Mercurial > repos > siwaa > gama_desc
diff README.md @ 0:23b15c0eabff draft default tip
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_DESC/galaxy-tools commit 6b9b95de1fe709f27a28d83797f81e91469edf79-dirty
author | siwaa |
---|---|
date | Mon, 18 Nov 2024 13:57:51 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Nov 18 13:57:51 2024 +0000 @@ -0,0 +1,86 @@ +# Galaxy tool Util for GAMA model + +# Desc + +The **gama_desc.xml** Galaxy tool provides some utils for Gama models : +it produces a **description JSON data** of a **GAML model file**. + +The **gama_desc.xml** Galaxy tool result can help to define inputs of the +**gama_legacy_gen** Galaxy tool +(see [more](./../../GAMA_HEADLESS_LEGACY/galaxy-tools/README.md)). + +The **gama_desc.xml** Galaxy tool relies on a container providing **python3** +(only required). + +# Galaxy tool gama_desc.xml + +- **Inputs** : + + - model_gaml + +- **Outputs** : + + - desc_json : information about the GAML model file + (names of the GAML model experiments of 'type': 'gui' ...) + + - Note : **desc_json** (cf **names of experiments of 'type': 'gui'**) can + be useful to identify and choose the **experiment_name** input value of + the **gama_legacy_gen** Galaxy tool + (see [more](./../../GAMA_HEADLESS_LEGACY/galaxy-tools/README.md)). + +# Local run by 'planemo serve' + +**Installs** : + + - Install Singularity : singularity version 3.8.5 + + - Install Galaxy code : + ``` + cd ~/DEVS + git clone https://github.com/galaxyproject/galaxy.git + ``` + + Note : Galaxy requiring at least singularity 3.7 + (cf singularity exec : --no-mount option) + + - Install Planemo into a Python virtualenv : + ``` + pip3 install --upgrade pip wheel setuptools virtualenv + + mkdir -p _fab + cd _fab + + python3 -m venv _venv_planemo + source _venv_planemo/bin/activate + + python3 -m pip install planemo + ``` + +**Use** : + + ``` + source _fab/_venv_planemo/bin/activate + ``` + + - Survey : + ``` + htop + ``` + + - Check tool syntax : + ``` + planemo lint --report_level all --fail_level error gama_desc.xml + ``` + + - Run tool : + ``` + make serveGAMA_DESC + ``` + + => http://127.0.0.1:9090 + +Use this Galaxy tool +==================== + +See [use-tools](../use-tools). +