/dev/null 2>&1; then \
+		python -m venv .venv; \
+	else \
+		echo "Python interpreter not found" >&2; exit 1; \
+	fi
 	@echo "\nSummary +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
 	@echo "Virtual environment created successfully."
 	@echo "To activate the environment for this shell session, run:"
 	@echo "source .venv/bin/activate"
 
 .PHONY: v
-v: venv
+v: venv

docs/guides/guide-admin/cloudregistry.md

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+## Synopsis
+
+GA4GH Service Registry API implementation for the ELIXIR Cloud.
+
+Service entries comply with the [external service schema](https://github.com/ga4gh-discovery/ga4gh-service-registry/blob/8c45be52940db92c2fa1cd821519c271c22b1c4c/service-registry.yaml#L158) defined in the [GA4GH Service Registry API][ga4gh-service-registry]
+
+Developers can find the API documentation [here](https://cloud-registry.readthedocs.io/en/latest/)
+
+## Installation
+
+You can find a Helm chart in the [GitHub repository](https://github.com/elixir-cloud-aai/cloud-registry/tree/dev/deployment) of Cloud-registry
+
+Follow these instructions
+
+- Install [Helm][helm-install]
+- Clone the [Cloud-registry repository](https://github.com/elixir-cloud-aai/cloud-registry/)
+
+    ```sh
+    git clone https://github.com/elixir-cloud-aai/cloud-registry.git
+    ```
+
+- Browse to `deployment` to find the `Chart.yaml` and the `values.yaml` files
+
+## Usage
+
+First you must create a namespace in Kubernetes in which to deploy Cloud-registry. The
+commands below assume that everything is created in the context of this
+namespace. How the namespace is created depends on the cluster, so we won't
+document it here.
+
+You need to edit the `values.yaml` file 
+
+After this you can deploy Cloud-registry using `helm`:
+
+```bash
+helm install cloud-registry . -f values.yaml
+```
+
+### Updates
+
+If you want to edit any of the Deployments, you can update them with
+`helm` and the `values.yaml` file. Once edited, you can run this command:
+
+```bash
+helm upgrade cloud-registry . -f values.yaml
+```
+
+## Technical details
+
+### MongoDB
+
+The MongoDB database is deployed using:
+
+- `templates/mongo-deploy.yaml`
+
+### Cloud-registry
+
+TRS-Filer is deployed using:
+
+- `templates/cloud-registry-deploy.yaml`
+
+## Destroy
+
+Simply run:
+
+```bash
+helm uninstall cloud-registry
+```
+

docs/guides/guide-admin/cwlwes.md

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+## Synopsis
+
+Microservice implementing the [Global Alliance for Genomics and
+Health][ga4gh] (GA4GH) [Workflow Execution Service][ga4gh-wes] (WES)
+API specification for the execution of workflows written in the [Common
+Workflow Language](https://www.commonwl.org/) (CWL).
+
+cwl-WES is a core service of the [ELIXIR Cloud & AAI
+project][elixir-cloud-aai-github].
+
+## Description
+
+cwl-WES (formerly: WES-ELIXIR) is a Flask/Gunicorn
+application that makes use of [Connexion](https://github.com/ga4gh/workflow-execution-service-schemas) to implement the
+[GA4GH WES OpenAPI specification][ga4gh-wes]. It enables clients/users
+to execute [CWL](https://www.commonwl.org) workflows in the cloud via a [GA4GH Task Execution
+Service][ga4gh-tes] (TES)-compatible execution backend (e.g.,
+[TESK][tesk] or [Funnel][funnel]). Workflows can be sent for execution,
+previous runs can be listed, and the status and run information of individual
+runs can be queried. The service leverages [cwl-tes][res-cwl-tes] to
+interpret [CWL](https://www.commonwl.org) workflows, break them down into individual tasks and
+emit [GA4GH TES][ga4gh-tes]-compatible HTTP requests to a configured
+[TES][ga4gh-tes] instance. Access to endpoints can be configured to require
+JSON Web Token-based access tokens, such as those issued by
+[ELIXIR AAI](https://elixir-europe.org/platforms/compute/aai). Run information is stored in a
+MongoDB database.
+
+Note that development is currently in beta stage.
+Further test deployments can be found at the [ELIXIR Cloud & AAI's resource
+listings](https://github.com/elixir-cloud-aai/elixir-cloud-aai/blob/dev/resources/resources.md).
+
+cwl-WES is developed and maintained by the [ELIXIR Cloud & AAI
+project][elixir-cloud], a multinational effort aimed at establishing and
+implementing [FAIR][fair] research in the Life Sciences.
+
+## Installation
+
+You can find a Helm chart in the [GitHub repository](https://github.com/elixir-cloud-aai/cwl-wes/tree/dev/deployment) of CWL-WES
+
+Follow these instructions
+
+- Install [Helm][helm-install]
+- Clone the [CWL-WES repository](https://github.com/elixir-cloud-aai/cwl-wes/)
+
+    ```sh
+    git clone https://github.com/elixir-cloud-aai/cwl-wes.git
+    ```
+
+- Browse to `deployment` to find the `Chart.yaml` and the `values.yaml` files
+
+## Usage
+
+First you must create a namespace in Kubernetes in which to deploy CWL-WES. The
+commands below assume that everything is created in the context of this
+namespace. How the namespace is created depends on the cluster, so we won't
+document it here.
+
+You need to edit the `values.yaml` file 
+
+After this you can deploy CWL-WES using `helm`:
+
+```bash
+helm install CWL-WES . -f values.yaml
+```
+
+### Updates
+
+If you want to edit any of the Deployments, you can update them with
+`helm` and the `values.yaml` file. Once edited, you can run this command:
+
+```bash
+helm upgrade CWL-WES . -f values.yaml
+```
+
+## Technical details
+
+### MongoDB
+
+The MongoDB database is deployed using:
+
+- `templates/mongodb-deployment.yaml`
+
+### RabbitMQ
+
+The message broker RabbitMQ that allows the app to communicate with the
+worker is deployed using:
+
+- `templates/rabbitmq/rabbitmq-deployment.yaml`
+
+### CWL-WES
+
+CWL-WES consists of a Flask server and a Celery worker.
+There are deployed using:
+
+- `templates/wes-deployment.yaml`
+- `templates/celery-deployment.yaml`
+
+## Destroy
+
+Simply run:
+
+```bash
+helm uninstall cwl-wes
+```
+

docs/guides/guide-admin/drsfiler.md

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+## Synopsis
+
+Microservice implementing the [Global Alliance for Genomics and
+Health (GA4GH)][ga4gh] [Data Repository Service][ga4gh-drs] (DRS)
+API specification.
+
+## Installation
+
+You can find a Helm chart in the [GitHub repository](https://github.com/elixir-cloud-aai/drs-filer/tree/dev/deployment) of DRS-Filer
+
+Follow these instructions
+
+- Install [Helm][helm-install]
+- Clone the [DRS-Filer repository](https://github.com/elixir-cloud-aai/drs-filer/)
+
+    ```sh
+    git clone https://github.com/elixir-cloud-aai/drs-filer.git
+    ```
+
+- Browse to `deployment` to find the `Chart.yaml` and the `values.yaml` files
+
+## Usage
+
+First you must create a namespace in Kubernetes in which to deploy DRS-Filer. The
+commands below assume that everything is created in the context of this
+namespace. How the namespace is created depends on the cluster, so we won't
+document it here.
+
+You need to edit the `values.yaml` file 
+
+After this you can deploy DRS-Filer using `helm`:
+
+```bash
+helm install drs-filer . -f values.yaml
+```
+
+### Updates
+
+If you want to edit any of the Deployments, you can update them with
+`helm` and the `values.yaml` file. Once edited, you can run this command:
+
+```bash
+helm upgrade drs-filer . -f values.yaml
+```
+
+## Technical details
+
+### MongoDB
+
+The MongoDB database is deployed using:
+
+- `templates/mongo-deploy.yaml`
+
+### DRS-Filer
+
+DRS-Filer is deployed using:
+
+- `templates/drs-filer-deploy.yaml`
+
+## Destroy
+
+Simply run:
+
+```bash
+helm uninstall drs-filer
+```
+

docs/guides/guide-admin/funnel.md

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+Follow these instructions if you wish to deploy a TES endpoint in front of your
+HPC/HTC cluster (currently tested with [Slurm][slurm] and [OpenPBS][openpbs].
+
+- Make sure the build dependencies `make` and [Go 1.21+][go-install] are
+  installed, `GOPATH` is set and `GOPATH/bin` is added to `PATH`.
+
+    For example, in Ubuntu this can be achieved via:
+
+    ```sh
+    sudo apt update
+    sudo apt install make golang-go
+    export GOPATH=/your/desired/path
+    export PATH=$GOPATH/bin:$PATH
+    go version
+    ```
+
+- Clone the repository:
+
+    ```sh
+    git clone https://github.com/ohsu-comp-bio/funnel.git
+    ```
+
+- Build Funnel:
+
+    ```sh
+    cd funnel
+    make
+    ```
+
+- Test the installation by starting the Funnel server with:
+
+    ```sh
+    funnel server run
+    ```
+
+If all works, Funnel should be ready for deployment on your HPC/HTC.
+
+Alternatively, you can install Funnel via Homebrew:
+
+```sh
+brew tap ohsu-comp-bio/formula
+brew install [email protected]
+```
+
+Source: [Funnel website](https://ohsu-comp-bio.github.io/funnel/)
+
+### Slurm
+
+For the use of Funnel with Slurm, make sure the following conditions are met:
+
+1. The `funnel` binary must be placed in a server with access to Slurm.
+2. A config file must be created and placed on the same server. [This
+   file][funnel-config-slurm] can be used as a starting point.
+3. If we would like to deploy Funnel as a Systemd service,
+   [this file][funnel-config-slurm-service] can be used as a template. Set the
+   correct paths to the `funnel` binary and config file.
+
+If successful, Funnel should be listening on port `8080`.
+
+### OpenPBS
+
+!!! warning "Under construction"
+    More info coming soon...