modelblocks-org/module_euro_industry

None

Overview

Latest release: None, Last update: 2026-10-15

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=modelblocks-org/module_euro_industry

Quality control: linting: failed formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/modelblocks-org/module_euro_industry . --tag None

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

Configuration

This workflow is part of the clio project. Please consult our documentation for more details. Other useful resources are:

  • INTERFACE.yaml: user input files (placed in resources/user) and module output files (placed in results).

  • workflow/internal/config.schema.yaml: general configuration options.

  • tests/integration/: a simple example of how to use this module.

Linting and formatting

Linting results
  1/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/google/auth/transport/grpc.py:43: FutureWarning: grpcio < 1.83.0 does not support Post-Quantum Cryptography (PQC). Support for non-PQC environments is deprecated. In April 2027, google-auth will raise its minimum requirements to enforce grpcio >= 1.83.0. For more details on Google Cloud's post-quantum security migration, visit: https://cloud.google.com/security/resources/post-quantum-cryptography
  2  warnings.warn(
  3Using workflow specific profile workflow/profiles/default for setting default command line arguments.
  4Lints for rule download_eurostat (line 22, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
  5    * Specify a conda environment or container for each rule.:
  6      This way, the used software for each specific step is documented, and the
  7      workflow can be executed on any machine without prerequisites.
  8      Also see:
  9      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 10      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 11
 12Lints for rule download_jrc_idees (line 35, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 13    * Specify a conda environment or container for each rule.:
 14      This way, the used software for each specific step is documented, and the
 15      workflow can be executed on any machine without prerequisites.
 16      Also see:
 17      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 18      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 19
 20Lints for rule download_hotmaps (line 48, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 21    * Specify a conda environment or container for each rule.:
 22      This way, the used software for each specific step is documented, and the
 23      workflow can be executed on any machine without prerequisites.
 24      Also see:
 25      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 26      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 27
 28Lints for rule download_ammonia_usgs (line 61, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 29    * Specify a conda environment or container for each rule.:
 30      This way, the used software for each specific step is documented, and the
 31      workflow can be executed on any machine without prerequisites.
 32      Also see:
 33      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 34      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 35
 36Lints for rule download_ammonia_plants (line 74, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 37    * Specify a conda environment or container for each rule.:
 38      This way, the used software for each specific step is documented, and the
 39      workflow can be executed on any machine without prerequisites.
 40      Also see:
 41      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 42      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 43
 44Lints for rule download_GEM_SPT (line 87, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 45    * Specify a conda environment or container for each rule.:
 46      This way, the used software for each specific step is documented, and the
 47      workflow can be executed on any machine without prerequisites.
 48      Also see:
 49      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 50      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 51
 52Lints for rule download_cement_non_eu (line 100, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 53    * Specify a conda environment or container for each rule.:
 54      This way, the used software for each specific step is documented, and the
 55      workflow can be executed on any machine without prerequisites.
 56      Also see:
 57      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 58      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 59
 60Lints for rule download_refineries_non_eu (line 113, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 61    * Specify a conda environment or container for each rule.:
 62      This way, the used software for each specific step is documented, and the
 63      workflow can be executed on any machine without prerequisites.
 64      Also see:
 65      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 66      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 67
 68Lints for rule download_CHE_industry (line 126, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 69    * Specify a conda environment or container for each rule.:
 70      This way, the used software for each specific step is documented, and the
 71      workflow can be executed on any machine without prerequisites.
 72      Also see:
 73      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 74      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 75
 76Lints for rule unzip_eurostat (line 139, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 77    * Specify a conda environment or container for each rule.:
 78      This way, the used software for each specific step is documented, and the
 79      workflow can be executed on any machine without prerequisites.
 80      Also see:
 81      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 82      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 83
 84Lints for rule unzip_jrc_idees (line 152, /tmp/tmpcxsmkz8u/workflow/rules/automatic.smk):
 85    * Specify a conda environment or container for each rule.:
 86      This way, the used software for each specific step is documented, and the
 87      workflow can be executed on any machine without prerequisites.
 88      Also see:
 89      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 90      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 91
 92Lints for rule prepare_ammonia_production (line 13, /tmp/tmpcxsmkz8u/workflow/rules/prepare.smk):
 93    * Specify a conda environment or container for each rule.:
 94      This way, the used software for each specific step is documented, and the
 95      workflow can be executed on any machine without prerequisites.
 96      Also see:
 97      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 98      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 99
100Lints for rule prepare_coke_transformation (line 29, /tmp/tmpcxsmkz8u/workflow/rules/prepare.smk):
101    * Specify a conda environment or container for each rule.:
102      This way, the used software for each specific step is documented, and the
103      workflow can be executed on any machine without prerequisites.
104      Also see:
105      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
106      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
107
108Lints for rule prepare_current_production (line 48, /tmp/tmpcxsmkz8u/workflow/rules/prepare.smk):
109    * Specify a conda environment or container for each rule.:
110      This way, the used software for each specific step is documented, and the
111      workflow can be executed on any machine without prerequisites.
112      Also see:
113      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
114      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
115
116Lints for rule prepare_current_energy_demand (line 73, /tmp/tmpcxsmkz8u/workflow/rules/prepare.smk):
117    * Specify a conda environment or container for each rule.:
118      This way, the used software for each specific step is documented, and the
119      workflow can be executed on any machine without prerequisites.
120      Also see:
121      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
122      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
123
124Lints for rule project_production (line 4, /tmp/tmpcxsmkz8u/workflow/rules/projections.smk):
125    * Specify a conda environment or container for each rule.:
126      This way, the used software for each specific step is documented, and the
127      workflow can be executed on any machine without prerequisites.
128      Also see:
129      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
130      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
131
132Lints for rule transform_industrial_demand (line 7, /tmp/tmpcxsmkz8u/workflow/rules/transformations.smk):
133    * Specify a conda environment or container for each rule.:
134      This way, the used software for each specific step is documented, and the
135      workflow can be executed on any machine without prerequisites.
136      Also see:
137      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
138      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
139
140Lints for rule plot_results (line 25, /tmp/tmpcxsmkz8u/workflow/rules/visualizations.smk):
141    * Specify a conda environment or container for each rule.:
142      This way, the used software for each specific step is documented, and the
143      workflow can be executed on any machine without prerequisites.
144      Also see:
145      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
146      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
147
148Lints for rule plot_spatial_maps (line 44, /tmp/tmpcxsmkz8u/workflow/rules/visualizations.smk):
149    * Specify a conda environment or container for each rule.:
150      This way, the used software for each specific step is documented, and the
151      workflow can be executed on any machine without prerequisites.
152      Also see:
153      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
154      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
155    * Param output_dir is a prefix of input or output file but hardcoded:
156      If this is meant to represent a file path prefix, it will fail when
157      running workflow in environments without a shared filesystem. Instead,
158      provide a function that infers the appropriate prefix from the input or
159      output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
160      Also see:
161      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
162      https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
163
164Lints for rule build_industrial_distribution_keys (line 19, /tmp/tmpcxsmkz8u/workflow/rules/spatial.smk):
165    * Specify a conda environment or container for each rule.:
166      This way, the used software for each specific step is documented, and the
167      workflow can be executed on any machine without prerequisites.
168      Also see:
169      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
170      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
171
172Lints for rule disaggregate_industrial_energy_demand (line 42, /tmp/tmpcxsmkz8u/workflow/rules/spatial.smk):
173    * Specify a conda environment or container for each rule.:
174      This way, the used software for each specific step is documented, and the
175      workflow can be executed on any machine without prerequisites.
176      Also see:
177      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
178      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
179
180Lints for rule disaggregate_route_production (line 63, /tmp/tmpcxsmkz8u/workflow/rules/spatial.smk):
181    * Specify a conda environment or container for each rule.:
182      This way, the used software for each specific step is documented, and the
183      workflow can be executed on any machine without prerequisites.
184      Also see:
185      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
186      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
Formatting results
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13[DEBUG] 
14[DEBUG] In file "/tmp/tmpcxsmkz8u/workflow/rules/automatic.smk":  Formatted content is different from original
15[INFO] 7 file(s) would be changed 😬
16
17snakefmt version: 0.11.5