From 21ee61c6f6733986b24dbe06b07ec23a9984d883 Mon Sep 17 00:00:00 2001
From: Steven Weaver <sweaver@temple.edu>
Date: Wed, 27 Nov 2024 08:25:12 -0800
Subject: [PATCH] veg/datamonkey-js#752 -- adding new meme options

---
 app/meme/meme.js | 27 ++++++++++++++++++++-------
 app/meme/meme.sh | 17 +++++++----------
 2 files changed, 27 insertions(+), 17 deletions(-)

diff --git a/app/meme/meme.js b/app/meme/meme.js
index 50168c6..4b6b713 100644
--- a/app/meme/meme.js
+++ b/app/meme/meme.js
@@ -5,7 +5,7 @@ var config = require("../../config.json"),
   fs = require("fs"),
   path = require("path");
 
-var meme = function(socket, stream, params) {
+var meme = function (socket, stream, params) {
   var self = this;
   self.socket = socket;
   self.stream = stream;
@@ -26,6 +26,12 @@ var meme = function(socket, stream, params) {
   self.bootstrap = self.params.analysis.bootstrap;
   self.resample = self.params.analysis.resample;
 
+  self.multiple_hits = self.params.multiple_hits;
+  self.site_multihit = self.params.site_multihit;
+  self.rates = self.params.rates;
+  self.resample = self.params.resample;
+  self.impute_states = self.params.impute_states;
+
   // parameter-derived attributes
   self.fn = __dirname + "/output/" + self.id;
   self.output_dir = path.dirname(self.fn);
@@ -36,10 +42,7 @@ var meme = function(socket, stream, params) {
   self.tree_fn = self.fn + ".tre";
 
   self.qsub_params = [
-    "-l walltime=" + 
-    config.meme_walltime + 
-    ",nodes=1:ppn=" + 
-    config.meme_procs,
+    "-l walltime=" + config.meme_walltime + ",nodes=1:ppn=" + config.meme_procs,
     "-q",
     config.qsub_queue,
     "-v",
@@ -59,6 +62,16 @@ var meme = function(socket, stream, params) {
       self.bootstrap +
       ",resample=" +
       self.resample +
+      ",multiple_hits=" +
+      self.multiple_hits +
+      ",site_multihit=" +
+      self.site_multihit +
+      ",rates=" +
+      self.rates +
+      ",resample=" +
+      self.resample +
+      ",impute_states=" +
+      self.impute_states +
       ",genetic_code=" +
       self.genetic_code +
       ",analysis_type=" +
@@ -73,11 +86,11 @@ var meme = function(socket, stream, params) {
     self.output_dir,
     "-e",
     self.output_dir,
-    self.qsub_script
+    self.qsub_script,
   ];
 
   // Write tree to a file
-  fs.writeFile(self.tree_fn, self.nj, function(err) {
+  fs.writeFile(self.tree_fn, self.nj, function (err) {
     if (err) throw err;
   });
 
diff --git a/app/meme/meme.sh b/app/meme/meme.sh
index 69fe491..32200a4 100755
--- a/app/meme/meme.sh
+++ b/app/meme/meme.sh
@@ -11,8 +11,11 @@ CWD=$cwd
 TREE_FN=$tree_fn
 STATUS_FILE=$sfn
 PROGRESS_FILE=$pfn
-#BOOTSTRAP=$bootstrap
-#RESAMPLE=$resample
+MULTIPLE_HITS="$multiple_hits"
+SITE_MULTIHIT="$site_multihit"
+RATES="$rates"
+RESAMPLE="$resample"
+IMPUTE_STATES="$impute_states"
 RESULTS_FN=$fn.MEME.json
 GENETIC_CODE=$genetic_code
 PROCS=$procs
@@ -24,13 +27,7 @@ export HYPHY_PATH=$HYPHY_PATH
 
 trap 'echo "Error" > $STATUS_FILE; exit 1' ERR
 
-#if [ $BOOTSTRAP = "true" ]
-#then
-echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH   meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE"
-mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;"  meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE
-#else
-#  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH   meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE"
-#  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;"  meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE
-#fi
+echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT --rates $RATES --resample $RESAMPLE --impute-states $IMPUTE_STATES >> $PROGRESS_FILE"
+mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT --rates $RATES --resample $RESAMPLE --impute-states $IMPUTE_STATES >> $PROGRESS_FILE
 
 echo "Completed" > $STATUS_FILE