Initial ARC template

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LICENSE

+MIT License
+
+Copyright (c) 2020 DataPLANT
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

+# ARCs
+
+for details, see <https://github.com/nfdi4plants/ARC-specification>
+
+## ARC directory structure
+
+`/isa.investigation.xlsx`
+: main investigation file (in XLSX format), contains top-level information about the investigation and links to studies and assays
+
+`/LICENSE`
+: license file for the arc
+
+`/arc.cwl`
+: (optional) executes all runs
+
+### Studies
+
+All input material or (external) data resources are considered studies (immutable input data)
+
+`/assays/<yourStudyName>`
+: folder for an essay, name is arbitrary
+
+`/assays/<yourStudyName>/resources`
+: assay dataset
+
+`/assays/<yourStudyName>/protocols`
+: assay protocol as text (e.g SOP)
+
+`/assays/<yourStudyName>/isa.study.xlsx`
+: per-assay ISA file, contains only info about this assay (in XLSX format)
+
+### Assays
+
+All measurement (self-generated) datasets are considered assays (immutable input data)
+
+`/assays/<yourAssayName>`
+: folder for an essay, name is arbitrary
+
+`/assays/<yourAssayName>/dataset`
+: assay dataset
+
+`/assays/<yourAssayName>/protocols`
+: assay protocol as text (e.g SOP)
+
+`/assays/<yourAssayName>/isa.assay.xlsx`
+: per-assay ISA file, contains only info about this assay (in XLSX format)
+
+### Workflows
+
+All programmatic components of an ARC should go here, in the form of code and environment.
+
+`/workflows/<yourWorkflowName>/`
+: folder for code and its environment (workflow specifications), contains all files needed to specify a workflow. Also packages and other includes needed should go here.
+
+`/workflows/<yourWorkflowName>/Dockerfile`
+: top-level Dockerfile [optional] in which all code/workflow should execute
+
+`/workflows/<yourWorkflowName>/[codefiles;...]`
+: code files/scripts for computation
+
+### Runs
+
+Runs are all artifacts that result by computation from studies, assays or other runs.
+
+`/runs/<yourRunResultName>`
+: folder for results of your run aka. workflow execution
+
+`/runs/<yourRunResultName>/[files;...]`
+: run result files (plots, tables, etc.)
+
+`/runs/<yourRunResultName>.cwl`
+: executes a script or workflow and produces run results accordingly.
+
+
+<!-- 
+### arc setup via arcCommander
+arc init
+arc i create -i yourInvestigationName
+arc a add -s yourStudyName -a yourAssayName
+-->

assays/yourAssayName/dataset/README.md

+## ARCs
+### Assays
+
+`/assays/<yourAssayName>/dataset`
+: assay dataset

assays/yourAssayName/protocols/README.md

+## ARCs
+### Assays
+
+`/assays/<yourAssayName>/protocols`
+: assay protocol as text (e.g SOP)

runs/yourRunName.cwl

+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: [fsi.exe, //workflows/FSharpCodespace/script1.fsx]
+inputs:
+  inputFiles:
+    type:
+      type: array
+      items: string
+    inputBinding:
+      position: 1
+outputs:
+  plotted_data:
+    type: File
+    outputBinding:
+      glob: $(inputs.plot)

runs/yourRunName.yml

+inputFiles:
+  - /…/assays/yourAssay/dataset/Sample1.txt
+  - /…/assays/yourAssay/dataset/Sample2.dat
+  - /…/assays/yourAssay/dataset/Sample3.txt
+plot: ./yourRunResultName/plot1.html

runs/yourRunResultName/README.md

+# ARCs
+
+## ARC directory structure
+
+`./runs/<yourRunResultName>`
+: folder for results of your run aka. workflow execution

runs/yourRunResultName/plot1.html

+
+<!DOCTYPE html>
+<html>
+    <head>
+        <!-- Plotly.js -->
+        <meta http-equiv="X-UA-Compatible" content="IE=11" >
+        <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
+        <style>
+        .container {
+          padding-right: 25px;
+          padding-left: 25px;
+          margin-right: 0 auto;
+          margin-left: 0 auto;
+        }
+        @media (min-width: 768px) {
+          .container {
+            width: 750px;
+          }
+        }
+        @media (min-width: 992px) {
+          .container {
+            width: 970px;
+          }
+        }
+        @media (min-width: 1200px) {
+          .container {
+            width: 1170px;
+          }
+        }
+        </style>
+    </head>
+    <body>
+      <div id="47e0f579-9104-4805-94b5-51152897c859" style="width: 600px; height: 600px;"><!-- Plotly chart will be drawn inside this DIV --></div>
+<script type="text/javascript">
+
+            var renderPlotly = function() {
+            var fsharpPlotlyRequire = requirejs.config({context:'fsharp-plotly',paths:{plotly:'https://cdn.plot.ly/plotly-latest.min'}});
+            fsharpPlotlyRequire(['plotly'], function(Plotly) {
+
+            var data = [{"type":"scatter","x":[1.0],"y":[2.0],"mode":"markers","marker":{}}];
+            var layout = {};
+            var config = {};
+            Plotly.newPlot('47e0f579-9104-4805-94b5-51152897c859', data, layout, config);
+});
+            };
+            if ((typeof(requirejs) !==  typeof(Function)) || (typeof(requirejs.config) !== typeof(Function))) { 
+                var script = document.createElement("script"); 
+                script.setAttribute("src", "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js"); 
+                script.onload = function(){
+                    renderPlotly();
+                };
+                document.getElementsByTagName("head")[0].appendChild(script); 
+            }
+            else {
+                renderPlotly();
+            }
+</script>
+
+      
+    </body>
+</html>
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