caddforge-docs 0.3.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- caddforge_docs/__init__.py +1 -0
- caddforge_docs/cli.py +20 -0
- caddforge_docs/server.py +124 -0
- caddforge_docs/site/404.html +2118 -0
- caddforge_docs/site/assets/_mkdocstrings.css +237 -0
- caddforge_docs/site/assets/images/favicon.png +0 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
- caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
- caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
- caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
- caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
- caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
- caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
- caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
- caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
- caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
- caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
- caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
- caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
- caddforge_docs/site/core/cli/index.html +2446 -0
- caddforge_docs/site/core/concepts/index.html +2340 -0
- caddforge_docs/site/core/configuration/index.html +2300 -0
- caddforge_docs/site/core/index.html +2170 -0
- caddforge_docs/site/core/jobs-results/index.html +2315 -0
- caddforge_docs/site/core/plugins/index.html +2200 -0
- caddforge_docs/site/core/slurm/index.html +2562 -0
- caddforge_docs/site/development/ci-publishing/index.html +2345 -0
- caddforge_docs/site/development/contributing/index.html +2311 -0
- caddforge_docs/site/development/documentation/index.html +2380 -0
- caddforge_docs/site/development/index.html +2201 -0
- caddforge_docs/site/development/release-notes/index.html +2504 -0
- caddforge_docs/site/development/release-readiness/index.html +2333 -0
- caddforge_docs/site/development/security/index.html +2181 -0
- caddforge_docs/site/development/tool-authoring/index.html +2435 -0
- caddforge_docs/site/examples/index.html +2465 -0
- caddforge_docs/site/examples/manifest.json +158 -0
- caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
- caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
- caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
- caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
- caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
- caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
- caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
- caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
- caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
- caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
- caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
- caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
- caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
- caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
- caddforge_docs/site/examples/quickstart/index.html +2172 -0
- caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
- caddforge_docs/site/examples/quickstart/run.py +18 -0
- caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
- caddforge_docs/site/examples/quickstart/scores.csv +7 -0
- caddforge_docs/site/examples/quickstart/values.csv +31 -0
- caddforge_docs/site/examples/run_tool.py +40 -0
- caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
- caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
- caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
- caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
- caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
- caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
- caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
- caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
- caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
- caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
- caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
- caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
- caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
- caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
- caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
- caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
- caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
- caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
- caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
- caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
- caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
- caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
- caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
- caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
- caddforge_docs/site/explanation/references/index.html +2218 -0
- caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
- caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
- caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
- caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
- caddforge_docs/site/getting-started/index.html +2200 -0
- caddforge_docs/site/getting-started/installation/index.html +2541 -0
- caddforge_docs/site/gui/index.html +2267 -0
- caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
- caddforge_docs/site/gui/walkthrough/index.html +2181 -0
- caddforge_docs/site/how-to/jobs/index.html +2195 -0
- caddforge_docs/site/how-to/scatter/index.html +2193 -0
- caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
- caddforge_docs/site/index.html +2359 -0
- caddforge_docs/site/objects.inv +0 -0
- caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
- caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
- caddforge_docs/site/pipelines/examples/index.html +3186 -0
- caddforge_docs/site/pipelines/index.html +2164 -0
- caddforge_docs/site/pipelines/specification/index.html +2278 -0
- caddforge_docs/site/plugins/datascience/index.html +2405 -0
- caddforge_docs/site/plugins/descriptors/index.html +2609 -0
- caddforge_docs/site/plugins/docking/index.html +2480 -0
- caddforge_docs/site/plugins/fep/index.html +2508 -0
- caddforge_docs/site/plugins/index.html +2216 -0
- caddforge_docs/site/plugins/md/index.html +3795 -0
- caddforge_docs/site/plugins/ml/index.html +2815 -0
- caddforge_docs/site/plugins/qm/index.html +2309 -0
- caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
- caddforge_docs/site/reference/api/index.html +4414 -0
- caddforge_docs/site/reference/index.html +2166 -0
- caddforge_docs/site/search/search_index.json +1 -0
- caddforge_docs/site/sitemap.xml +191 -0
- caddforge_docs/site/sitemap.xml.gz +0 -0
- caddforge_docs-0.3.0.dist-info/METADATA +158 -0
- caddforge_docs-0.3.0.dist-info/RECORD +152 -0
- caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
- caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
- caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
|
@@ -0,0 +1,2300 @@
|
|
|
1
|
+
|
|
2
|
+
<!doctype html>
|
|
3
|
+
<html lang="en" class="no-js">
|
|
4
|
+
<head>
|
|
5
|
+
|
|
6
|
+
<meta charset="utf-8">
|
|
7
|
+
<meta name="viewport" content="width=device-width,initial-scale=1">
|
|
8
|
+
|
|
9
|
+
<meta name="description" content="Central documentation for the CADDForge CADD toolbox framework.">
|
|
10
|
+
|
|
11
|
+
|
|
12
|
+
|
|
13
|
+
<link rel="canonical" href="https://idorsia.github.io/caddforge-docs/core/configuration/">
|
|
14
|
+
|
|
15
|
+
|
|
16
|
+
<link rel="prev" href="../concepts/">
|
|
17
|
+
|
|
18
|
+
|
|
19
|
+
<link rel="next" href="../cli/">
|
|
20
|
+
|
|
21
|
+
|
|
22
|
+
|
|
23
|
+
|
|
24
|
+
|
|
25
|
+
<link rel="icon" href="../../assets/images/favicon.png">
|
|
26
|
+
<meta name="generator" content="mkdocs-ProperDocs 1.6.7, mkdocs-material-9.7.7">
|
|
27
|
+
|
|
28
|
+
|
|
29
|
+
|
|
30
|
+
<title>Configuration - CADDForge</title>
|
|
31
|
+
|
|
32
|
+
|
|
33
|
+
|
|
34
|
+
<link rel="stylesheet" href="../../assets/stylesheets/main.ec1eaa64.min.css">
|
|
35
|
+
|
|
36
|
+
|
|
37
|
+
<link rel="stylesheet" href="../../assets/stylesheets/palette.ab4e12ef.min.css">
|
|
38
|
+
|
|
39
|
+
|
|
40
|
+
|
|
41
|
+
|
|
42
|
+
|
|
43
|
+
|
|
44
|
+
|
|
45
|
+
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
|
|
50
|
+
<link rel="stylesheet" href="../../assets/_mkdocstrings.css">
|
|
51
|
+
|
|
52
|
+
<script>__md_scope=new URL("../..",location),__md_hash=e=>[...e].reduce(((e,_)=>(e<<5)-e+_.charCodeAt(0)),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
|
|
53
|
+
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
|
|
57
|
+
|
|
58
|
+
</head>
|
|
59
|
+
|
|
60
|
+
|
|
61
|
+
|
|
62
|
+
|
|
63
|
+
|
|
64
|
+
|
|
65
|
+
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
<body dir="ltr" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="teal">
|
|
69
|
+
|
|
70
|
+
|
|
71
|
+
<input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
|
|
72
|
+
<input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
|
|
73
|
+
<label class="md-overlay" for="__drawer"></label>
|
|
74
|
+
<div data-md-component="skip">
|
|
75
|
+
|
|
76
|
+
|
|
77
|
+
<a href="#configuration" class="md-skip">
|
|
78
|
+
Skip to content
|
|
79
|
+
</a>
|
|
80
|
+
|
|
81
|
+
</div>
|
|
82
|
+
<div data-md-component="announce">
|
|
83
|
+
|
|
84
|
+
</div>
|
|
85
|
+
|
|
86
|
+
|
|
87
|
+
|
|
88
|
+
|
|
89
|
+
|
|
90
|
+
|
|
91
|
+
<header class="md-header md-header--shadow" data-md-component="header">
|
|
92
|
+
<nav class="md-header__inner md-grid" aria-label="Header">
|
|
93
|
+
<a href="../.." title="CADDForge" class="md-header__button md-logo" aria-label="CADDForge" data-md-component="logo">
|
|
94
|
+
|
|
95
|
+
|
|
96
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
|
|
97
|
+
|
|
98
|
+
</a>
|
|
99
|
+
<label class="md-header__button md-icon" for="__drawer">
|
|
100
|
+
|
|
101
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z"/></svg>
|
|
102
|
+
</label>
|
|
103
|
+
<div class="md-header__title" data-md-component="header-title">
|
|
104
|
+
<div class="md-header__ellipsis">
|
|
105
|
+
<div class="md-header__topic">
|
|
106
|
+
<span class="md-ellipsis">
|
|
107
|
+
CADDForge
|
|
108
|
+
</span>
|
|
109
|
+
</div>
|
|
110
|
+
<div class="md-header__topic" data-md-component="header-topic">
|
|
111
|
+
<span class="md-ellipsis">
|
|
112
|
+
|
|
113
|
+
Configuration
|
|
114
|
+
|
|
115
|
+
</span>
|
|
116
|
+
</div>
|
|
117
|
+
</div>
|
|
118
|
+
</div>
|
|
119
|
+
|
|
120
|
+
|
|
121
|
+
<form class="md-header__option" data-md-component="palette">
|
|
122
|
+
|
|
123
|
+
|
|
124
|
+
|
|
125
|
+
|
|
126
|
+
<input class="md-option" data-md-color-media="(prefers-color-scheme: light)" data-md-color-scheme="default" data-md-color-primary="blue" data-md-color-accent="teal" aria-label="Switch to dark mode" type="radio" name="__palette" id="__palette_0">
|
|
127
|
+
|
|
128
|
+
<label class="md-header__button md-icon" title="Switch to dark mode" for="__palette_1" hidden>
|
|
129
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="m17.75 4.09-2.53 1.94.91 3.06-2.63-1.81-2.63 1.81.91-3.06-2.53-1.94L12.44 4l1.06-3 1.06 3zm3.5 6.91-1.64 1.25.59 1.98-1.7-1.17-1.7 1.17.59-1.98L15.75 11l2.06-.05L18.5 9l.69 1.95zm-2.28 4.95c.83-.08 1.72 1.1 1.19 1.85-.32.45-.66.87-1.08 1.27C15.17 23 8.84 23 4.94 19.07c-3.91-3.9-3.91-10.24 0-14.14.4-.4.82-.76 1.27-1.08.75-.53 1.93.36 1.85 1.19-.27 2.86.69 5.83 2.89 8.02a9.96 9.96 0 0 0 8.02 2.89m-1.64 2.02a12.08 12.08 0 0 1-7.8-3.47c-2.17-2.19-3.33-5-3.49-7.82-2.81 3.14-2.7 7.96.31 10.98 3.02 3.01 7.84 3.12 10.98.31"/></svg>
|
|
130
|
+
</label>
|
|
131
|
+
|
|
132
|
+
|
|
133
|
+
|
|
134
|
+
|
|
135
|
+
|
|
136
|
+
<input class="md-option" data-md-color-media="(prefers-color-scheme: dark)" data-md-color-scheme="slate" data-md-color-primary="blue" data-md-color-accent="teal" aria-label="Switch to light mode" type="radio" name="__palette" id="__palette_1">
|
|
137
|
+
|
|
138
|
+
<label class="md-header__button md-icon" title="Switch to light mode" for="__palette_0" hidden>
|
|
139
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 7a5 5 0 0 1 5 5 5 5 0 0 1-5 5 5 5 0 0 1-5-5 5 5 0 0 1 5-5m0 2a3 3 0 0 0-3 3 3 3 0 0 0 3 3 3 3 0 0 0 3-3 3 3 0 0 0-3-3m0-7 2.39 3.42C13.65 5.15 12.84 5 12 5s-1.65.15-2.39.42zM3.34 7l4.16-.35A7.2 7.2 0 0 0 5.94 8.5c-.44.74-.69 1.5-.83 2.29zm.02 10 1.76-3.77a7.131 7.131 0 0 0 2.38 4.14zM20.65 7l-1.77 3.79a7.02 7.02 0 0 0-2.38-4.15zm-.01 10-4.14.36c.59-.51 1.12-1.14 1.54-1.86.42-.73.69-1.5.83-2.29zM12 22l-2.41-3.44c.74.27 1.55.44 2.41.44.82 0 1.63-.17 2.37-.44z"/></svg>
|
|
140
|
+
</label>
|
|
141
|
+
|
|
142
|
+
|
|
143
|
+
</form>
|
|
144
|
+
|
|
145
|
+
|
|
146
|
+
|
|
147
|
+
<script>var palette=__md_get("__palette");if(palette&&palette.color){if("(prefers-color-scheme)"===palette.color.media){var media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']");palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent")}for(var[key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script>
|
|
148
|
+
|
|
149
|
+
|
|
150
|
+
|
|
151
|
+
|
|
152
|
+
|
|
153
|
+
<label class="md-header__button md-icon" for="__search">
|
|
154
|
+
|
|
155
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.52 6.52 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5"/></svg>
|
|
156
|
+
</label>
|
|
157
|
+
<div class="md-search" data-md-component="search" role="dialog">
|
|
158
|
+
<label class="md-search__overlay" for="__search"></label>
|
|
159
|
+
<div class="md-search__inner" role="search">
|
|
160
|
+
<form class="md-search__form" name="search">
|
|
161
|
+
<input type="text" class="md-search__input" name="query" aria-label="Search" placeholder="Search" autocapitalize="off" autocorrect="off" autocomplete="off" spellcheck="false" data-md-component="search-query" required>
|
|
162
|
+
<label class="md-search__icon md-icon" for="__search">
|
|
163
|
+
|
|
164
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.52 6.52 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5"/></svg>
|
|
165
|
+
|
|
166
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M20 11v2H8l5.5 5.5-1.42 1.42L4.16 12l7.92-7.92L13.5 5.5 8 11z"/></svg>
|
|
167
|
+
</label>
|
|
168
|
+
<nav class="md-search__options" aria-label="Search">
|
|
169
|
+
|
|
170
|
+
<button type="reset" class="md-search__icon md-icon" title="Clear" aria-label="Clear" tabindex="-1">
|
|
171
|
+
|
|
172
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"/></svg>
|
|
173
|
+
</button>
|
|
174
|
+
</nav>
|
|
175
|
+
|
|
176
|
+
<div class="md-search__suggest" data-md-component="search-suggest"></div>
|
|
177
|
+
|
|
178
|
+
</form>
|
|
179
|
+
<div class="md-search__output">
|
|
180
|
+
<div class="md-search__scrollwrap" tabindex="0" data-md-scrollfix>
|
|
181
|
+
<div class="md-search-result" data-md-component="search-result">
|
|
182
|
+
<div class="md-search-result__meta">
|
|
183
|
+
Initializing search
|
|
184
|
+
</div>
|
|
185
|
+
<ol class="md-search-result__list" role="presentation"></ol>
|
|
186
|
+
</div>
|
|
187
|
+
</div>
|
|
188
|
+
</div>
|
|
189
|
+
</div>
|
|
190
|
+
</div>
|
|
191
|
+
|
|
192
|
+
|
|
193
|
+
|
|
194
|
+
<div class="md-header__source">
|
|
195
|
+
<a href="https://github.com/idorsia/caddforge-docs" title="Go to repository" class="md-source" data-md-component="source">
|
|
196
|
+
<div class="md-source__icon md-icon">
|
|
197
|
+
|
|
198
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 7.1.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2025 Fonticons, Inc.--><path d="M439.6 236.1 244 40.5c-5.4-5.5-12.8-8.5-20.4-8.5s-15 3-20.4 8.4L162.5 81l51.5 51.5c27.1-9.1 52.7 16.8 43.4 43.7l49.7 49.7c34.2-11.8 61.2 31 35.5 56.7-26.5 26.5-70.2-2.9-56-37.3L240.3 199v121.9c25.3 12.5 22.3 41.8 9.1 55-6.4 6.4-15.2 10.1-24.3 10.1s-17.8-3.6-24.3-10.1c-17.6-17.6-11.1-46.9 11.2-56v-123c-20.8-8.5-24.6-30.7-18.6-45L142.6 101 8.5 235.1C3 240.6 0 247.9 0 255.5s3 15 8.5 20.4l195.6 195.7c5.4 5.4 12.7 8.4 20.4 8.4s15-3 20.4-8.4l194.7-194.7c5.4-5.4 8.4-12.8 8.4-20.4s-3-15-8.4-20.4"/></svg>
|
|
199
|
+
</div>
|
|
200
|
+
<div class="md-source__repository">
|
|
201
|
+
caddforge-docs
|
|
202
|
+
</div>
|
|
203
|
+
</a>
|
|
204
|
+
</div>
|
|
205
|
+
|
|
206
|
+
</nav>
|
|
207
|
+
|
|
208
|
+
</header>
|
|
209
|
+
|
|
210
|
+
<div class="md-container" data-md-component="container">
|
|
211
|
+
|
|
212
|
+
|
|
213
|
+
|
|
214
|
+
|
|
215
|
+
|
|
216
|
+
|
|
217
|
+
<main class="md-main" data-md-component="main">
|
|
218
|
+
<div class="md-main__inner md-grid">
|
|
219
|
+
|
|
220
|
+
|
|
221
|
+
|
|
222
|
+
<div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
|
|
223
|
+
<div class="md-sidebar__scrollwrap">
|
|
224
|
+
<div class="md-sidebar__inner">
|
|
225
|
+
|
|
226
|
+
|
|
227
|
+
|
|
228
|
+
|
|
229
|
+
<nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
|
|
230
|
+
<label class="md-nav__title" for="__drawer">
|
|
231
|
+
<a href="../.." title="CADDForge" class="md-nav__button md-logo" aria-label="CADDForge" data-md-component="logo">
|
|
232
|
+
|
|
233
|
+
|
|
234
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54"/></svg>
|
|
235
|
+
|
|
236
|
+
</a>
|
|
237
|
+
CADDForge
|
|
238
|
+
</label>
|
|
239
|
+
|
|
240
|
+
<div class="md-nav__source">
|
|
241
|
+
<a href="https://github.com/idorsia/caddforge-docs" title="Go to repository" class="md-source" data-md-component="source">
|
|
242
|
+
<div class="md-source__icon md-icon">
|
|
243
|
+
|
|
244
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 7.1.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2025 Fonticons, Inc.--><path d="M439.6 236.1 244 40.5c-5.4-5.5-12.8-8.5-20.4-8.5s-15 3-20.4 8.4L162.5 81l51.5 51.5c27.1-9.1 52.7 16.8 43.4 43.7l49.7 49.7c34.2-11.8 61.2 31 35.5 56.7-26.5 26.5-70.2-2.9-56-37.3L240.3 199v121.9c25.3 12.5 22.3 41.8 9.1 55-6.4 6.4-15.2 10.1-24.3 10.1s-17.8-3.6-24.3-10.1c-17.6-17.6-11.1-46.9 11.2-56v-123c-20.8-8.5-24.6-30.7-18.6-45L142.6 101 8.5 235.1C3 240.6 0 247.9 0 255.5s3 15 8.5 20.4l195.6 195.7c5.4 5.4 12.7 8.4 20.4 8.4s15-3 20.4-8.4l194.7-194.7c5.4-5.4 8.4-12.8 8.4-20.4s-3-15-8.4-20.4"/></svg>
|
|
245
|
+
</div>
|
|
246
|
+
<div class="md-source__repository">
|
|
247
|
+
caddforge-docs
|
|
248
|
+
</div>
|
|
249
|
+
</a>
|
|
250
|
+
</div>
|
|
251
|
+
|
|
252
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
253
|
+
|
|
254
|
+
|
|
255
|
+
|
|
256
|
+
|
|
257
|
+
|
|
258
|
+
|
|
259
|
+
|
|
260
|
+
<li class="md-nav__item">
|
|
261
|
+
<a href="../.." class="md-nav__link">
|
|
262
|
+
|
|
263
|
+
|
|
264
|
+
|
|
265
|
+
<span class="md-ellipsis">
|
|
266
|
+
|
|
267
|
+
|
|
268
|
+
Home
|
|
269
|
+
|
|
270
|
+
|
|
271
|
+
|
|
272
|
+
</span>
|
|
273
|
+
|
|
274
|
+
|
|
275
|
+
|
|
276
|
+
</a>
|
|
277
|
+
</li>
|
|
278
|
+
|
|
279
|
+
|
|
280
|
+
|
|
281
|
+
|
|
282
|
+
|
|
283
|
+
|
|
284
|
+
|
|
285
|
+
|
|
286
|
+
|
|
287
|
+
|
|
288
|
+
|
|
289
|
+
|
|
290
|
+
|
|
291
|
+
|
|
292
|
+
|
|
293
|
+
|
|
294
|
+
|
|
295
|
+
|
|
296
|
+
|
|
297
|
+
|
|
298
|
+
|
|
299
|
+
|
|
300
|
+
|
|
301
|
+
|
|
302
|
+
|
|
303
|
+
|
|
304
|
+
|
|
305
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
306
|
+
|
|
307
|
+
|
|
308
|
+
|
|
309
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
|
|
310
|
+
|
|
311
|
+
|
|
312
|
+
<div class="md-nav__link md-nav__container">
|
|
313
|
+
<a href="../../getting-started/" class="md-nav__link ">
|
|
314
|
+
|
|
315
|
+
|
|
316
|
+
|
|
317
|
+
<span class="md-ellipsis">
|
|
318
|
+
|
|
319
|
+
|
|
320
|
+
Getting Started
|
|
321
|
+
|
|
322
|
+
|
|
323
|
+
|
|
324
|
+
</span>
|
|
325
|
+
|
|
326
|
+
|
|
327
|
+
|
|
328
|
+
</a>
|
|
329
|
+
|
|
330
|
+
|
|
331
|
+
<label class="md-nav__link " for="__nav_2" id="__nav_2_label" tabindex="">
|
|
332
|
+
<span class="md-nav__icon md-icon"></span>
|
|
333
|
+
</label>
|
|
334
|
+
|
|
335
|
+
</div>
|
|
336
|
+
|
|
337
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
|
|
338
|
+
<label class="md-nav__title" for="__nav_2">
|
|
339
|
+
<span class="md-nav__icon md-icon"></span>
|
|
340
|
+
|
|
341
|
+
|
|
342
|
+
Getting Started
|
|
343
|
+
|
|
344
|
+
|
|
345
|
+
</label>
|
|
346
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
347
|
+
|
|
348
|
+
|
|
349
|
+
|
|
350
|
+
|
|
351
|
+
|
|
352
|
+
|
|
353
|
+
|
|
354
|
+
<li class="md-nav__item">
|
|
355
|
+
<a href="../../getting-started/installation/" class="md-nav__link">
|
|
356
|
+
|
|
357
|
+
|
|
358
|
+
|
|
359
|
+
<span class="md-ellipsis">
|
|
360
|
+
|
|
361
|
+
|
|
362
|
+
Installation
|
|
363
|
+
|
|
364
|
+
|
|
365
|
+
|
|
366
|
+
</span>
|
|
367
|
+
|
|
368
|
+
|
|
369
|
+
|
|
370
|
+
</a>
|
|
371
|
+
</li>
|
|
372
|
+
|
|
373
|
+
|
|
374
|
+
|
|
375
|
+
|
|
376
|
+
|
|
377
|
+
|
|
378
|
+
|
|
379
|
+
|
|
380
|
+
|
|
381
|
+
|
|
382
|
+
<li class="md-nav__item">
|
|
383
|
+
<a href="../../getting-started/first-workflow/" class="md-nav__link">
|
|
384
|
+
|
|
385
|
+
|
|
386
|
+
|
|
387
|
+
<span class="md-ellipsis">
|
|
388
|
+
|
|
389
|
+
|
|
390
|
+
First Workflow
|
|
391
|
+
|
|
392
|
+
|
|
393
|
+
|
|
394
|
+
</span>
|
|
395
|
+
|
|
396
|
+
|
|
397
|
+
|
|
398
|
+
</a>
|
|
399
|
+
</li>
|
|
400
|
+
|
|
401
|
+
|
|
402
|
+
|
|
403
|
+
|
|
404
|
+
|
|
405
|
+
|
|
406
|
+
|
|
407
|
+
|
|
408
|
+
|
|
409
|
+
|
|
410
|
+
<li class="md-nav__item">
|
|
411
|
+
<a href="../../getting-started/first-pipeline/" class="md-nav__link">
|
|
412
|
+
|
|
413
|
+
|
|
414
|
+
|
|
415
|
+
<span class="md-ellipsis">
|
|
416
|
+
|
|
417
|
+
|
|
418
|
+
First Pipeline
|
|
419
|
+
|
|
420
|
+
|
|
421
|
+
|
|
422
|
+
</span>
|
|
423
|
+
|
|
424
|
+
|
|
425
|
+
|
|
426
|
+
</a>
|
|
427
|
+
</li>
|
|
428
|
+
|
|
429
|
+
|
|
430
|
+
|
|
431
|
+
|
|
432
|
+
</ul>
|
|
433
|
+
</nav>
|
|
434
|
+
|
|
435
|
+
</li>
|
|
436
|
+
|
|
437
|
+
|
|
438
|
+
|
|
439
|
+
|
|
440
|
+
|
|
441
|
+
|
|
442
|
+
|
|
443
|
+
|
|
444
|
+
|
|
445
|
+
|
|
446
|
+
|
|
447
|
+
|
|
448
|
+
|
|
449
|
+
|
|
450
|
+
|
|
451
|
+
|
|
452
|
+
|
|
453
|
+
|
|
454
|
+
|
|
455
|
+
|
|
456
|
+
|
|
457
|
+
|
|
458
|
+
|
|
459
|
+
|
|
460
|
+
|
|
461
|
+
|
|
462
|
+
|
|
463
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
464
|
+
|
|
465
|
+
|
|
466
|
+
|
|
467
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
|
|
468
|
+
|
|
469
|
+
|
|
470
|
+
<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
|
|
471
|
+
|
|
472
|
+
|
|
473
|
+
|
|
474
|
+
<span class="md-ellipsis">
|
|
475
|
+
|
|
476
|
+
|
|
477
|
+
How-to Guides
|
|
478
|
+
|
|
479
|
+
|
|
480
|
+
|
|
481
|
+
</span>
|
|
482
|
+
|
|
483
|
+
|
|
484
|
+
|
|
485
|
+
<span class="md-nav__icon md-icon"></span>
|
|
486
|
+
</label>
|
|
487
|
+
|
|
488
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
|
|
489
|
+
<label class="md-nav__title" for="__nav_3">
|
|
490
|
+
<span class="md-nav__icon md-icon"></span>
|
|
491
|
+
|
|
492
|
+
|
|
493
|
+
How-to Guides
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
</label>
|
|
497
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
498
|
+
|
|
499
|
+
|
|
500
|
+
|
|
501
|
+
|
|
502
|
+
|
|
503
|
+
|
|
504
|
+
|
|
505
|
+
<li class="md-nav__item">
|
|
506
|
+
<a href="../../how-to/jobs/" class="md-nav__link">
|
|
507
|
+
|
|
508
|
+
|
|
509
|
+
|
|
510
|
+
<span class="md-ellipsis">
|
|
511
|
+
|
|
512
|
+
|
|
513
|
+
Jobs and Results
|
|
514
|
+
|
|
515
|
+
|
|
516
|
+
|
|
517
|
+
</span>
|
|
518
|
+
|
|
519
|
+
|
|
520
|
+
|
|
521
|
+
</a>
|
|
522
|
+
</li>
|
|
523
|
+
|
|
524
|
+
|
|
525
|
+
|
|
526
|
+
|
|
527
|
+
|
|
528
|
+
|
|
529
|
+
|
|
530
|
+
|
|
531
|
+
|
|
532
|
+
|
|
533
|
+
<li class="md-nav__item">
|
|
534
|
+
<a href="../../how-to/scatter/" class="md-nav__link">
|
|
535
|
+
|
|
536
|
+
|
|
537
|
+
|
|
538
|
+
<span class="md-ellipsis">
|
|
539
|
+
|
|
540
|
+
|
|
541
|
+
Scatter and Reduce
|
|
542
|
+
|
|
543
|
+
|
|
544
|
+
|
|
545
|
+
</span>
|
|
546
|
+
|
|
547
|
+
|
|
548
|
+
|
|
549
|
+
</a>
|
|
550
|
+
</li>
|
|
551
|
+
|
|
552
|
+
|
|
553
|
+
|
|
554
|
+
|
|
555
|
+
|
|
556
|
+
|
|
557
|
+
|
|
558
|
+
|
|
559
|
+
|
|
560
|
+
|
|
561
|
+
<li class="md-nav__item">
|
|
562
|
+
<a href="../../how-to/troubleshooting/" class="md-nav__link">
|
|
563
|
+
|
|
564
|
+
|
|
565
|
+
|
|
566
|
+
<span class="md-ellipsis">
|
|
567
|
+
|
|
568
|
+
|
|
569
|
+
Troubleshooting
|
|
570
|
+
|
|
571
|
+
|
|
572
|
+
|
|
573
|
+
</span>
|
|
574
|
+
|
|
575
|
+
|
|
576
|
+
|
|
577
|
+
</a>
|
|
578
|
+
</li>
|
|
579
|
+
|
|
580
|
+
|
|
581
|
+
|
|
582
|
+
|
|
583
|
+
</ul>
|
|
584
|
+
</nav>
|
|
585
|
+
|
|
586
|
+
</li>
|
|
587
|
+
|
|
588
|
+
|
|
589
|
+
|
|
590
|
+
|
|
591
|
+
|
|
592
|
+
|
|
593
|
+
|
|
594
|
+
|
|
595
|
+
|
|
596
|
+
|
|
597
|
+
|
|
598
|
+
|
|
599
|
+
|
|
600
|
+
|
|
601
|
+
|
|
602
|
+
|
|
603
|
+
|
|
604
|
+
|
|
605
|
+
|
|
606
|
+
|
|
607
|
+
|
|
608
|
+
|
|
609
|
+
|
|
610
|
+
|
|
611
|
+
|
|
612
|
+
|
|
613
|
+
|
|
614
|
+
|
|
615
|
+
|
|
616
|
+
|
|
617
|
+
|
|
618
|
+
|
|
619
|
+
|
|
620
|
+
|
|
621
|
+
|
|
622
|
+
<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
|
|
623
|
+
|
|
624
|
+
|
|
625
|
+
|
|
626
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
|
|
627
|
+
|
|
628
|
+
|
|
629
|
+
<div class="md-nav__link md-nav__container">
|
|
630
|
+
<a href="../" class="md-nav__link ">
|
|
631
|
+
|
|
632
|
+
|
|
633
|
+
|
|
634
|
+
<span class="md-ellipsis">
|
|
635
|
+
|
|
636
|
+
|
|
637
|
+
Core
|
|
638
|
+
|
|
639
|
+
|
|
640
|
+
|
|
641
|
+
</span>
|
|
642
|
+
|
|
643
|
+
|
|
644
|
+
|
|
645
|
+
</a>
|
|
646
|
+
|
|
647
|
+
|
|
648
|
+
<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
649
|
+
<span class="md-nav__icon md-icon"></span>
|
|
650
|
+
</label>
|
|
651
|
+
|
|
652
|
+
</div>
|
|
653
|
+
|
|
654
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
|
|
655
|
+
<label class="md-nav__title" for="__nav_4">
|
|
656
|
+
<span class="md-nav__icon md-icon"></span>
|
|
657
|
+
|
|
658
|
+
|
|
659
|
+
Core
|
|
660
|
+
|
|
661
|
+
|
|
662
|
+
</label>
|
|
663
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
664
|
+
|
|
665
|
+
|
|
666
|
+
|
|
667
|
+
|
|
668
|
+
|
|
669
|
+
|
|
670
|
+
|
|
671
|
+
<li class="md-nav__item">
|
|
672
|
+
<a href="../concepts/" class="md-nav__link">
|
|
673
|
+
|
|
674
|
+
|
|
675
|
+
|
|
676
|
+
<span class="md-ellipsis">
|
|
677
|
+
|
|
678
|
+
|
|
679
|
+
Concepts
|
|
680
|
+
|
|
681
|
+
|
|
682
|
+
|
|
683
|
+
</span>
|
|
684
|
+
|
|
685
|
+
|
|
686
|
+
|
|
687
|
+
</a>
|
|
688
|
+
</li>
|
|
689
|
+
|
|
690
|
+
|
|
691
|
+
|
|
692
|
+
|
|
693
|
+
|
|
694
|
+
|
|
695
|
+
|
|
696
|
+
|
|
697
|
+
|
|
698
|
+
|
|
699
|
+
|
|
700
|
+
|
|
701
|
+
<li class="md-nav__item md-nav__item--active">
|
|
702
|
+
|
|
703
|
+
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
|
704
|
+
|
|
705
|
+
|
|
706
|
+
|
|
707
|
+
|
|
708
|
+
|
|
709
|
+
<label class="md-nav__link md-nav__link--active" for="__toc">
|
|
710
|
+
|
|
711
|
+
|
|
712
|
+
|
|
713
|
+
<span class="md-ellipsis">
|
|
714
|
+
|
|
715
|
+
|
|
716
|
+
Configuration
|
|
717
|
+
|
|
718
|
+
|
|
719
|
+
|
|
720
|
+
</span>
|
|
721
|
+
|
|
722
|
+
|
|
723
|
+
|
|
724
|
+
<span class="md-nav__icon md-icon"></span>
|
|
725
|
+
</label>
|
|
726
|
+
|
|
727
|
+
<a href="./" class="md-nav__link md-nav__link--active">
|
|
728
|
+
|
|
729
|
+
|
|
730
|
+
|
|
731
|
+
<span class="md-ellipsis">
|
|
732
|
+
|
|
733
|
+
|
|
734
|
+
Configuration
|
|
735
|
+
|
|
736
|
+
|
|
737
|
+
|
|
738
|
+
</span>
|
|
739
|
+
|
|
740
|
+
|
|
741
|
+
|
|
742
|
+
</a>
|
|
743
|
+
|
|
744
|
+
|
|
745
|
+
|
|
746
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
747
|
+
|
|
748
|
+
|
|
749
|
+
|
|
750
|
+
|
|
751
|
+
|
|
752
|
+
|
|
753
|
+
<label class="md-nav__title" for="__toc">
|
|
754
|
+
<span class="md-nav__icon md-icon"></span>
|
|
755
|
+
Table of contents
|
|
756
|
+
</label>
|
|
757
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
758
|
+
|
|
759
|
+
<li class="md-nav__item">
|
|
760
|
+
<a href="#transparent-compressed-inputs" class="md-nav__link">
|
|
761
|
+
<span class="md-ellipsis">
|
|
762
|
+
|
|
763
|
+
Transparent compressed inputs
|
|
764
|
+
|
|
765
|
+
</span>
|
|
766
|
+
</a>
|
|
767
|
+
|
|
768
|
+
</li>
|
|
769
|
+
|
|
770
|
+
<li class="md-nav__item">
|
|
771
|
+
<a href="#shared-slurm-environment-options" class="md-nav__link">
|
|
772
|
+
<span class="md-ellipsis">
|
|
773
|
+
|
|
774
|
+
Shared Slurm environment options
|
|
775
|
+
|
|
776
|
+
</span>
|
|
777
|
+
</a>
|
|
778
|
+
|
|
779
|
+
</li>
|
|
780
|
+
|
|
781
|
+
</ul>
|
|
782
|
+
|
|
783
|
+
</nav>
|
|
784
|
+
|
|
785
|
+
</li>
|
|
786
|
+
|
|
787
|
+
|
|
788
|
+
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
|
|
792
|
+
|
|
793
|
+
|
|
794
|
+
|
|
795
|
+
|
|
796
|
+
<li class="md-nav__item">
|
|
797
|
+
<a href="../cli/" class="md-nav__link">
|
|
798
|
+
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
<span class="md-ellipsis">
|
|
802
|
+
|
|
803
|
+
|
|
804
|
+
CLI
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
|
|
808
|
+
</span>
|
|
809
|
+
|
|
810
|
+
|
|
811
|
+
|
|
812
|
+
</a>
|
|
813
|
+
</li>
|
|
814
|
+
|
|
815
|
+
|
|
816
|
+
|
|
817
|
+
|
|
818
|
+
|
|
819
|
+
|
|
820
|
+
|
|
821
|
+
|
|
822
|
+
|
|
823
|
+
|
|
824
|
+
<li class="md-nav__item">
|
|
825
|
+
<a href="../jobs-results/" class="md-nav__link">
|
|
826
|
+
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
<span class="md-ellipsis">
|
|
830
|
+
|
|
831
|
+
|
|
832
|
+
Jobs and Results
|
|
833
|
+
|
|
834
|
+
|
|
835
|
+
|
|
836
|
+
</span>
|
|
837
|
+
|
|
838
|
+
|
|
839
|
+
|
|
840
|
+
</a>
|
|
841
|
+
</li>
|
|
842
|
+
|
|
843
|
+
|
|
844
|
+
|
|
845
|
+
|
|
846
|
+
|
|
847
|
+
|
|
848
|
+
|
|
849
|
+
|
|
850
|
+
|
|
851
|
+
|
|
852
|
+
<li class="md-nav__item">
|
|
853
|
+
<a href="../slurm/" class="md-nav__link">
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
<span class="md-ellipsis">
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
Slurm Backend
|
|
861
|
+
|
|
862
|
+
|
|
863
|
+
|
|
864
|
+
</span>
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
</a>
|
|
869
|
+
</li>
|
|
870
|
+
|
|
871
|
+
|
|
872
|
+
|
|
873
|
+
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
|
|
877
|
+
|
|
878
|
+
|
|
879
|
+
|
|
880
|
+
<li class="md-nav__item">
|
|
881
|
+
<a href="../plugins/" class="md-nav__link">
|
|
882
|
+
|
|
883
|
+
|
|
884
|
+
|
|
885
|
+
<span class="md-ellipsis">
|
|
886
|
+
|
|
887
|
+
|
|
888
|
+
Plugins
|
|
889
|
+
|
|
890
|
+
|
|
891
|
+
|
|
892
|
+
</span>
|
|
893
|
+
|
|
894
|
+
|
|
895
|
+
|
|
896
|
+
</a>
|
|
897
|
+
</li>
|
|
898
|
+
|
|
899
|
+
|
|
900
|
+
|
|
901
|
+
|
|
902
|
+
</ul>
|
|
903
|
+
</nav>
|
|
904
|
+
|
|
905
|
+
</li>
|
|
906
|
+
|
|
907
|
+
|
|
908
|
+
|
|
909
|
+
|
|
910
|
+
|
|
911
|
+
|
|
912
|
+
|
|
913
|
+
|
|
914
|
+
|
|
915
|
+
|
|
916
|
+
|
|
917
|
+
|
|
918
|
+
|
|
919
|
+
|
|
920
|
+
|
|
921
|
+
|
|
922
|
+
|
|
923
|
+
|
|
924
|
+
|
|
925
|
+
|
|
926
|
+
|
|
927
|
+
|
|
928
|
+
|
|
929
|
+
|
|
930
|
+
|
|
931
|
+
|
|
932
|
+
|
|
933
|
+
|
|
934
|
+
|
|
935
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
936
|
+
|
|
937
|
+
|
|
938
|
+
|
|
939
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
|
940
|
+
|
|
941
|
+
|
|
942
|
+
<div class="md-nav__link md-nav__container">
|
|
943
|
+
<a href="../../pipelines/" class="md-nav__link ">
|
|
944
|
+
|
|
945
|
+
|
|
946
|
+
|
|
947
|
+
<span class="md-ellipsis">
|
|
948
|
+
|
|
949
|
+
|
|
950
|
+
Pipelines
|
|
951
|
+
|
|
952
|
+
|
|
953
|
+
|
|
954
|
+
</span>
|
|
955
|
+
|
|
956
|
+
|
|
957
|
+
|
|
958
|
+
</a>
|
|
959
|
+
|
|
960
|
+
|
|
961
|
+
<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
|
962
|
+
<span class="md-nav__icon md-icon"></span>
|
|
963
|
+
</label>
|
|
964
|
+
|
|
965
|
+
</div>
|
|
966
|
+
|
|
967
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
|
968
|
+
<label class="md-nav__title" for="__nav_5">
|
|
969
|
+
<span class="md-nav__icon md-icon"></span>
|
|
970
|
+
|
|
971
|
+
|
|
972
|
+
Pipelines
|
|
973
|
+
|
|
974
|
+
|
|
975
|
+
</label>
|
|
976
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
977
|
+
|
|
978
|
+
|
|
979
|
+
|
|
980
|
+
|
|
981
|
+
|
|
982
|
+
|
|
983
|
+
|
|
984
|
+
<li class="md-nav__item">
|
|
985
|
+
<a href="../../pipelines/specification/" class="md-nav__link">
|
|
986
|
+
|
|
987
|
+
|
|
988
|
+
|
|
989
|
+
<span class="md-ellipsis">
|
|
990
|
+
|
|
991
|
+
|
|
992
|
+
Specification
|
|
993
|
+
|
|
994
|
+
|
|
995
|
+
|
|
996
|
+
</span>
|
|
997
|
+
|
|
998
|
+
|
|
999
|
+
|
|
1000
|
+
</a>
|
|
1001
|
+
</li>
|
|
1002
|
+
|
|
1003
|
+
|
|
1004
|
+
|
|
1005
|
+
|
|
1006
|
+
|
|
1007
|
+
|
|
1008
|
+
|
|
1009
|
+
|
|
1010
|
+
|
|
1011
|
+
|
|
1012
|
+
<li class="md-nav__item">
|
|
1013
|
+
<a href="../../pipelines/artifacts/" class="md-nav__link">
|
|
1014
|
+
|
|
1015
|
+
|
|
1016
|
+
|
|
1017
|
+
<span class="md-ellipsis">
|
|
1018
|
+
|
|
1019
|
+
|
|
1020
|
+
Artifacts
|
|
1021
|
+
|
|
1022
|
+
|
|
1023
|
+
|
|
1024
|
+
</span>
|
|
1025
|
+
|
|
1026
|
+
|
|
1027
|
+
|
|
1028
|
+
</a>
|
|
1029
|
+
</li>
|
|
1030
|
+
|
|
1031
|
+
|
|
1032
|
+
|
|
1033
|
+
|
|
1034
|
+
|
|
1035
|
+
|
|
1036
|
+
|
|
1037
|
+
|
|
1038
|
+
|
|
1039
|
+
|
|
1040
|
+
<li class="md-nav__item">
|
|
1041
|
+
<a href="../../pipelines/built-ins/" class="md-nav__link">
|
|
1042
|
+
|
|
1043
|
+
|
|
1044
|
+
|
|
1045
|
+
<span class="md-ellipsis">
|
|
1046
|
+
|
|
1047
|
+
|
|
1048
|
+
Built-in Stages
|
|
1049
|
+
|
|
1050
|
+
|
|
1051
|
+
|
|
1052
|
+
</span>
|
|
1053
|
+
|
|
1054
|
+
|
|
1055
|
+
|
|
1056
|
+
</a>
|
|
1057
|
+
</li>
|
|
1058
|
+
|
|
1059
|
+
|
|
1060
|
+
|
|
1061
|
+
|
|
1062
|
+
|
|
1063
|
+
|
|
1064
|
+
|
|
1065
|
+
|
|
1066
|
+
|
|
1067
|
+
|
|
1068
|
+
<li class="md-nav__item">
|
|
1069
|
+
<a href="../../pipelines/examples/" class="md-nav__link">
|
|
1070
|
+
|
|
1071
|
+
|
|
1072
|
+
|
|
1073
|
+
<span class="md-ellipsis">
|
|
1074
|
+
|
|
1075
|
+
|
|
1076
|
+
Examples
|
|
1077
|
+
|
|
1078
|
+
|
|
1079
|
+
|
|
1080
|
+
</span>
|
|
1081
|
+
|
|
1082
|
+
|
|
1083
|
+
|
|
1084
|
+
</a>
|
|
1085
|
+
</li>
|
|
1086
|
+
|
|
1087
|
+
|
|
1088
|
+
|
|
1089
|
+
|
|
1090
|
+
</ul>
|
|
1091
|
+
</nav>
|
|
1092
|
+
|
|
1093
|
+
</li>
|
|
1094
|
+
|
|
1095
|
+
|
|
1096
|
+
|
|
1097
|
+
|
|
1098
|
+
|
|
1099
|
+
|
|
1100
|
+
|
|
1101
|
+
|
|
1102
|
+
|
|
1103
|
+
|
|
1104
|
+
|
|
1105
|
+
|
|
1106
|
+
|
|
1107
|
+
|
|
1108
|
+
|
|
1109
|
+
|
|
1110
|
+
|
|
1111
|
+
|
|
1112
|
+
|
|
1113
|
+
|
|
1114
|
+
|
|
1115
|
+
|
|
1116
|
+
|
|
1117
|
+
|
|
1118
|
+
|
|
1119
|
+
|
|
1120
|
+
|
|
1121
|
+
|
|
1122
|
+
|
|
1123
|
+
|
|
1124
|
+
|
|
1125
|
+
|
|
1126
|
+
|
|
1127
|
+
|
|
1128
|
+
|
|
1129
|
+
|
|
1130
|
+
|
|
1131
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1132
|
+
|
|
1133
|
+
|
|
1134
|
+
|
|
1135
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
|
|
1136
|
+
|
|
1137
|
+
|
|
1138
|
+
<div class="md-nav__link md-nav__container">
|
|
1139
|
+
<a href="../../plugins/" class="md-nav__link ">
|
|
1140
|
+
|
|
1141
|
+
|
|
1142
|
+
|
|
1143
|
+
<span class="md-ellipsis">
|
|
1144
|
+
|
|
1145
|
+
|
|
1146
|
+
Plugins
|
|
1147
|
+
|
|
1148
|
+
|
|
1149
|
+
|
|
1150
|
+
</span>
|
|
1151
|
+
|
|
1152
|
+
|
|
1153
|
+
|
|
1154
|
+
</a>
|
|
1155
|
+
|
|
1156
|
+
|
|
1157
|
+
<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
|
1158
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1159
|
+
</label>
|
|
1160
|
+
|
|
1161
|
+
</div>
|
|
1162
|
+
|
|
1163
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
|
1164
|
+
<label class="md-nav__title" for="__nav_6">
|
|
1165
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1166
|
+
|
|
1167
|
+
|
|
1168
|
+
Plugins
|
|
1169
|
+
|
|
1170
|
+
|
|
1171
|
+
</label>
|
|
1172
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1173
|
+
|
|
1174
|
+
|
|
1175
|
+
|
|
1176
|
+
|
|
1177
|
+
|
|
1178
|
+
|
|
1179
|
+
|
|
1180
|
+
<li class="md-nav__item">
|
|
1181
|
+
<a href="../../plugins/version-matrix/" class="md-nav__link">
|
|
1182
|
+
|
|
1183
|
+
|
|
1184
|
+
|
|
1185
|
+
<span class="md-ellipsis">
|
|
1186
|
+
|
|
1187
|
+
|
|
1188
|
+
Version Matrix
|
|
1189
|
+
|
|
1190
|
+
|
|
1191
|
+
|
|
1192
|
+
</span>
|
|
1193
|
+
|
|
1194
|
+
|
|
1195
|
+
|
|
1196
|
+
</a>
|
|
1197
|
+
</li>
|
|
1198
|
+
|
|
1199
|
+
|
|
1200
|
+
|
|
1201
|
+
|
|
1202
|
+
|
|
1203
|
+
|
|
1204
|
+
|
|
1205
|
+
|
|
1206
|
+
|
|
1207
|
+
|
|
1208
|
+
<li class="md-nav__item">
|
|
1209
|
+
<a href="../../plugins/docking/" class="md-nav__link">
|
|
1210
|
+
|
|
1211
|
+
|
|
1212
|
+
|
|
1213
|
+
<span class="md-ellipsis">
|
|
1214
|
+
|
|
1215
|
+
|
|
1216
|
+
Docking
|
|
1217
|
+
|
|
1218
|
+
|
|
1219
|
+
|
|
1220
|
+
</span>
|
|
1221
|
+
|
|
1222
|
+
|
|
1223
|
+
|
|
1224
|
+
</a>
|
|
1225
|
+
</li>
|
|
1226
|
+
|
|
1227
|
+
|
|
1228
|
+
|
|
1229
|
+
|
|
1230
|
+
|
|
1231
|
+
|
|
1232
|
+
|
|
1233
|
+
|
|
1234
|
+
|
|
1235
|
+
|
|
1236
|
+
<li class="md-nav__item">
|
|
1237
|
+
<a href="../../plugins/descriptors/" class="md-nav__link">
|
|
1238
|
+
|
|
1239
|
+
|
|
1240
|
+
|
|
1241
|
+
<span class="md-ellipsis">
|
|
1242
|
+
|
|
1243
|
+
|
|
1244
|
+
Descriptors
|
|
1245
|
+
|
|
1246
|
+
|
|
1247
|
+
|
|
1248
|
+
</span>
|
|
1249
|
+
|
|
1250
|
+
|
|
1251
|
+
|
|
1252
|
+
</a>
|
|
1253
|
+
</li>
|
|
1254
|
+
|
|
1255
|
+
|
|
1256
|
+
|
|
1257
|
+
|
|
1258
|
+
|
|
1259
|
+
|
|
1260
|
+
|
|
1261
|
+
|
|
1262
|
+
|
|
1263
|
+
|
|
1264
|
+
<li class="md-nav__item">
|
|
1265
|
+
<a href="../../plugins/md/" class="md-nav__link">
|
|
1266
|
+
|
|
1267
|
+
|
|
1268
|
+
|
|
1269
|
+
<span class="md-ellipsis">
|
|
1270
|
+
|
|
1271
|
+
|
|
1272
|
+
MD
|
|
1273
|
+
|
|
1274
|
+
|
|
1275
|
+
|
|
1276
|
+
</span>
|
|
1277
|
+
|
|
1278
|
+
|
|
1279
|
+
|
|
1280
|
+
</a>
|
|
1281
|
+
</li>
|
|
1282
|
+
|
|
1283
|
+
|
|
1284
|
+
|
|
1285
|
+
|
|
1286
|
+
|
|
1287
|
+
|
|
1288
|
+
|
|
1289
|
+
|
|
1290
|
+
|
|
1291
|
+
|
|
1292
|
+
<li class="md-nav__item">
|
|
1293
|
+
<a href="../../plugins/fep/" class="md-nav__link">
|
|
1294
|
+
|
|
1295
|
+
|
|
1296
|
+
|
|
1297
|
+
<span class="md-ellipsis">
|
|
1298
|
+
|
|
1299
|
+
|
|
1300
|
+
FEP
|
|
1301
|
+
|
|
1302
|
+
|
|
1303
|
+
|
|
1304
|
+
</span>
|
|
1305
|
+
|
|
1306
|
+
|
|
1307
|
+
|
|
1308
|
+
</a>
|
|
1309
|
+
</li>
|
|
1310
|
+
|
|
1311
|
+
|
|
1312
|
+
|
|
1313
|
+
|
|
1314
|
+
|
|
1315
|
+
|
|
1316
|
+
|
|
1317
|
+
|
|
1318
|
+
|
|
1319
|
+
|
|
1320
|
+
<li class="md-nav__item">
|
|
1321
|
+
<a href="../../plugins/qm/" class="md-nav__link">
|
|
1322
|
+
|
|
1323
|
+
|
|
1324
|
+
|
|
1325
|
+
<span class="md-ellipsis">
|
|
1326
|
+
|
|
1327
|
+
|
|
1328
|
+
QM
|
|
1329
|
+
|
|
1330
|
+
|
|
1331
|
+
|
|
1332
|
+
</span>
|
|
1333
|
+
|
|
1334
|
+
|
|
1335
|
+
|
|
1336
|
+
</a>
|
|
1337
|
+
</li>
|
|
1338
|
+
|
|
1339
|
+
|
|
1340
|
+
|
|
1341
|
+
|
|
1342
|
+
|
|
1343
|
+
|
|
1344
|
+
|
|
1345
|
+
|
|
1346
|
+
|
|
1347
|
+
|
|
1348
|
+
<li class="md-nav__item">
|
|
1349
|
+
<a href="../../plugins/ml/" class="md-nav__link">
|
|
1350
|
+
|
|
1351
|
+
|
|
1352
|
+
|
|
1353
|
+
<span class="md-ellipsis">
|
|
1354
|
+
|
|
1355
|
+
|
|
1356
|
+
ML
|
|
1357
|
+
|
|
1358
|
+
|
|
1359
|
+
|
|
1360
|
+
</span>
|
|
1361
|
+
|
|
1362
|
+
|
|
1363
|
+
|
|
1364
|
+
</a>
|
|
1365
|
+
</li>
|
|
1366
|
+
|
|
1367
|
+
|
|
1368
|
+
|
|
1369
|
+
|
|
1370
|
+
|
|
1371
|
+
|
|
1372
|
+
|
|
1373
|
+
|
|
1374
|
+
|
|
1375
|
+
|
|
1376
|
+
<li class="md-nav__item">
|
|
1377
|
+
<a href="../../plugins/datascience/" class="md-nav__link">
|
|
1378
|
+
|
|
1379
|
+
|
|
1380
|
+
|
|
1381
|
+
<span class="md-ellipsis">
|
|
1382
|
+
|
|
1383
|
+
|
|
1384
|
+
Data Science
|
|
1385
|
+
|
|
1386
|
+
|
|
1387
|
+
|
|
1388
|
+
</span>
|
|
1389
|
+
|
|
1390
|
+
|
|
1391
|
+
|
|
1392
|
+
</a>
|
|
1393
|
+
</li>
|
|
1394
|
+
|
|
1395
|
+
|
|
1396
|
+
|
|
1397
|
+
|
|
1398
|
+
</ul>
|
|
1399
|
+
</nav>
|
|
1400
|
+
|
|
1401
|
+
</li>
|
|
1402
|
+
|
|
1403
|
+
|
|
1404
|
+
|
|
1405
|
+
|
|
1406
|
+
|
|
1407
|
+
|
|
1408
|
+
|
|
1409
|
+
|
|
1410
|
+
|
|
1411
|
+
|
|
1412
|
+
|
|
1413
|
+
|
|
1414
|
+
|
|
1415
|
+
|
|
1416
|
+
|
|
1417
|
+
|
|
1418
|
+
|
|
1419
|
+
|
|
1420
|
+
|
|
1421
|
+
|
|
1422
|
+
|
|
1423
|
+
|
|
1424
|
+
|
|
1425
|
+
|
|
1426
|
+
|
|
1427
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1428
|
+
|
|
1429
|
+
|
|
1430
|
+
|
|
1431
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_7" >
|
|
1432
|
+
|
|
1433
|
+
|
|
1434
|
+
<div class="md-nav__link md-nav__container">
|
|
1435
|
+
<a href="../../gui/" class="md-nav__link ">
|
|
1436
|
+
|
|
1437
|
+
|
|
1438
|
+
|
|
1439
|
+
<span class="md-ellipsis">
|
|
1440
|
+
|
|
1441
|
+
|
|
1442
|
+
GUI
|
|
1443
|
+
|
|
1444
|
+
|
|
1445
|
+
|
|
1446
|
+
</span>
|
|
1447
|
+
|
|
1448
|
+
|
|
1449
|
+
|
|
1450
|
+
</a>
|
|
1451
|
+
|
|
1452
|
+
|
|
1453
|
+
<label class="md-nav__link " for="__nav_7" id="__nav_7_label" tabindex="">
|
|
1454
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1455
|
+
</label>
|
|
1456
|
+
|
|
1457
|
+
</div>
|
|
1458
|
+
|
|
1459
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
|
|
1460
|
+
<label class="md-nav__title" for="__nav_7">
|
|
1461
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1462
|
+
|
|
1463
|
+
|
|
1464
|
+
GUI
|
|
1465
|
+
|
|
1466
|
+
|
|
1467
|
+
</label>
|
|
1468
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1469
|
+
|
|
1470
|
+
|
|
1471
|
+
|
|
1472
|
+
|
|
1473
|
+
|
|
1474
|
+
|
|
1475
|
+
|
|
1476
|
+
<li class="md-nav__item">
|
|
1477
|
+
<a href="../../gui/walkthrough/" class="md-nav__link">
|
|
1478
|
+
|
|
1479
|
+
|
|
1480
|
+
|
|
1481
|
+
<span class="md-ellipsis">
|
|
1482
|
+
|
|
1483
|
+
|
|
1484
|
+
Walkthrough
|
|
1485
|
+
|
|
1486
|
+
|
|
1487
|
+
|
|
1488
|
+
</span>
|
|
1489
|
+
|
|
1490
|
+
|
|
1491
|
+
|
|
1492
|
+
</a>
|
|
1493
|
+
</li>
|
|
1494
|
+
|
|
1495
|
+
|
|
1496
|
+
|
|
1497
|
+
|
|
1498
|
+
|
|
1499
|
+
|
|
1500
|
+
|
|
1501
|
+
|
|
1502
|
+
|
|
1503
|
+
|
|
1504
|
+
<li class="md-nav__item">
|
|
1505
|
+
<a href="../../gui/plugin-authoring/" class="md-nav__link">
|
|
1506
|
+
|
|
1507
|
+
|
|
1508
|
+
|
|
1509
|
+
<span class="md-ellipsis">
|
|
1510
|
+
|
|
1511
|
+
|
|
1512
|
+
Plugin GUI Authoring
|
|
1513
|
+
|
|
1514
|
+
|
|
1515
|
+
|
|
1516
|
+
</span>
|
|
1517
|
+
|
|
1518
|
+
|
|
1519
|
+
|
|
1520
|
+
</a>
|
|
1521
|
+
</li>
|
|
1522
|
+
|
|
1523
|
+
|
|
1524
|
+
|
|
1525
|
+
|
|
1526
|
+
</ul>
|
|
1527
|
+
</nav>
|
|
1528
|
+
|
|
1529
|
+
</li>
|
|
1530
|
+
|
|
1531
|
+
|
|
1532
|
+
|
|
1533
|
+
|
|
1534
|
+
|
|
1535
|
+
|
|
1536
|
+
|
|
1537
|
+
|
|
1538
|
+
|
|
1539
|
+
|
|
1540
|
+
|
|
1541
|
+
|
|
1542
|
+
|
|
1543
|
+
|
|
1544
|
+
|
|
1545
|
+
|
|
1546
|
+
|
|
1547
|
+
|
|
1548
|
+
|
|
1549
|
+
|
|
1550
|
+
|
|
1551
|
+
|
|
1552
|
+
|
|
1553
|
+
|
|
1554
|
+
|
|
1555
|
+
|
|
1556
|
+
|
|
1557
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1558
|
+
|
|
1559
|
+
|
|
1560
|
+
|
|
1561
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8" >
|
|
1562
|
+
|
|
1563
|
+
|
|
1564
|
+
<div class="md-nav__link md-nav__container">
|
|
1565
|
+
<a href="../../reference/" class="md-nav__link ">
|
|
1566
|
+
|
|
1567
|
+
|
|
1568
|
+
|
|
1569
|
+
<span class="md-ellipsis">
|
|
1570
|
+
|
|
1571
|
+
|
|
1572
|
+
Reference
|
|
1573
|
+
|
|
1574
|
+
|
|
1575
|
+
|
|
1576
|
+
</span>
|
|
1577
|
+
|
|
1578
|
+
|
|
1579
|
+
|
|
1580
|
+
</a>
|
|
1581
|
+
|
|
1582
|
+
|
|
1583
|
+
<label class="md-nav__link " for="__nav_8" id="__nav_8_label" tabindex="">
|
|
1584
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1585
|
+
</label>
|
|
1586
|
+
|
|
1587
|
+
</div>
|
|
1588
|
+
|
|
1589
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false">
|
|
1590
|
+
<label class="md-nav__title" for="__nav_8">
|
|
1591
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1592
|
+
|
|
1593
|
+
|
|
1594
|
+
Reference
|
|
1595
|
+
|
|
1596
|
+
|
|
1597
|
+
</label>
|
|
1598
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1599
|
+
|
|
1600
|
+
|
|
1601
|
+
|
|
1602
|
+
|
|
1603
|
+
|
|
1604
|
+
|
|
1605
|
+
|
|
1606
|
+
<li class="md-nav__item">
|
|
1607
|
+
<a href="../../reference/api/" class="md-nav__link">
|
|
1608
|
+
|
|
1609
|
+
|
|
1610
|
+
|
|
1611
|
+
<span class="md-ellipsis">
|
|
1612
|
+
|
|
1613
|
+
|
|
1614
|
+
Public Python API
|
|
1615
|
+
|
|
1616
|
+
|
|
1617
|
+
|
|
1618
|
+
</span>
|
|
1619
|
+
|
|
1620
|
+
|
|
1621
|
+
|
|
1622
|
+
</a>
|
|
1623
|
+
</li>
|
|
1624
|
+
|
|
1625
|
+
|
|
1626
|
+
|
|
1627
|
+
|
|
1628
|
+
|
|
1629
|
+
|
|
1630
|
+
|
|
1631
|
+
|
|
1632
|
+
|
|
1633
|
+
|
|
1634
|
+
<li class="md-nav__item">
|
|
1635
|
+
<a href="../../examples/" class="md-nav__link">
|
|
1636
|
+
|
|
1637
|
+
|
|
1638
|
+
|
|
1639
|
+
<span class="md-ellipsis">
|
|
1640
|
+
|
|
1641
|
+
|
|
1642
|
+
Example Library
|
|
1643
|
+
|
|
1644
|
+
|
|
1645
|
+
|
|
1646
|
+
</span>
|
|
1647
|
+
|
|
1648
|
+
|
|
1649
|
+
|
|
1650
|
+
</a>
|
|
1651
|
+
</li>
|
|
1652
|
+
|
|
1653
|
+
|
|
1654
|
+
|
|
1655
|
+
|
|
1656
|
+
|
|
1657
|
+
|
|
1658
|
+
|
|
1659
|
+
|
|
1660
|
+
|
|
1661
|
+
|
|
1662
|
+
<li class="md-nav__item">
|
|
1663
|
+
<a href="../../examples/quickstart/" class="md-nav__link">
|
|
1664
|
+
|
|
1665
|
+
|
|
1666
|
+
|
|
1667
|
+
<span class="md-ellipsis">
|
|
1668
|
+
|
|
1669
|
+
|
|
1670
|
+
Example Data Provenance
|
|
1671
|
+
|
|
1672
|
+
|
|
1673
|
+
|
|
1674
|
+
</span>
|
|
1675
|
+
|
|
1676
|
+
|
|
1677
|
+
|
|
1678
|
+
</a>
|
|
1679
|
+
</li>
|
|
1680
|
+
|
|
1681
|
+
|
|
1682
|
+
|
|
1683
|
+
|
|
1684
|
+
</ul>
|
|
1685
|
+
</nav>
|
|
1686
|
+
|
|
1687
|
+
</li>
|
|
1688
|
+
|
|
1689
|
+
|
|
1690
|
+
|
|
1691
|
+
|
|
1692
|
+
|
|
1693
|
+
|
|
1694
|
+
|
|
1695
|
+
|
|
1696
|
+
|
|
1697
|
+
|
|
1698
|
+
|
|
1699
|
+
|
|
1700
|
+
|
|
1701
|
+
|
|
1702
|
+
|
|
1703
|
+
|
|
1704
|
+
|
|
1705
|
+
|
|
1706
|
+
|
|
1707
|
+
|
|
1708
|
+
|
|
1709
|
+
|
|
1710
|
+
|
|
1711
|
+
|
|
1712
|
+
|
|
1713
|
+
|
|
1714
|
+
|
|
1715
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1716
|
+
|
|
1717
|
+
|
|
1718
|
+
|
|
1719
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
|
|
1720
|
+
|
|
1721
|
+
|
|
1722
|
+
<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
1723
|
+
|
|
1724
|
+
|
|
1725
|
+
|
|
1726
|
+
<span class="md-ellipsis">
|
|
1727
|
+
|
|
1728
|
+
|
|
1729
|
+
Explanation
|
|
1730
|
+
|
|
1731
|
+
|
|
1732
|
+
|
|
1733
|
+
</span>
|
|
1734
|
+
|
|
1735
|
+
|
|
1736
|
+
|
|
1737
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1738
|
+
</label>
|
|
1739
|
+
|
|
1740
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
|
1741
|
+
<label class="md-nav__title" for="__nav_9">
|
|
1742
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1743
|
+
|
|
1744
|
+
|
|
1745
|
+
Explanation
|
|
1746
|
+
|
|
1747
|
+
|
|
1748
|
+
</label>
|
|
1749
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1750
|
+
|
|
1751
|
+
|
|
1752
|
+
|
|
1753
|
+
|
|
1754
|
+
|
|
1755
|
+
|
|
1756
|
+
|
|
1757
|
+
<li class="md-nav__item">
|
|
1758
|
+
<a href="../../explanation/reproducibility/" class="md-nav__link">
|
|
1759
|
+
|
|
1760
|
+
|
|
1761
|
+
|
|
1762
|
+
<span class="md-ellipsis">
|
|
1763
|
+
|
|
1764
|
+
|
|
1765
|
+
Reproducibility
|
|
1766
|
+
|
|
1767
|
+
|
|
1768
|
+
|
|
1769
|
+
</span>
|
|
1770
|
+
|
|
1771
|
+
|
|
1772
|
+
|
|
1773
|
+
</a>
|
|
1774
|
+
</li>
|
|
1775
|
+
|
|
1776
|
+
|
|
1777
|
+
|
|
1778
|
+
|
|
1779
|
+
|
|
1780
|
+
|
|
1781
|
+
|
|
1782
|
+
|
|
1783
|
+
|
|
1784
|
+
|
|
1785
|
+
<li class="md-nav__item">
|
|
1786
|
+
<a href="../../explanation/references/" class="md-nav__link">
|
|
1787
|
+
|
|
1788
|
+
|
|
1789
|
+
|
|
1790
|
+
<span class="md-ellipsis">
|
|
1791
|
+
|
|
1792
|
+
|
|
1793
|
+
Method References
|
|
1794
|
+
|
|
1795
|
+
|
|
1796
|
+
|
|
1797
|
+
</span>
|
|
1798
|
+
|
|
1799
|
+
|
|
1800
|
+
|
|
1801
|
+
</a>
|
|
1802
|
+
</li>
|
|
1803
|
+
|
|
1804
|
+
|
|
1805
|
+
|
|
1806
|
+
|
|
1807
|
+
|
|
1808
|
+
|
|
1809
|
+
|
|
1810
|
+
|
|
1811
|
+
|
|
1812
|
+
|
|
1813
|
+
<li class="md-nav__item">
|
|
1814
|
+
<a href="../../explanation/third-party-notices/" class="md-nav__link">
|
|
1815
|
+
|
|
1816
|
+
|
|
1817
|
+
|
|
1818
|
+
<span class="md-ellipsis">
|
|
1819
|
+
|
|
1820
|
+
|
|
1821
|
+
Third-party Notices
|
|
1822
|
+
|
|
1823
|
+
|
|
1824
|
+
|
|
1825
|
+
</span>
|
|
1826
|
+
|
|
1827
|
+
|
|
1828
|
+
|
|
1829
|
+
</a>
|
|
1830
|
+
</li>
|
|
1831
|
+
|
|
1832
|
+
|
|
1833
|
+
|
|
1834
|
+
|
|
1835
|
+
</ul>
|
|
1836
|
+
</nav>
|
|
1837
|
+
|
|
1838
|
+
</li>
|
|
1839
|
+
|
|
1840
|
+
|
|
1841
|
+
|
|
1842
|
+
|
|
1843
|
+
|
|
1844
|
+
|
|
1845
|
+
|
|
1846
|
+
|
|
1847
|
+
|
|
1848
|
+
|
|
1849
|
+
|
|
1850
|
+
|
|
1851
|
+
|
|
1852
|
+
|
|
1853
|
+
|
|
1854
|
+
|
|
1855
|
+
|
|
1856
|
+
|
|
1857
|
+
|
|
1858
|
+
|
|
1859
|
+
|
|
1860
|
+
|
|
1861
|
+
|
|
1862
|
+
|
|
1863
|
+
|
|
1864
|
+
|
|
1865
|
+
|
|
1866
|
+
|
|
1867
|
+
|
|
1868
|
+
|
|
1869
|
+
|
|
1870
|
+
|
|
1871
|
+
|
|
1872
|
+
|
|
1873
|
+
|
|
1874
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1875
|
+
|
|
1876
|
+
|
|
1877
|
+
|
|
1878
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_10" >
|
|
1879
|
+
|
|
1880
|
+
|
|
1881
|
+
<div class="md-nav__link md-nav__container">
|
|
1882
|
+
<a href="../../development/" class="md-nav__link ">
|
|
1883
|
+
|
|
1884
|
+
|
|
1885
|
+
|
|
1886
|
+
<span class="md-ellipsis">
|
|
1887
|
+
|
|
1888
|
+
|
|
1889
|
+
Development
|
|
1890
|
+
|
|
1891
|
+
|
|
1892
|
+
|
|
1893
|
+
</span>
|
|
1894
|
+
|
|
1895
|
+
|
|
1896
|
+
|
|
1897
|
+
</a>
|
|
1898
|
+
|
|
1899
|
+
|
|
1900
|
+
<label class="md-nav__link " for="__nav_10" id="__nav_10_label" tabindex="">
|
|
1901
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1902
|
+
</label>
|
|
1903
|
+
|
|
1904
|
+
</div>
|
|
1905
|
+
|
|
1906
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_10_label" aria-expanded="false">
|
|
1907
|
+
<label class="md-nav__title" for="__nav_10">
|
|
1908
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1909
|
+
|
|
1910
|
+
|
|
1911
|
+
Development
|
|
1912
|
+
|
|
1913
|
+
|
|
1914
|
+
</label>
|
|
1915
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1916
|
+
|
|
1917
|
+
|
|
1918
|
+
|
|
1919
|
+
|
|
1920
|
+
|
|
1921
|
+
|
|
1922
|
+
|
|
1923
|
+
<li class="md-nav__item">
|
|
1924
|
+
<a href="../../development/release-notes/" class="md-nav__link">
|
|
1925
|
+
|
|
1926
|
+
|
|
1927
|
+
|
|
1928
|
+
<span class="md-ellipsis">
|
|
1929
|
+
|
|
1930
|
+
|
|
1931
|
+
Release Notes
|
|
1932
|
+
|
|
1933
|
+
|
|
1934
|
+
|
|
1935
|
+
</span>
|
|
1936
|
+
|
|
1937
|
+
|
|
1938
|
+
|
|
1939
|
+
</a>
|
|
1940
|
+
</li>
|
|
1941
|
+
|
|
1942
|
+
|
|
1943
|
+
|
|
1944
|
+
|
|
1945
|
+
|
|
1946
|
+
|
|
1947
|
+
|
|
1948
|
+
|
|
1949
|
+
|
|
1950
|
+
|
|
1951
|
+
<li class="md-nav__item">
|
|
1952
|
+
<a href="../../development/tool-authoring/" class="md-nav__link">
|
|
1953
|
+
|
|
1954
|
+
|
|
1955
|
+
|
|
1956
|
+
<span class="md-ellipsis">
|
|
1957
|
+
|
|
1958
|
+
|
|
1959
|
+
Tool Authoring
|
|
1960
|
+
|
|
1961
|
+
|
|
1962
|
+
|
|
1963
|
+
</span>
|
|
1964
|
+
|
|
1965
|
+
|
|
1966
|
+
|
|
1967
|
+
</a>
|
|
1968
|
+
</li>
|
|
1969
|
+
|
|
1970
|
+
|
|
1971
|
+
|
|
1972
|
+
|
|
1973
|
+
|
|
1974
|
+
|
|
1975
|
+
|
|
1976
|
+
|
|
1977
|
+
|
|
1978
|
+
|
|
1979
|
+
<li class="md-nav__item">
|
|
1980
|
+
<a href="../../development/documentation/" class="md-nav__link">
|
|
1981
|
+
|
|
1982
|
+
|
|
1983
|
+
|
|
1984
|
+
<span class="md-ellipsis">
|
|
1985
|
+
|
|
1986
|
+
|
|
1987
|
+
Documentation
|
|
1988
|
+
|
|
1989
|
+
|
|
1990
|
+
|
|
1991
|
+
</span>
|
|
1992
|
+
|
|
1993
|
+
|
|
1994
|
+
|
|
1995
|
+
</a>
|
|
1996
|
+
</li>
|
|
1997
|
+
|
|
1998
|
+
|
|
1999
|
+
|
|
2000
|
+
|
|
2001
|
+
|
|
2002
|
+
|
|
2003
|
+
|
|
2004
|
+
|
|
2005
|
+
|
|
2006
|
+
|
|
2007
|
+
<li class="md-nav__item">
|
|
2008
|
+
<a href="../../development/contributing/" class="md-nav__link">
|
|
2009
|
+
|
|
2010
|
+
|
|
2011
|
+
|
|
2012
|
+
<span class="md-ellipsis">
|
|
2013
|
+
|
|
2014
|
+
|
|
2015
|
+
Contributing
|
|
2016
|
+
|
|
2017
|
+
|
|
2018
|
+
|
|
2019
|
+
</span>
|
|
2020
|
+
|
|
2021
|
+
|
|
2022
|
+
|
|
2023
|
+
</a>
|
|
2024
|
+
</li>
|
|
2025
|
+
|
|
2026
|
+
|
|
2027
|
+
|
|
2028
|
+
|
|
2029
|
+
|
|
2030
|
+
|
|
2031
|
+
|
|
2032
|
+
|
|
2033
|
+
|
|
2034
|
+
|
|
2035
|
+
<li class="md-nav__item">
|
|
2036
|
+
<a href="../../development/security/" class="md-nav__link">
|
|
2037
|
+
|
|
2038
|
+
|
|
2039
|
+
|
|
2040
|
+
<span class="md-ellipsis">
|
|
2041
|
+
|
|
2042
|
+
|
|
2043
|
+
Security Reporting
|
|
2044
|
+
|
|
2045
|
+
|
|
2046
|
+
|
|
2047
|
+
</span>
|
|
2048
|
+
|
|
2049
|
+
|
|
2050
|
+
|
|
2051
|
+
</a>
|
|
2052
|
+
</li>
|
|
2053
|
+
|
|
2054
|
+
|
|
2055
|
+
|
|
2056
|
+
|
|
2057
|
+
|
|
2058
|
+
|
|
2059
|
+
|
|
2060
|
+
|
|
2061
|
+
|
|
2062
|
+
|
|
2063
|
+
<li class="md-nav__item">
|
|
2064
|
+
<a href="../../development/release-readiness/" class="md-nav__link">
|
|
2065
|
+
|
|
2066
|
+
|
|
2067
|
+
|
|
2068
|
+
<span class="md-ellipsis">
|
|
2069
|
+
|
|
2070
|
+
|
|
2071
|
+
Release Readiness
|
|
2072
|
+
|
|
2073
|
+
|
|
2074
|
+
|
|
2075
|
+
</span>
|
|
2076
|
+
|
|
2077
|
+
|
|
2078
|
+
|
|
2079
|
+
</a>
|
|
2080
|
+
</li>
|
|
2081
|
+
|
|
2082
|
+
|
|
2083
|
+
|
|
2084
|
+
|
|
2085
|
+
|
|
2086
|
+
|
|
2087
|
+
|
|
2088
|
+
|
|
2089
|
+
|
|
2090
|
+
|
|
2091
|
+
<li class="md-nav__item">
|
|
2092
|
+
<a href="../../development/ci-publishing/" class="md-nav__link">
|
|
2093
|
+
|
|
2094
|
+
|
|
2095
|
+
|
|
2096
|
+
<span class="md-ellipsis">
|
|
2097
|
+
|
|
2098
|
+
|
|
2099
|
+
CI and Publishing
|
|
2100
|
+
|
|
2101
|
+
|
|
2102
|
+
|
|
2103
|
+
</span>
|
|
2104
|
+
|
|
2105
|
+
|
|
2106
|
+
|
|
2107
|
+
</a>
|
|
2108
|
+
</li>
|
|
2109
|
+
|
|
2110
|
+
|
|
2111
|
+
|
|
2112
|
+
|
|
2113
|
+
</ul>
|
|
2114
|
+
</nav>
|
|
2115
|
+
|
|
2116
|
+
</li>
|
|
2117
|
+
|
|
2118
|
+
|
|
2119
|
+
|
|
2120
|
+
</ul>
|
|
2121
|
+
</nav>
|
|
2122
|
+
</div>
|
|
2123
|
+
</div>
|
|
2124
|
+
</div>
|
|
2125
|
+
|
|
2126
|
+
|
|
2127
|
+
|
|
2128
|
+
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
|
|
2129
|
+
<div class="md-sidebar__scrollwrap">
|
|
2130
|
+
<div class="md-sidebar__inner">
|
|
2131
|
+
|
|
2132
|
+
|
|
2133
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
2134
|
+
|
|
2135
|
+
|
|
2136
|
+
|
|
2137
|
+
|
|
2138
|
+
|
|
2139
|
+
|
|
2140
|
+
<label class="md-nav__title" for="__toc">
|
|
2141
|
+
<span class="md-nav__icon md-icon"></span>
|
|
2142
|
+
Table of contents
|
|
2143
|
+
</label>
|
|
2144
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
2145
|
+
|
|
2146
|
+
<li class="md-nav__item">
|
|
2147
|
+
<a href="#transparent-compressed-inputs" class="md-nav__link">
|
|
2148
|
+
<span class="md-ellipsis">
|
|
2149
|
+
|
|
2150
|
+
Transparent compressed inputs
|
|
2151
|
+
|
|
2152
|
+
</span>
|
|
2153
|
+
</a>
|
|
2154
|
+
|
|
2155
|
+
</li>
|
|
2156
|
+
|
|
2157
|
+
<li class="md-nav__item">
|
|
2158
|
+
<a href="#shared-slurm-environment-options" class="md-nav__link">
|
|
2159
|
+
<span class="md-ellipsis">
|
|
2160
|
+
|
|
2161
|
+
Shared Slurm environment options
|
|
2162
|
+
|
|
2163
|
+
</span>
|
|
2164
|
+
</a>
|
|
2165
|
+
|
|
2166
|
+
</li>
|
|
2167
|
+
|
|
2168
|
+
</ul>
|
|
2169
|
+
|
|
2170
|
+
</nav>
|
|
2171
|
+
</div>
|
|
2172
|
+
</div>
|
|
2173
|
+
</div>
|
|
2174
|
+
|
|
2175
|
+
|
|
2176
|
+
|
|
2177
|
+
<div class="md-content" data-md-component="content">
|
|
2178
|
+
|
|
2179
|
+
<article class="md-content__inner md-typeset">
|
|
2180
|
+
|
|
2181
|
+
|
|
2182
|
+
|
|
2183
|
+
|
|
2184
|
+
|
|
2185
|
+
|
|
2186
|
+
|
|
2187
|
+
|
|
2188
|
+
<h1 id="configuration">Configuration<a class="headerlink" href="#configuration" title="Permanent link">¶</a></h1>
|
|
2189
|
+
<p>CADDForge separates static configuration from runtime execution.</p>
|
|
2190
|
+
<p>Tool configs are validated Python objects, usually Pydantic models. They should be:</p>
|
|
2191
|
+
<ul>
|
|
2192
|
+
<li>constructible from Python code</li>
|
|
2193
|
+
<li>loadable from YAML or JSON</li>
|
|
2194
|
+
<li>explicit about required inputs and defaults</li>
|
|
2195
|
+
<li>responsible for validation, not execution</li>
|
|
2196
|
+
</ul>
|
|
2197
|
+
<p>Example config:</p>
|
|
2198
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
|
|
2199
|
+
<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nt">export_results</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
|
|
2200
|
+
<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="nt">receptor_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">protein.pdbqt</span>
|
|
2201
|
+
<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="nt">ligand_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ligand.sdf</span>
|
|
2202
|
+
</code></pre></div>
|
|
2203
|
+
<p><code>export_results</code> is a shared core option. It defaults to <code>false</code>, which keeps outputs under the
|
|
2204
|
+
standard run directory. Set it to <code>true</code> when a workflow should automatically copy its <code>results/</code>
|
|
2205
|
+
directory back to the submission working directory after completion.</p>
|
|
2206
|
+
<p>Use the CLI to inspect templates exposed by installed plugins:</p>
|
|
2207
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>docking<span class="w"> </span>unidock
|
|
2208
|
+
</code></pre></div>
|
|
2209
|
+
<p>Workflows receive validated config objects and use them to prepare and run jobs.</p>
|
|
2210
|
+
<h2 id="transparent-compressed-inputs">Transparent compressed inputs<a class="headerlink" href="#transparent-compressed-inputs" title="Permanent link">¶</a></h2>
|
|
2211
|
+
<p>At declared plugin boundaries, <code>.csv.gz</code>, <code>.tsv.gz</code>, and <code>.sdf.gz</code> inputs remain compressed on
|
|
2212
|
+
shared storage and are expanded only when the tool starts. Local jobs use job-scoped temporary
|
|
2213
|
+
storage, single-node Slurm jobs use node-local scratch, and multi-node jobs use a private shared
|
|
2214
|
+
staging directory. Saved configuration and results retain the original compressed source path, and
|
|
2215
|
+
runtime materializations are removed after the job.</p>
|
|
2216
|
+
<p>Only paths declared by a plugin input contract are staged. Formats that natively consume gzip,
|
|
2217
|
+
such as selected large-space inputs or tool-specific compressed formats, remain compressed when the
|
|
2218
|
+
plugin marks them as native. Plain inputs keep their existing behavior.</p>
|
|
2219
|
+
<p>Pipeline splitting can stream <code>.csv.gz</code>, <code>.tsv.gz</code>, and <code>.sdf.gz</code> sources into compressed shards;
|
|
2220
|
+
each shard job expands only its own input. A compressed output is finalized atomically from a plain
|
|
2221
|
+
tool output when the output port declares its configuration field.</p>
|
|
2222
|
+
<h2 id="shared-slurm-environment-options">Shared Slurm environment options<a class="headerlink" href="#shared-slurm-environment-options" title="Permanent link">¶</a></h2>
|
|
2223
|
+
<p>Packed environments use the following shared fields:</p>
|
|
2224
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">slurm</span>
|
|
2225
|
+
<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="nt">slurm_env_pack_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/shared/envs/caddforge.tar.gz</span>
|
|
2226
|
+
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nt">slurm_env_cache_enabled</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2227
|
+
<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># Optional absolute path on compute nodes:</span>
|
|
2228
|
+
<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="c1"># slurm_env_cache_dir: /scratch/caddforge_environments/my-user</span>
|
|
2229
|
+
</code></pre></div>
|
|
2230
|
+
<p><code>slurm_env_cache_enabled</code> defaults to <code>true</code>. With caching enabled, CADDForge reuses unpacked
|
|
2231
|
+
environments in per-user node-local storage. Set it to <code>false</code> to use the original behavior where
|
|
2232
|
+
every job unpacks its own environment under job-private scratch.</p>
|
|
2233
|
+
<p><code>slurm_env_cache_dir</code> overrides the automatically selected node-local cache root and must be an
|
|
2234
|
+
absolute compute-node path. Cache retention and lock timeouts are core policies and are not
|
|
2235
|
+
configured per job.</p>
|
|
2236
|
+
<p><code>slurm_env_pack_path</code> is mutually exclusive with <code>slurm_wheelhouse_path</code> and
|
|
2237
|
+
<code>slurm_requirements_path</code>. See the <a href="../slurm/">Slurm backend guide</a> for complete environment setup.</p>
|
|
2238
|
+
|
|
2239
|
+
|
|
2240
|
+
|
|
2241
|
+
|
|
2242
|
+
|
|
2243
|
+
|
|
2244
|
+
|
|
2245
|
+
|
|
2246
|
+
|
|
2247
|
+
|
|
2248
|
+
|
|
2249
|
+
|
|
2250
|
+
|
|
2251
|
+
</article>
|
|
2252
|
+
</div>
|
|
2253
|
+
|
|
2254
|
+
|
|
2255
|
+
<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
|
|
2256
|
+
</div>
|
|
2257
|
+
|
|
2258
|
+
<button type="button" class="md-top md-icon" data-md-component="top" hidden>
|
|
2259
|
+
|
|
2260
|
+
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg>
|
|
2261
|
+
Back to top
|
|
2262
|
+
</button>
|
|
2263
|
+
|
|
2264
|
+
</main>
|
|
2265
|
+
|
|
2266
|
+
<footer class="md-footer">
|
|
2267
|
+
|
|
2268
|
+
<div class="md-footer-meta md-typeset">
|
|
2269
|
+
<div class="md-footer-meta__inner md-grid">
|
|
2270
|
+
<div class="md-copyright">
|
|
2271
|
+
|
|
2272
|
+
|
|
2273
|
+
Made with
|
|
2274
|
+
<a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
|
|
2275
|
+
Material for MkDocs
|
|
2276
|
+
</a>
|
|
2277
|
+
|
|
2278
|
+
</div>
|
|
2279
|
+
|
|
2280
|
+
</div>
|
|
2281
|
+
</div>
|
|
2282
|
+
</footer>
|
|
2283
|
+
|
|
2284
|
+
</div>
|
|
2285
|
+
<div class="md-dialog" data-md-component="dialog">
|
|
2286
|
+
<div class="md-dialog__inner md-typeset"></div>
|
|
2287
|
+
</div>
|
|
2288
|
+
|
|
2289
|
+
|
|
2290
|
+
|
|
2291
|
+
|
|
2292
|
+
|
|
2293
|
+
<script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": ["navigation.instant", "navigation.sections", "navigation.indexes", "navigation.top", "search.highlight", "search.suggest", "content.code.copy"], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
|
|
2294
|
+
|
|
2295
|
+
|
|
2296
|
+
<script src="../../assets/javascripts/bundle.d7400e89.min.js"></script>
|
|
2297
|
+
|
|
2298
|
+
|
|
2299
|
+
</body>
|
|
2300
|
+
</html>
|