Merge pull request #184 from veg/develop

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veg · Mar 1, 2021 · 50e066e · 50e066e
2 parents dbcba35 + 2491142
commit 50e066e
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Showing 5 changed files with 171 additions and 163 deletions.
diff --git a/.eslintrc.yml b/.eslintrc.yml
@@ -0,0 +1,11 @@
+env:
+  browser: true
+  commonjs: true
+  es6: true
+extends: 'eslint:recommended'
+globals:
+  Atomics: readonly
+  SharedArrayBuffer: readonly
+parserOptions:
+  ecmaVersion: 11
+rules: {}
diff --git a/app/gard/gard.js b/app/gard/gard.js
@@ -12,7 +12,7 @@ const client = redis.createClient({ host: config.redis_host, port: config.redis_
 
 var gard = function(socket, stream, params) {
 
-  var self = this;
+  const self = this;
 
   const variation_map = { none: "None", general_discrete: "GDD", beta_gamma: "Gamma" };
 
@@ -32,6 +32,7 @@ var gard = function(socket, stream, params) {
     variation_map[self.params.analysis.site_to_site_variation];
   self.rate_classes = self.params.analysis.rate_classes || 2;
   self.genetic_code = self.params.msa[0].gencodeid + 1;
+  self.run_mode = self.params.analysis.run_mode == "1" ? "Faster": "Normal";
   self.datatype = self.params.analysis.datatype || "0";
   self.datatype = datatypes[self.datatype];
   self.nj = self.params.msa[0].nj;
@@ -75,6 +76,8 @@ var gard = function(socket, stream, params) {
       self.rate_classes +
       ",datatype=" +
       self.datatype+
+      ",run_mode=" +
+      self.run_mode+
       ",analysis_type=" +
       self.type +
       ",cwd=" +

diff --git a/app/gard/gard.sh b/app/gard/gard.sh
@@ -16,6 +16,7 @@ GENETIC_CODE=$genetic_code
 RATE_VARIATION=$rate_var
 RATE_CLASSES=$rate_classes
 DATATYPE=$datatype
+RUN_MODE=$run_mode
 
 PROCS=$procs
 
@@ -36,8 +37,8 @@ export HYPHY_PATH=$HYPHY_PATH
 
 trap 'echo "Error" > $STATUS_FILE; exit 1' ERR
 
-echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN"
-mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
+echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN"
+mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $GARD --type $DATATYPE --alignment $FN --model $MODEL --mode $RUN_MODE --rv $RATE_VARIATION --rate-classes $RATE_CLASSES --output $RESULTS_FN > $PROGRESS_FILE
 
 echo "Completed" > $STATUS_FILE
 

diff --git a/package.json b/package.json
@@ -31,7 +31,7 @@
     "winston": "^3.2.1"
   },
   "devDependencies": {
-    "eslint": "^7.6.0",
+    "eslint": "^7.9.0",
     "heapdump": "^0.3.15",
     "socket.io-client": "1.x.x"
   }