Add rdeval

recipes/rdeval/Makefile.patch

@@ -0,0 +1,25 @@
+--- a/Makefile
++++ b/Makefile
+@@ -12,7 +12,12 @@
+ INCLUDE = include
+ BINDIR := $(BUILD)/.o
+
+-LDFLAGS := -pthread
++ifeq ($(origin LDFLAGS), undefined)
++    LDFLAGS := -pthread
++else
++    LDFLAGS := $(LDFLAGS) -pthread
++endif
++
+ LIBS = -lz
+
+ OBJS := main input reads
+@@ -27,7 +32,7 @@
+ all: head validate regenerate
+
+ $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
+
+ .PHONY: gfalibs
+ gfalibs:

recipes/rdeval/build.sh

@@ -2,13 +2,21 @@
 
 set -o errexit
 set -o nounset
-set -o xtrace
+
+if [ -e "$PREFIX/include" ]; then
+    export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I$PREFIX/include"
+fi
+
+if [ -e "$PREFIX/lib" ]; then
+    export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L$PREFIX/lib"
+fi
+
+echo "CPPFLAGS=\"$CPPFLAGS\""
+echo "LDFLAGS=\"$LDFLAGS\""
 
 cd "$SRC_DIR"
 
-export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include"
-export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
+make
 
-make -j"${CPU_COUNT}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -Wno-unused-command-line-argument" LDFLAGS="${LDFLAGS}"
 install -d "$PREFIX/bin"
 install -v -m 0755 build/bin/rdeval "$PREFIX/bin/"

recipes/rdeval/gfalibs-Makefile.patch

@@ -0,0 +1,25 @@
+--- a/gfalibs/Makefile
++++ b/gfalibs/Makefile
+@@ -1,4 +1,4 @@
+-CXX = g++
++CXX ?= g++
+ INCLUDE_DIR = -I./include
+ WARNINGS = -Wall -Wextra
+
+@@ -8,15 +8,13 @@
+ BUILD = build/bin
+ SOURCE = src
+ INCLUDE = include
+-LDFLAGS :=
+
+ SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory)
+
+ all: $(SOURCES)
+-	@
+
+ %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
+
+ clean:
+ 	$(RM) *.o

recipes/rdeval/meta.yaml

@@ -9,12 +9,11 @@ source:
   url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip
   sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d
   patches:
-    - zlib.patch
-    - foo.patch
-    - gfalibs.patch
+    - Makefile.patch
+    - gfalibs-Makefile.patch
 
 build: 
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x.x") }}
 
@@ -23,7 +22,6 @@ requirements:
     - {{ compiler('cxx') }}
     - make
   host:
-    - pthread-stubs
     - zlib
 
 test:

recipes/rdeval/reads.patch

@@ -0,0 +1,10 @@
+--- a/src/reads.cpp
++++ b/src/reads.cpp
+@@ -178,7 +178,6 @@
+
+                 StreamObj streamObj;
+                 stream = streamObj.openStream(userInput, 'r', i);
+-                Sequences* readBatch = new Sequences;
+
+                 while (getline(*stream, newLine)) {
+