LinhHo/module_area_potentials

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Overview

Latest release: None, Last update: 2025-06-30

Linting: linting: failed, Formatting: formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.

When using Mamba, run

mamba create -c conda-forge -c bioconda --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

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/LinhHo/module_area_potentials . --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

  1Using workflow specific profile workflow/profiles/default for setting default command line arguments.
  2Lints for rule download_cutout_slope (line 3, /tmp/tmpz157ya54/workflow/rules/automatic.smk):
  3    * No log directive defined:
  4      Without a log directive, all output will be printed to the terminal. In
  5      distributed environments, this means that errors are harder to discover.
  6      In local environments, output of concurrent jobs will be mixed and become
  7      unreadable.
  8      Also see:
  9      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 10
 11Lints for rule download_cutout_bathymetry (line 15, /tmp/tmpz157ya54/workflow/rules/automatic.smk):
 12    * No log directive defined:
 13      Without a log directive, all output will be printed to the terminal. In
 14      distributed environments, this means that errors are harder to discover.
 15      In local environments, output of concurrent jobs will be mixed and become
 16      unreadable.
 17      Also see:
 18      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 19
 20Lints for rule download_wdpa (line 27, /tmp/tmpz157ya54/workflow/rules/automatic.smk):
 21    * No log directive defined:
 22      Without a log directive, all output will be printed to the terminal. In
 23      distributed environments, this means that errors are harder to discover.
 24      In local environments, output of concurrent jobs will be mixed and become
 25      unreadable.
 26      Also see:
 27      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 28
 29Lints for rule unzip_wdpa (line 39, /tmp/tmpz157ya54/workflow/rules/automatic.smk):
 30    * No log directive defined:
 31      Without a log directive, all output will be printed to the terminal. In
 32      distributed environments, this means that errors are harder to discover.
 33      In local environments, output of concurrent jobs will be mixed and become
 34      unreadable.
 35      Also see:
 36      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 37
 38Lints for rule download_globcover (line 58, /tmp/tmpz157ya54/workflow/rules/automatic.smk):
 39    * No log directive defined:
 40      Without a log directive, all output will be printed to the terminal. In
 41      distributed environments, this means that errors are harder to discover.
 42      In local environments, output of concurrent jobs will be mixed and become
 43      unreadable.
 44      Also see:
 45      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 46
 47Lints for rule download_ghsl (line 95, /tmp/tmpz157ya54/workflow/rules/automatic.smk):
 48    * No log directive defined:
 49      Without a log directive, all output will be printed to the terminal. In
 50      distributed environments, this means that errors are harder to discover.
 51      In local environments, output of concurrent jobs will be mixed and become
 52      unreadable.
 53      Also see:
 54      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 55
 56Lints for rule unzip_ghsl (line 107, /tmp/tmpz157ya54/workflow/rules/automatic.smk):
 57    * No log directive defined:
 58      Without a log directive, all output will be printed to the terminal. In
 59      distributed environments, this means that errors are harder to discover.
 60      In local environments, output of concurrent jobs will be mixed and become
 61      unreadable.
 62      Also see:
 63      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 64
 65Lints for rule cutout_landcover (line 3, /tmp/tmpz157ya54/workflow/rules/prepare.smk):
 66    * No log directive defined:
 67      Without a log directive, all output will be printed to the terminal. In
 68      distributed environments, this means that errors are harder to discover.
 69      In local environments, output of concurrent jobs will be mixed and become
 70      unreadable.
 71      Also see:
 72      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 73
 74Lints for rule cutout_landseamask (line 18, /tmp/tmpz157ya54/workflow/rules/prepare.smk):
 75    * No log directive defined:
 76      Without a log directive, all output will be printed to the terminal. In
 77      distributed environments, this means that errors are harder to discover.
 78      In local environments, output of concurrent jobs will be mixed and become
 79      unreadable.
 80      Also see:
 81      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 82
 83Lints for rule cutout_settlement (line 33, /tmp/tmpz157ya54/workflow/rules/prepare.smk):
 84    * No log directive defined:
 85      Without a log directive, all output will be printed to the terminal. In
 86      distributed environments, this means that errors are harder to discover.
 87      In local environments, output of concurrent jobs will be mixed and become
 88      unreadable.
 89      Also see:
 90      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 91
 92Lints for rule slope_too_steep (line 4, /tmp/tmpz157ya54/workflow/rules/process.smk):
 93    * No log directive defined:
 94      Without a log directive, all output will be printed to the terminal. In
 95      distributed environments, this means that errors are harder to discover.
 96      In local environments, output of concurrent jobs will be mixed and become
 97      unreadable.
 98      Also see:
 99      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
100
101Lints for rule suitable_land_cover (line 19, /tmp/tmpz157ya54/workflow/rules/process.smk):
102    * No log directive defined:
103      Without a log directive, all output will be printed to the terminal. In
104      distributed environments, this means that errors are harder to discover.
105      In local environments, output of concurrent jobs will be mixed and become
106      unreadable.
107      Also see:
108      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
109
110Lints for rule resample_same_resolution (line 34, /tmp/tmpz157ya54/workflow/rules/process.smk):
111    * No log directive defined:
112      Without a log directive, all output will be printed to the terminal. In
113      distributed environments, this means that errors are harder to discover.
114      In local environments, output of concurrent jobs will be mixed and become
115      unreadable.
116      Also see:
117      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
118
119Lints for rule technical_mask (line 59, /tmp/tmpz157ya54/workflow/rules/process.smk):
120    * No log directive defined:
121      Without a log directive, all output will be printed to the terminal. In
122      distributed environments, this means that errors are harder to discover.
123      In local environments, output of concurrent jobs will be mixed and become
124      unreadable.
125      Also see:
126      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
127
128Lints for rule area_potential (line 78, /tmp/tmpz157ya54/workflow/rules/process.smk):
129    * No log directive defined:
130      Without a log directive, all output will be printed to the terminal. In
131      distributed environments, this means that errors are harder to discover.
132      In local environments, output of concurrent jobs will be mixed and become
133      unreadable.
134      Also see:
135      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files

Formatting results

 1[DEBUG] 
 2[DEBUG] 
 3[DEBUG] In file "/tmp/tmpz157ya54/workflow/rules/process.smk":  Formatted content is different from original
 4[DEBUG] 
 5[DEBUG] In file "/tmp/tmpz157ya54/workflow/rules/prepare.smk":  Formatted content is different from original
 6[DEBUG] 
 7[DEBUG] In file "/tmp/tmpz157ya54/workflow/rules/automatic.smk":  Formatted content is different from original
 8[INFO] 3 file(s) would be changed 😬
 9[INFO] 1 file(s) would be left unchanged 🎉
10
11snakefmt version: 0.11.0