adding RDEVAL (#52070)

* initial attempt

* adding make as a dependency

* new hash

* adding test

* fixing build.sh

* using version with submodules

* adding zlib

* updates

* update

* foo

* quote

* u

* a

* patch

* zlib

* zlib

* foo

* clean up recipe

* clean up patches

* Update build.sh

* add gfalibs patch

* Update meta.yaml

* Update meta.yaml

* add gfalibs patch

* edit foo.patch

* Update foo.patch

* edit foo.patch

* edit foo.patch

* Update build.sh

---------

Co-authored-by: Richard C. Burhans <[email protected]>
Co-authored-by: mencian <[email protected]>
Co-authored-by: Joshua Zhuang <[email protected]>

Author: 3 people

recipes/rdeval/build.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o nounset
+set -o xtrace
+
+cd "$SRC_DIR"
+
+export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include"
+export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
+
+make -j"${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/foo.patch

@@ -0,0 +1,38 @@
+diff --git a/Makefile b/Makefile
+index 5823f28..6f4a60f 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+-CXX ?= g++
+-INCLUDE_DIR = -I./include -I./gfalibs/include
++CXX ?= ${CXX}
++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include
+ WARNINGS = -Wall -Wextra
+ 
+ CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS)
+@@ -12,8 +12,8 @@ SOURCE = src
+ INCLUDE = include
+ BINDIR := $(BUILD)/.o
+ 
+-LDFLAGS := -pthread
+-LIBS = -lz
++LDFLAGS := -pthread -L${PREFIX}/lib
++LIBS := -lz -lpthread
+ 
+ OBJS := main input reads
+ BINS := $(addprefix $(BINDIR)/, $(OBJS))
+@@ -22,12 +22,12 @@ BINS := $(addprefix $(BINDIR)/, $(OBJS))
+ GFALIBS_DIR := $(CURDIR)/gfalibs
+ 
+ head: $(BINS) gfalibs | $(BUILD)
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
++	$(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
+ 	
+ all: head validate regenerate
+ 
+ $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
++	$(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS)
+ 
+ .PHONY: gfalibs
+ gfalibs:

recipes/rdeval/gfalibs.patch

@@ -0,0 +1,30 @@
+diff --git a/gfalibs/Makefile b/gfalibs/Makefile
+index de9ab9b..90a703c 100644
+--- a/gfalibs/Makefile
++++ b/gfalibs/Makefile
+@@ -1,5 +1,5 @@
+-CXX = g++
+-INCLUDE_DIR = -I./include
++CXX = $(CXX)
++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap
+ WARNINGS = -Wall -Wextra
+ 
+ CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS)
+@@ -8,7 +8,7 @@ TARGET = gfalibs
+ BUILD = build/bin
+ SOURCE = src
+ INCLUDE = include
+-LDFLAGS :=
++LDFLAGS := -L${PREFIX}/lib -pthread
+ 
+ SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory)
+ 
+@@ -16,7 +16,7 @@ all: $(SOURCES)
+ 	@
+ 
+ %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
++	$(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz -lpthread
+     
+ clean:
+ 	$(RM) *.o

recipes/rdeval/meta.yaml

@@ -0,0 +1,45 @@
+{% set name = "rdeval" %}
+{% set version = "0.0.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+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
+
+build: 
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - make
+  host:
+    - pthread-stubs
+    - zlib
+
+test:
+  commands:
+    - rdeval --help
+
+about:
+  home: https://github.com/vgl-hub/{{ name }}
+  summary: A general purpose, multithreaded read analysis and manipulation tool.
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  dev_url: https://github.com/vgl-hub/{{ name }}
+  doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

recipes/rdeval/zlib.patch

@@ -0,0 +1,52 @@
+diff --git a/gfalibs/include/output.h b/gfalibs/include/output.h
+index aabbec0..20f0dc1 100644
+--- a/gfalibs/include/output.h
++++ b/gfalibs/include/output.h
+@@ -12,7 +12,7 @@
+ #include "gfa-lines.h"
+ #include "gfa.h"
+ 
+-#include "zlib.h"
++#include <zlib.h>
+ #include "zstream/zstream_common.hpp"
+ #include "zstream/ozstream.hpp"
+ #include "zstream/ozstream_impl.hpp"
+diff --git a/gfalibs/include/stream-obj.h b/gfalibs/include/stream-obj.h
+index 1faa4df..8e28bf6 100644
+--- a/gfalibs/include/stream-obj.h
++++ b/gfalibs/include/stream-obj.h
+@@ -2,7 +2,7 @@
+ #define STREAM_OBJ_H
+ 
+ #include <fstream>
+-#include "zlib.h"
++#include <zlib.h>
+ 
+ class membuf : public std::streambuf {
+     
+diff --git a/gfalibs/src/stream-obj.cpp b/gfalibs/src/stream-obj.cpp
+index e9694ee..c6eca26 100644
+--- a/gfalibs/src/stream-obj.cpp
++++ b/gfalibs/src/stream-obj.cpp
+@@ -5,7 +5,7 @@
+ 
+ #include "bed.h"
+ #include "struct.h"
+-#include "zlib.h"
++#include <zlib.h>
+ #include "global.h"
+ #include "log.h"
+ #include "threadpool.h"
+diff --git a/src/reads.cpp b/src/reads.cpp
+index 866f49b..ac714cf 100644
+--- a/src/reads.cpp
++++ b/src/reads.cpp
+@@ -14,7 +14,7 @@
+ #include "functions.h" // global functions
+ #include "stream-obj.h"
+ 
+-#include "zlib.h"
++#include <zlib.h>
+ #include "zstream/zstream_common.hpp"
+ #include "zstream/ozstream.hpp"
+ #include "zstream/ozstream_impl.hpp"