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| # positional-carbon13-enrichment | ||
| [](https://dl.circleci.com/status-badge/redirect/gh/p2m2/positional-carbon13-enrichment/tree/develop) | ||
| # Calculations of <sup>13</sup>C-Positional Enrichments | ||
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| https://p2m2.github.io/positional-carbon13-enrichment/ | ||
| [](https://app.circleci.com/pipelines/github/p2m2) | ||
| [](https://p2m2.github.io/positional-carbon13-enrichment/) | ||
| [](https://doi.org/10.3390/metabo13040466) | ||
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| ## install | ||
| <sup>13</sup>C-positional enrichments were calculated by combining mean <sup>13</sup>C enrichments | ||
| of several mass fragments that shared part of the carbon backbone from the same TMS | ||
| derivative. A workflow has been created to calculate these <sup>13</sup>C-positional enrichments | ||
| directly from the outputs of our <sup>13</sup>C-processing method | ||
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| ### Node.js with JSDOM | ||
| To use the software without prior installation and obtain a visual rendering, please visit the site https://p2m2.github.io/positional-carbon13-enrichment/ | ||
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| check [scala.js installation page](https://www.scala-js.org/doc/project/js-environments.html) | ||
| For a precise description of the method, refer to the publication [*"Evaluation of GC/MS-Based <sup>13</sup>C-Positional Approaches for TMS Derivatives of Organic and Amino Acids and Application to Plant <sup>13</sup>C-Labeled Experiments"*](https://doi.org/10.3390/metabo13040466) | ||
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| ```bash | ||
| runMain fr.inrae.p2m2.tools.PositionalCarbon13EnrichmentMain src/test/resources/galaxy430_res.tsv | ||
| ``` | ||
| ## Software programming environment | ||
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| ### test app | ||
| - [SBT](https://www.scala-sbt.org/) | ||
| - [Scala](https://www.scala-lang.org/) | ||
| - [ScalaJS - Node.js with JSDOM](https://www.scala-js.org/doc/project/js-environments.html) | ||
| - [Node.js](https://nodejs.org/en) | ||
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| ```bash | ||
| sbt positionalCarbonSourcesJVM/test | ||
| sbt positionalCarbonSourcesJS/test | ||
| ``` | ||
| ### Dependencies for HTML generation | ||
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| - [Chart.js](https://www.chartjs.org/) | ||
| - [ScalaTags](https://com-lihaoyi.github.io/scalatags/) | ||
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| ### command line | ||
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| #### run tests | ||
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| ```shell | ||
| sbt positionalCarbonSourcesJVM/run jvm/src/test/resources/galaxy430_res.tsv | ||
| sbt test | ||
| ``` | ||
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| ### jar | ||
| ### Html | ||
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| #### Development version | ||
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| ``` | ||
| sbt positionalCarbonSourcesJVM/assembly | ||
| ```shell | ||
| sbt fastOptJS::webpack | ||
| # open html/index.html | ||
| ``` | ||
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| ### Html | ||
| #### Release | ||
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| ```shell | ||
| sbt fastLinkJS | ||
| sbt fullOptJS::webpack | ||
| cp target/scala-2.13/scalajs-bundler/main/positional-carbon13-enrichment-opt-bundle.js docs/ | ||
| # open docs/index.html | ||
| ``` | ||
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| ```main | ||
| fullOptJS | ||
| # --> js/target/scala-2.13/positionalcarbonsources-opt | ||
| ``` | ||
| ## Information about the authors and the software | ||
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| *Y. Dellero, O. Filangi, A . Bouchereau* | ||
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| - [Institute for Genetics, Environment and Plant Protection (IGEPP), National Research Institute for Agriculture, Food and Environment (INRAE), Institut Agro, Université Rennes, 35650 Le Rheu, France](https://www6.rennes.inrae.fr/igepp) | ||
| - [Metabolic Profiling and Metabolomic Platform (P2M2), Biopolymers Interactions Assemblies, Institute for Genetics, Environment and Plant Protection, 35650 Le Rheu, France](https://www6.inrae.fr/p2m2/) | ||
| - [MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 35650 Le Rheu, France](https://www.metabohub.fr/) | ||
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| This code is released under the MIT License. | ||
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| open [index](./html/index.html) |
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@@ -15,11 +15,18 @@ ThisBuild / developers := List( | |
| Developer("ofilangi", "Olivier Filangi", "[email protected]",url("https://github.com/ofilangi")) | ||
| ) | ||
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| lazy val root = (project in file(".")) | ||
| .aggregate(positionalCarbonSources.js, positionalCarbonSources.jvm) | ||
| lazy val root = (project in file(".")). | ||
| enablePlugins(ScalaJSPlugin). | ||
| enablePlugins(ScalaJSBundlerPlugin). | ||
| // add the `it` configuration | ||
| configs(IntegrationTest). | ||
| // add `it` tasks | ||
| settings(Defaults.itSettings: _*). | ||
| // add Scala.js-specific settings and tasks to the `it` configuration | ||
| settings(inConfig(IntegrationTest)(ScalaJSPlugin.testConfigSettings): _*) | ||
| .settings( | ||
| name := "positional-carbon13-enrichment", | ||
| version := "0.1.0-SNAPSHOT", | ||
| version := "1.0.0", | ||
| credentials += { | ||
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| val realm = scala.util.Properties.envOrElse("REALM_CREDENTIAL", "") | ||
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@@ -45,63 +52,34 @@ lazy val root = (project in file(".")) | |
| publishLocalConfiguration := publishLocalConfiguration.value.withOverwrite(true), | ||
| pomIncludeRepository := { _ => false }, | ||
| publishMavenStyle := true, | ||
| coverageMinimumStmtTotal := 70, | ||
| coverageMinimumBranchTotal := 30, | ||
| coverageMinimumStmtPerPackage := 70, | ||
| coverageMinimumBranchPerPackage := 30, | ||
| coverageMinimumStmtPerFile := 70, | ||
| coverageMinimumBranchPerFile := 30, | ||
| coverageFailOnMinimum := true, | ||
| coverageHighlighting := true | ||
| ) | ||
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| // Project containing source code shared between the JS and JVM projects. | ||
| // This project should never be compiled or packages but is simply an IntelliJ IDEA | ||
| // friendly alternative to a shared code directory. Projects depending on this | ||
| // projects source code should declare a dependency as 'Provided' AND append | ||
| // this projects source directory manually to 'unmanagedSourceDirectories'. | ||
| lazy val PositionalCarbon13EnrichmentShared = project.in(file("shared")) | ||
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| lazy val PositionalCarbon13EnrichmentSharedSettings = Seq( | ||
| name := "foo", | ||
| version := "0.1-SNAPSHOT", | ||
| // NOTE: The following line will generate a warning in IntelliJ IDEA, which can be ignored: | ||
| // "The following source roots are outside the corresponding base directories" | ||
| Compile / unmanagedSourceDirectories += ( (PositionalCarbon13EnrichmentShared / Compile) / scalaSource).value | ||
| ) | ||
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| lazy val positionalCarbonSources = crossProject(JSPlatform, JVMPlatform).in(file(".")). | ||
| settings( | ||
| libraryDependencies ++= Seq( | ||
| "com.lihaoyi" %%% "utest" % "0.8.1" % Test | ||
| ), | ||
| testFrameworks += new TestFramework("utest.runner.Framework") | ||
| ). | ||
| jvmSettings( | ||
| buildInfoKeys := Seq[BuildInfoKey](name, version, scalaVersion, sbtVersion), | ||
| coverageMinimumStmtTotal := 20, | ||
| coverageFailOnMinimum := false, | ||
| coverageHighlighting := true, | ||
| libraryDependencies ++= Seq( | ||
| "com.lihaoyi" %% "utest" % "0.8.1" % Test, | ||
| "com.github.scopt" %% "scopt" % "4.1.0" | ||
| "com.lihaoyi" %%% "utest" % "0.8.1" % Test, | ||
| "com.lihaoyi" %%% "scalatags" % "0.12.0", | ||
| ), | ||
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| // Compile / unmanagedSourceDirectories += baseDirectory.value.getParentFile.getParentFile / "shared"/"src"/"main"/"scala", | ||
| // Test / unmanagedSourceDirectories += baseDirectory.value.getParentFile.getParentFile / "shared"/"src"/"test"/"scala", | ||
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| Compile / mainClass := Some("fr.inrae.p2m2.app.PositionalCarbon13EnrichmentMain") , | ||
| testFrameworks += new TestFramework("utest.runner.Framework"), | ||
| assembly / target := file("assembly"), | ||
| assembly / assemblyJarName := s"${name.value}-${version.value}.jar" | ||
| ) | ||
| .enablePlugins(BuildInfoPlugin) | ||
| .jsSettings( | ||
| // Add JS-specific settings here | ||
| scalaJSUseMainModuleInitializer := true, | ||
| jsEnv := new org.scalajs.jsenv.jsdomnodejs.JSDOMNodeJSEnv(), | ||
| libraryDependencies ++= Seq( | ||
| "com.lihaoyi" %%% "utest" % "0.8.1" % Test, | ||
| "org.scala-js" %%% "scalajs-dom" % "2.1.0", | ||
| "com.lihaoyi" %%% "scalatags" % "0.12.0" | ||
| ) | ||
| assembly / assemblyJarName := s"${name.value}-${version.value}.jar", | ||
| Compile / fastOptJS / scalaJSLinkerConfig ~= { | ||
| _.withOptimizer(false) | ||
| .withPrettyPrint(true) | ||
| .withSourceMap(true) | ||
| }, | ||
| Compile / fullOptJS / scalaJSLinkerConfig ~= { | ||
| _.withSourceMap(false) | ||
| .withModuleKind(ModuleKind.CommonJSModule) | ||
| }, | ||
| webpackBundlingMode := BundlingMode.LibraryAndApplication(), | ||
| Compile / npmDependencies ++= Seq( | ||
| "chart" -> "0.1.2", | ||
| ), | ||
| Test / npmDevDependencies ++= Seq( | ||
| "jsdom" -> "21.1.1" | ||
| ), | ||
| Compile / scalaJSUseMainModuleInitializer := true, | ||
| Test / requireJsDomEnv := true | ||
| ) | ||
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| Global / onChangedBuildSource := ReloadOnSourceChanges | ||
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