From 963b38131897e1e96a36962424779f81d5972d04 Mon Sep 17 00:00:00 2001
From: Sergey Koren <sergek@umd.edu>
Date: Tue, 8 Aug 2023 11:05:02 -0400
Subject: [PATCH] Check for required dependencies depending on what pipelien
 we're running (e.g. graphaligner only for ONT, bwa only for HiC, etc)

---
 src/verkko.sh | 53 ++++++++++++++++++++++++++++++---------------------
 1 file changed, 31 insertions(+), 22 deletions(-)

diff --git a/src/verkko.sh b/src/verkko.sh
index 4111f5bb..9f7a8261 100755
--- a/src/verkko.sh
+++ b/src/verkko.sh
@@ -675,34 +675,43 @@ elif [ ! -e "$mbg" ] ; then
     errors="${errors}Can't find MBG executable at '$mbg'.\n"
 fi
 
-if   [ "x$graphaligner" = "x" ] ; then
-    errors="${errors}Can't find GraphAligner executable in \$PATH or \$VERKKO/bin/GraphAligner.\n"
-elif [ ! -e "$graphaligner" ] ; then
-    errors="${errors}Can't find GraphAligner executable at '$graphaligner'.\n"
-fi
+# graphaligner and winnowmap are required when we have ONT data
+if [ "x$withont" = "xTrue" ] ; then
+    if   [ "x$graphaligner" = "x" ] ; then
+        errors="${errors}Can't find GraphAligner executable in \$PATH or \$VERKKO/bin/GraphAligner.\n"
+    elif [ ! -e "$graphaligner" ] ; then
+        errors="${errors}Can't find GraphAligner executable at '$graphaligner'.\n"
+    fi
 
-if   [ "x$mashmap" = "x" ] ; then
-    errors="${errors}Can't find MashMap executable in \$PATH or \$VERKKO/bin/mashmap.\n"
-elif [ ! -e "$mashmap" ] ; then
-    errors="${errors}Can't find MashMap executable at '$mashmap'.\n"
+    if   [ "x$winnowmap" = "x" ] ; then
+        errors="${errors}Can't find Winnowmap executable in \$PATH or \$VERKKO/bin/winnowmap.\n"
+    elif [ ! -e "$winnowmap" ] ; then
+        errors="${errors}Can't find Winnowmap executable at '$winnowmap'.\n"
+    fi
 fi
 
-if   [ "x$winnowmap" = "x" ] ; then
-    errors="${errors}Can't find Winnowmap executable in \$PATH or \$VERKKO/bin/winnowmap.\n"
-elif [ ! -e "$winnowmap" ] ; then
-    errors="${errors}Can't find Winnowmap executable at '$winnowmap'.\n"
+# mashmap required for hic and for screening contaminant
+if [ ! -z "$screen" -o "x$withhic" = "xTrue" ] ; then
+    if   [ "x$mashmap" = "x" ] ; then
+        errors="${errors}Can't find MashMap executable in \$PATH or \$VERKKO/bin/mashmap.\n"
+    elif [ ! -e "$mashmap" ] ; then
+        errors="${errors}Can't find MashMap executable at '$mashmap'.\n"
+    fi
 fi
 
-if   [ "x$bwa" = "x" ] ; then
-    errors="${errors}Can't find BWA executable in \$PATH or \$VERKKO/bin/bwa.\n"
-elif [ ! -e "$bwa" ] ; then
-    errors="${errors}Can't find BWA executable at '$bwa'.\n"
-fi
+# bwa and samtools required for HiC data
+if [ "x$withhic" = "xTrue" ] ; then
+    if   [ "x$bwa" = "x" ] ; then
+        errors="${errors}Can't find BWA executable in \$PATH or \$VERKKO/bin/bwa.\n"
+    elif [ ! -e "$bwa" ] ; then
+        errors="${errors}Can't find BWA executable at '$bwa'.\n"
+    fi
 
-if   [ "x$samtools" = "x" ] ; then
-    errors="${errors}Can't find Samtools executable in \$PATH or \$VERKKO/bin/samtools.\n"
-elif [ ! -e "$samtools" ] ; then
-    errors="${errors}Can't find Samtools executable at '$samtools'.\n"
+    if   [ "x$samtools" = "x" ] ; then
+        errors="${errors}Can't find Samtools executable in \$PATH or \$VERKKO/bin/samtools.\n"
+    elif [ ! -e "$samtools" ] ; then
+        errors="${errors}Can't find Samtools executable at '$samtools'.\n"
+    fi
 fi
 
 #