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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
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1 # Galaxy tool Util for GAMA model
2
3 # Desc
4
5 The **gama_desc.xml** Galaxy tool provides some utils for Gama models :
6 it produces a **description JSON data** of a **GAML model file**.
7
8 The **gama_desc.xml** Galaxy tool result can help to define inputs of the
9 **gama_legacy_gen** Galaxy tool
10 (see [more](./../../GAMA_HEADLESS_LEGACY/galaxy-tools/README.md)).
11
12 The **gama_desc.xml** Galaxy tool relies on a container providing **python3**
13 (only required).
14
15 # Galaxy tool gama_desc.xml
16
17 - **Inputs** :
18
19 - model_gaml
20
21 - **Outputs** :
22
23 - desc_json : information about the GAML model file
24 (names of the GAML model experiments of 'type': 'gui' ...)
25
26 - Note : **desc_json** (cf **names of experiments of 'type': 'gui'**) can
27 be useful to identify and choose the **experiment_name** input value of
28 the **gama_legacy_gen** Galaxy tool
29 (see [more](./../../GAMA_HEADLESS_LEGACY/galaxy-tools/README.md)).
30
31 # Local run by 'planemo serve'
32
33 **Installs** :
34
35 - Install Singularity : singularity version 3.8.5
36
37 - Install Galaxy code :
38 ```
39 cd ~/DEVS
40 git clone https://github.com/galaxyproject/galaxy.git
41 ```
42
43 Note : Galaxy requiring at least singularity 3.7
44 (cf singularity exec : --no-mount option)
45
46 - Install Planemo into a Python virtualenv :
47 ```
48 pip3 install --upgrade pip wheel setuptools virtualenv
49
50 mkdir -p _fab
51 cd _fab
52
53 python3 -m venv _venv_planemo
54 source _venv_planemo/bin/activate
55
56 python3 -m pip install planemo
57 ```
58
59 **Use** :
60
61 ```
62 source _fab/_venv_planemo/bin/activate
63 ```
64
65 - Survey :
66 ```
67 htop
68 ```
69
70 - Check tool syntax :
71 ```
72 planemo lint --report_level all --fail_level error gama_desc.xml
73 ```
74
75 - Run tool :
76 ```
77 make serveGAMA_DESC
78 ```
79
80 => http://127.0.0.1:9090
81
82 Use this Galaxy tool
83 ====================
84
85 See [use-tools](../use-tools).
86