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).
+