From 63aa78c741ca1a62fe125ee5a8fc7fdff55349e9 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 16 Dec 2024 23:20:26 +0000
Subject: [PATCH 1/5] Update parsnp to 2.1.2

---
 recipes/parsnp/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

From 1c345f998c860eed6e9968c61ec0e03884106cef Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 17 Dec 2024 18:54:02 -0600
Subject: [PATCH 2/5] Update build.sh

---
 recipes/parsnp/build.sh | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/recipes/parsnp/build.sh b/recipes/parsnp/build.sh
index 8c6ca7f6a253e..107375c471b54 100644
--- a/recipes/parsnp/build.sh
+++ b/recipes/parsnp/build.sh
@@ -1,41 +1,43 @@
 #!/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=$PREFIX CXXFLAGS='-fopenmp' --disable-shared 
+autoreconf -if
+if [[ `uname` == "Darwin" ]]; then
+    sed -i.bak '' '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
+    ./configure --prefix="$PREFIX" CXX="${CXX}" CXXFLAGS='${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" CXX="${CXX}" CXXFLAGS='${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

From 30d43739a5a185744d63ba9fa2441dd04b2a0d9a Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 17 Dec 2024 19:11:18 -0600
Subject: [PATCH 3/5] Update build.sh

---
 recipes/parsnp/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/parsnp/build.sh b/recipes/parsnp/build.sh
index 107375c471b54..f271ba23e90e9 100644
--- a/recipes/parsnp/build.sh
+++ b/recipes/parsnp/build.sh
@@ -13,10 +13,10 @@ cd muscle
 autoreconf -if
 if [[ `uname` == "Darwin" ]]; then
     sed -i.bak '' '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix="$PREFIX" CXX="${CXX}" CXXFLAGS='${CXXFLAGS} -O3 -fopenmp' --disable-shared 
+    ./configure --prefix="$PREFIX" CXXFLAGS='${CXXFLAGS} -O3 -fopenmp' --disable-shared 
 else
     sed -i.bak '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix="$PREFIX" CXX="${CXX}" CXXFLAGS='${CXXFLAGS} -O3 -fopenmp'
+    ./configure --prefix="$PREFIX" CXXFLAGS='${CXXFLAGS} -O3 -fopenmp'
 fi
 make -j"${CPU_COUNT}"
 make install

From 0dd015a852717cde6fddaed2749746edb3f90145 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 17 Dec 2024 19:36:13 -0600
Subject: [PATCH 4/5] Update build.sh

---
 recipes/parsnp/build.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/recipes/parsnp/build.sh b/recipes/parsnp/build.sh
index f271ba23e90e9..d610e4f91dbad 100644
--- a/recipes/parsnp/build.sh
+++ b/recipes/parsnp/build.sh
@@ -10,13 +10,12 @@ mkdir -p "$PREFIX/bin/bin"
 cd muscle
 
 ./autogen.sh
-autoreconf -if
 if [[ `uname` == "Darwin" ]]; then
     sed -i.bak '' '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix="$PREFIX" CXXFLAGS='${CXXFLAGS} -O3 -fopenmp' --disable-shared 
+    ./configure --prefix='$PREFIX' CXX='${CXX}' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp' --disable-shared 
 else
     sed -i.bak '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix="$PREFIX" CXXFLAGS='${CXXFLAGS} -O3 -fopenmp'
+    ./configure --prefix='$PREFIX' CXX='${CXX}' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp'
 fi
 make -j"${CPU_COUNT}"
 make install

From 00dc1197c2424bbe52150ea0f7dd0b726dee82c4 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 17 Dec 2024 20:10:31 -0600
Subject: [PATCH 5/5] Update build.sh

---
 recipes/parsnp/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/parsnp/build.sh b/recipes/parsnp/build.sh
index d610e4f91dbad..99b22a3173862 100644
--- a/recipes/parsnp/build.sh
+++ b/recipes/parsnp/build.sh
@@ -12,10 +12,10 @@ cd muscle
 ./autogen.sh
 if [[ `uname` == "Darwin" ]]; then
     sed -i.bak '' '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix='$PREFIX' CXX='${CXX}' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp' --disable-shared 
+    ./configure --prefix='$PREFIX' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp' --disable-shared 
 else
     sed -i.bak '/bin_PROGRAMS/d' ./libMUSCLE/Makefile.am
-    ./configure --prefix='$PREFIX' CXX='${CXX}' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp'
+    ./configure --prefix='$PREFIX' CXXFLAGS='${CXXFLAGS} -O3 -fopenmp'
 fi
 make -j"${CPU_COUNT}"
 make install