Merge pull request #243 from hybsearch/configurable-jml-and-mrbayes

Expose JML and MrBayes config to the UI
hybsearch · Apr 27, 2019 · 763adba · 763adba
2 parents 96b5cf7 + f26a43c
commit 763adba
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Showing 6 changed files with 74 additions and 25 deletions.
diff --git a/server/pipeline/pipelines/mbnb.js b/server/pipeline/pipelines/mbnb.js
@@ -37,6 +37,33 @@ let options = {
 		label: "BEAST's 'chainLength' parameter",
 		description: 'another desc',
 	},
+	mrBayesConfig: {
+		default: `
+set autoclose=yes nowarn=yes;
+lset nst=6 rates=invgamma;
+prset topologypr = uniform;
+prset brlenspr = clock:uniform;
+mcmc ngen=20000 samplefreq=100;
+sumt;`.trim(),
+		type: 'textarea',
+		label: 'MrBayes Config',
+		description: '',
+	},
+	jmlConfig: {
+		default: `
+# species and seqperspecies are automatically set,
+# but can be overridden here if needed
+locusrate = 1.0
+heredityscalar = 0.25
+seqgencommand = -mHKY -f0.2678,0.1604,0.2031,0.3687 -t1.5161 -i0 -a0.2195 -l810
+significancelevel = 0.9999
+burnin = 0
+thinning = 1
+seed = -1`.trim(),
+		type: 'textarea',
+		label: 'JML Config',
+		description: '',
+	},
 }
 
 let steps = [
@@ -64,7 +91,7 @@ let steps = [
 	{
 		// does whatever mrbayes does
 		input: ['aligned-nexus'],
-		transform: ([data]) => [mrBayes(data)],
+		transform: ([data], { mrBayesConfig }) => [mrBayes(data, mrBayesConfig)],
 		output: ['consensus-tree'],
 	},
 	{
@@ -149,11 +176,15 @@ let steps = [
 	{
 		// run JML
 		input: ['phylipified-trees', 'aligned-phylip', 'phylip-identifier-map'],
-		transform: ([phylipifiedTrees, alignedPhylip, phylipIdentMap]) => [
+		transform: (
+			[phylipifiedTrees, alignedPhylip, phylipIdentMap],
+			{ jmlConfig }
+		) => [
 			jml({
 				phylipData: alignedPhylip,
 				trees: phylipifiedTrees,
 				phylipMapping: phylipIdentMap,
+				config: jmlConfig,
 			}),
 		],
 		output: ['jml-output'],

diff --git a/server/ui/ui.js b/server/ui/ui.js
@@ -269,9 +269,15 @@ const handleNewSteps = payload => {
 		([key, val]) =>
 			// prettier-ignore
 			`<div class="option-row">
-				<label>${val.label}: <input name="${key}" type="${val.type}" value="${val.default}" placeholder="${val.description}"></label>
+				<label>
+					${val.label}:
+						${val.type === 'textarea'
+							? `<textarea name="${key}" placeholder="${val.description}">${val.default}</textarea>`
+							: `<input name="${key}" type="${val.type}" value="${val.default}" placeholder="${val.description}">`}
+				</label>
 			</div>`
 	)
+
 	if (options.length) {
 		optionsEl.removeAttribute('hidden')
 		optionsContainer.innerHTML = options.join('')

diff --git a/server/wrappers/jml/__tests__/__snapshots__/ctl.test.js.snap b/server/wrappers/jml/__tests__/__snapshots__/ctl.test.js.snap
@@ -3,23 +3,27 @@
 exports[`emydura-short.phy 1`] = `
 "species = tQwNDLi oTYwLH vwAqcZ CXTpAGBdz
 seqperspecies = 3 2 2 1
+
 locusrate = 1.0
 heredityscalar = 0.25
 seqgencommand = -mHKY -f0.2678,0.1604,0.2031,0.3687 -t1.5161 -i0 -a0.2195 -l810
 significancelevel = 0.9999
 burnin = 0
 thinning = 1
-seed = -1"
+seed = -1
+"
 `;
 
 exports[`smallerlepus.phy 1`] = `
 "species = igcfean abbdbkga cbcidpnh bkaabphc
 seqperspecies = 15 2 8 4
+
 locusrate = 1.0
 heredityscalar = 0.25
 seqgencommand = -mHKY -f0.2678,0.1604,0.2031,0.3687 -t1.5161 -i0 -a0.2195 -l810
 significancelevel = 0.9999
 burnin = 0
 thinning = 1
-seed = -1"
+seed = -1
+"
 `;
diff --git a/server/wrappers/jml/ctl.js b/server/wrappers/jml/ctl.js
@@ -3,16 +3,20 @@
 const mapValues = require('lodash/mapValues')
 const groupBy = require('lodash/groupBy')
 
-function makeControlData(speciesCounts) {
-	return `species = ${Object.keys(speciesCounts).join(' ')}
-seqperspecies = ${Object.values(speciesCounts).join(' ')}
+let defaultConfig = `
 locusrate = 1.0
 heredityscalar = 0.25
 seqgencommand = -mHKY -f0.2678,0.1604,0.2031,0.3687 -t1.5161 -i0 -a0.2195 -l810
 significancelevel = 0.9999
 burnin = 0
 thinning = 1
 seed = -1`
+
+function makeControlData(speciesCounts, config) {
+	return `species = ${Object.keys(speciesCounts).join(' ')}
+seqperspecies = ${Object.values(speciesCounts).join(' ')}
+${config || defaultConfig}
+`
 }
 
 function getSpeciesFromPhylip(phylipData) {
@@ -26,12 +30,12 @@ function getSpeciesFromPhylip(phylipData) {
 }
 
 module.exports = computeSpecies
-function computeSpecies(phylip) {
+function computeSpecies(phylip, config) {
 	let allSpecies = [...getSpeciesFromPhylip(phylip)]
 	let speciesCounts = mapValues(
 		groupBy(allSpecies, speciesName => speciesName.split('x')[0]),
 		speciesInstances => speciesInstances.length
 	)
 
-	return makeControlData(speciesCounts)
+	return makeControlData(speciesCounts, config)
 }
diff --git a/server/wrappers/jml/index.js b/server/wrappers/jml/index.js
@@ -28,7 +28,7 @@ const readJmlOutputFile = filepath => {
 }
 
 module.exports = jml
-async function jml({ phylipData, trees, phylipMapping }) {
+async function jml({ phylipData, trees, phylipMapping, config }) {
 	let workDir = tempy.directory()
 
 	let phylipFile = path.join(workDir, 'input.phy')
@@ -38,7 +38,7 @@ async function jml({ phylipData, trees, phylipMapping }) {
 	fs.writeFileSync(treesFile, trees, 'utf-8')
 
 	let controlFile = path.join(workDir, 'jml.input.ctl')
-	let controlData = generateControlFile(phylipData)
+	let controlData = generateControlFile(phylipData, config)
 	fs.writeFileSync(controlFile, controlData, 'utf-8')
 
 	// find binary via `which`

diff --git a/server/wrappers/mrbayes/index.js b/server/wrappers/mrbayes/index.js
@@ -21,26 +21,30 @@ $ mb
 # Created consensus tree file: {ORIG_FILENAME}.con.tre
 */
 
-function insertCommandBlock(data) {
-	let cmdBlock = dedent`
-	begin mrbayes;
-		set autoclose=yes nowarn=yes;
-		lset nst=6 rates=invgamma;
-		prset topologypr = uniform;
-		prset brlenspr = clock:uniform;
-		mcmc ngen=20000 samplefreq=100;
-		sumt;
-	end;`
-	return data.replace('end;', `end;\n${cmdBlock}\n`)
+let cmdBlock = `
+	set autoclose=yes nowarn=yes;
+	lset nst=6 rates=invgamma;
+	prset topologypr = uniform;
+	prset brlenspr = clock:uniform;
+	mcmc ngen=20000 samplefreq=100;
+	sumt;
+`
+
+function insertCommandBlock(data, config) {
+	config = dedent`
+		begin mrbayes;
+			${config || cmdBlock}
+		end;`
+	return data.replace('end;', `end;\n${config}\n`)
 }
 
 module.exports = mrbayes
-async function mrbayes(data) {
+async function mrbayes(data, config) {
 	const inputFile = tempy.file()
 	const outputFile = inputFile + '.con.tre'
 
 	// we can control mrbayes with a "command block"
-	data = insertCommandBlock(data)
+	data = insertCommandBlock(data, config)
 
 	fs.writeFileSync(inputFile, data, 'utf-8')