diff --git a/recipes/parsnp/build.sh b/recipes/parsnp/build.sh
index 8c6ca7f6a253e..99b22a3173862 100644
--- a/recipes/parsnp/build.sh
+++ b/recipes/parsnp/build.sh
@@ -1,41 +1,42 @@
 #!/bin/bash
 
-mkdir -p  "$PREFIX/bin"
-mkdir -p  "$PREFIX/bin/bin"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
+mkdir -p "$PREFIX/bin"
+mkdir -p "$PREFIX/bin/bin"
 
 cd muscle
 
 ./autogen.sh
-if [ `uname` == Darwin ]; then
-    sed -i '' '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix=$PREFIX CXXFLAGS='-fopenmp' --disable-shared 
+if [[ `uname` == "Darwin" ]]; then
+    sed -i.bak '' '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
+    ./configure --prefix='$PREFIX' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp' --disable-shared 
 else
-    sed -i '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix=$PREFIX CXXFLAGS='-fopenmp'
+    sed -i.bak '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
+    ./configure --prefix='$PREFIX' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp'
 fi
-make -j
+make -j"${CPU_COUNT}"
 make install
 
 cd ..
 
-# Patch automake update. remove for future release 
-#sed '1 s/.*/AC_INIT([parsnp],[1.6.1])/' configure.ac
-#sed '2 s/.*/AM_INIT_AUTOMAKE([-Wall])/' configure.ac
-
 ./autogen.sh
-./configure --with-libmuscle=$PREFIX/include
-make LDADD="$LDADD -lMUSCLE-3.7"
+autoreconf -if
+./configure CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3" --with-libmuscle="$PREFIX/include"
+make LDADD="$LDADD -lMUSCLE-3.7" -j"${CPU_COUNT}"
 make install
 
 rm -R muscle/libMUSCLE
 rm -R muscle/autom4te.cache
 rm -R muscle/m4
 
-cp parsnp $PREFIX/bin 
+install -v -m 0755 parsnp $PREFIX/bin
 cp extend.py $PREFIX/bin
 cp logger.py $PREFIX/bin
 cp partition.py $PREFIX/bin
-cp src/parsnp_core $PREFIX/bin/bin
+install -v -m 0755 src/parsnp_core $PREFIX/bin/bin
 cp template.ini $PREFIX/bin
 cp -R bin $PREFIX/bin 
 cp -R examples $PREFIX/bin
diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml
index 0a3982f7469da..dece37f1798bb 100644
--- a/recipes/parsnp/meta.yaml
+++ b/recipes/parsnp/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.1.1" %}
+{% set version = "2.1.2" %}
 
 package:
   name: parsnp
@@ -6,7 +6,7 @@ package:
 
 source:
   url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz"
-  sha256: 7887ee4030dad6f30a4b735f1ee463024204030adbdcb0fa96562e6e8664474e
+  sha256: accb60e70a1ea06fb707824955c4cd41b606356c41354f10e044a02cff4a984d
 
 build:
   number: 0