From 674dcc0281ebf08f9ccbc6688836394cdce2d2d9 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 10:43:37 -0500 Subject: [PATCH 01/55] initial attempt --- recipes/rdeval/build.sh | 30 ++++++++++++++++++++++++++++++ recipes/rdeval/meta.yaml | 30 ++++++++++++++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 recipes/rdeval/build.sh create mode 100644 recipes/rdeval/meta.yaml diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh new file mode 100644 index 0000000000000..9c443366babf4 --- /dev/null +++ b/recipes/rdeval/build.sh @@ -0,0 +1,30 @@ +#!/usr/bin/env bash + +set -o errexit +set -o nounset +set -o xtrace + +make + +# mkdir -vp "${PREFIX}/bin" + +# # Define installation manifest +# declare -A files=( +# ["bam_depth.sh"]="0755" +# ["halfdeep.sh"]="0755" +# ["halfdeep.r"]="0755" +# ["scaffold_lengths.py"]="0755" +# ) + +# # Install files +# for file in "${!files[@]}"; do +# if [[ ! -f "$SRC_DIR/$file" ]]; then +# echo "Source file $file not found in $SRC_DIR" >&2 +# exit 1 +# fi +# +# if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then +# echo "Failed to install $file" >&2 +# exit 1 +# fi +# done diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml new file mode 100644 index 0000000000000..97fc488104e5d --- /dev/null +++ b/recipes/rdeval/meta.yaml @@ -0,0 +1,30 @@ +{% set name = "rdeval" %} +{% set version = "0.0.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/vgl-hub/{{ name }}/archive/refs/tags/v{{ version }}.zip + sha256: 78500c88efa48f62f1907301bf36c9b689bd6933a59bd4a38974f0af393ed541 + +requirements: + build: + - {{ compiler('cxx') }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} + +test: + commands: + - ${PREFIX}/bin/genodsp --help + +about: + home: https://github.com/vgl-hub/{{ name }} + summary: A general purpose, multithreaded read analysis and manipulation tool. + license: MIT + license_file: LICENSE + license_url: https://github.com/vgl-hub/{{ name }}/blob/main/LICENSE From e33c5e28de6b5770d0778db5898df4c5fc6ed2c8 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 11:06:01 -0500 Subject: [PATCH 02/55] adding make as a dependency --- recipes/rdeval/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 97fc488104e5d..8cbc4b55bc68b 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -12,6 +12,7 @@ source: requirements: build: - {{ compiler('cxx') }} + - make build: number: 0 From 2b072df731ff3efdfccf882333b6d1a1b7bf2b45 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 11:16:39 -0500 Subject: [PATCH 03/55] new hash --- recipes/rdeval/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 8cbc4b55bc68b..34c96900ad6b6 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -7,7 +7,7 @@ package: source: url: https://github.com/vgl-hub/{{ name }}/archive/refs/tags/v{{ version }}.zip - sha256: 78500c88efa48f62f1907301bf36c9b689bd6933a59bd4a38974f0af393ed541 + sha256: 466ff3dd3f80aa544be4e0992d1d46bbde933279413392cf17a1fe3b6c2fc5be requirements: build: From 8231e37ae1c1bd68e41d095cd0166fe2f167c5cf Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 11:24:09 -0500 Subject: [PATCH 04/55] adding test --- recipes/rdeval/build.sh | 35 ++++++++++++++++------------------- recipes/rdeval/meta.yaml | 2 +- 2 files changed, 17 insertions(+), 20 deletions(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 9c443366babf4..c99823e1c4124 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -8,23 +8,20 @@ make # mkdir -vp "${PREFIX}/bin" -# # Define installation manifest -# declare -A files=( -# ["bam_depth.sh"]="0755" -# ["halfdeep.sh"]="0755" -# ["halfdeep.r"]="0755" -# ["scaffold_lengths.py"]="0755" -# ) +# Define installation manifest +declare -A files=( + ["rdeval"]="0755" +) -# # Install files -# for file in "${!files[@]}"; do -# if [[ ! -f "$SRC_DIR/$file" ]]; then -# echo "Source file $file not found in $SRC_DIR" >&2 -# exit 1 -# fi -# -# if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then -# echo "Failed to install $file" >&2 -# exit 1 -# fi -# done +# Install files +for file in "${!files[@]}"; do + if [[ ! -f "$SRC_DIR/$file" ]]; then + echo "Source file $file not found in $SRC_DIR" >&2 + exit 1 + fi + + if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then + echo "Failed to install $file" >&2 + exit 1 + fi +done diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 34c96900ad6b6..18baaa52cfeaf 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -21,7 +21,7 @@ build: test: commands: - - ${PREFIX}/bin/genodsp --help + - ${PREFIX}/bin/rdeval --help about: home: https://github.com/vgl-hub/{{ name }} From f4652bcf1f3e86c25cf8219650c8c7429d24b784 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 11:35:40 -0500 Subject: [PATCH 05/55] fixing build.sh --- recipes/rdeval/build.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index c99823e1c4124..d616e93fa49f3 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -4,6 +4,7 @@ set -o errexit set -o nounset set -o xtrace +cd "$SRC_DIR" make # mkdir -vp "${PREFIX}/bin" From 87296b0ab9f707d8d004d5ebce254224ba5c29d6 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 11:48:07 -0500 Subject: [PATCH 06/55] using version with submodules --- recipes/rdeval/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 18baaa52cfeaf..a8987305f2edc 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -6,8 +6,8 @@ package: version: {{ version }} source: - url: https://github.com/vgl-hub/{{ name }}/archive/refs/tags/v{{ version }}.zip - sha256: 466ff3dd3f80aa544be4e0992d1d46bbde933279413392cf17a1fe3b6c2fc5be + url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip + sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d requirements: build: From 9bd1425493042bbc2f31696f641f690f8ea23367 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 11:59:54 -0500 Subject: [PATCH 07/55] adding zlib --- recipes/rdeval/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index a8987305f2edc..b99ff132342a3 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -13,6 +13,7 @@ requirements: build: - {{ compiler('cxx') }} - make + - zlib build: number: 0 From 13e7bd6e6ec5c81ec5495c9b89da79412a27177e Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 12:27:03 -0500 Subject: [PATCH 08/55] updates --- recipes/rdeval/build.sh | 4 ++++ recipes/rdeval/meta.yaml | 2 ++ 2 files changed, 6 insertions(+) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index d616e93fa49f3..2f9eea9eb9f9e 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -5,6 +5,10 @@ set -o nounset set -o xtrace cd "$SRC_DIR" + +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" + make # mkdir -vp "${PREFIX}/bin" diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index b99ff132342a3..be27894384d2a 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -14,6 +14,8 @@ requirements: - {{ compiler('cxx') }} - make - zlib + run: + - zlib build: number: 0 From ce7037ffa479fd5e2369b4ca61b8a55edfe3d72e Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 12:46:11 -0500 Subject: [PATCH 09/55] update --- recipes/rdeval/build.sh | 21 +-------------------- 1 file changed, 1 insertion(+), 20 deletions(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 2f9eea9eb9f9e..08217978a5f9f 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -10,23 +10,4 @@ export CFLAGS="$CFLAGS -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" make - -# mkdir -vp "${PREFIX}/bin" - -# Define installation manifest -declare -A files=( - ["rdeval"]="0755" -) - -# Install files -for file in "${!files[@]}"; do - if [[ ! -f "$SRC_DIR/$file" ]]; then - echo "Source file $file not found in $SRC_DIR" >&2 - exit 1 - fi - - if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then - echo "Failed to install $file" >&2 - exit 1 - fi -done +install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" From b1a6e2b57490896a5e6e5f0948a84b6dd44d844d Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 12:56:29 -0500 Subject: [PATCH 10/55] foo --- recipes/rdeval/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 08217978a5f9f..189f8cbba1b77 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -6,7 +6,7 @@ set -o xtrace cd "$SRC_DIR" -export CFLAGS="$CFLAGS -I$PREFIX/include" +export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" make From 303792e65c2bff6ad0daaf0ee506706811b8909c Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 14:05:16 -0500 Subject: [PATCH 11/55] quote --- recipes/rdeval/meta.yaml | 4 ++-- recipes/rdeval/quote.patch | 25 +++++++++++++++++++++++++ 2 files changed, 27 insertions(+), 2 deletions(-) create mode 100644 recipes/rdeval/quote.patch diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index be27894384d2a..08ccf16e35704 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -8,14 +8,14 @@ package: source: url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d + patches: + - quote.patch requirements: build: - {{ compiler('cxx') }} - make - zlib - run: - - zlib build: number: 0 diff --git a/recipes/rdeval/quote.patch b/recipes/rdeval/quote.patch new file mode 100644 index 0000000000000..42944e0ada46e --- /dev/null +++ b/recipes/rdeval/quote.patch @@ -0,0 +1,25 @@ +diff --git a/Makefile b/Makefile +index 5823f28..7e1295c 100644 +--- a/Makefile ++++ b/Makefile +@@ -14,6 +14,7 @@ BINDIR := $(BUILD)/.o + + LDFLAGS := -pthread + LIBS = -lz ++-L/usr/lib/x86_64-linux-gnu -lz + + OBJS := main input reads + BINS := $(addprefix $(BINDIR)/, $(OBJS)) +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 + #include "zstream/zstream_common.hpp" + #include "zstream/ozstream.hpp" + #include "zstream/ozstream_impl.hpp" From 0ae2fef96f44bcb9707b89c2b02f2f527ecbb35e Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 14:38:54 -0500 Subject: [PATCH 12/55] u --- recipes/rdeval/libs.patch | 13 +++++++++++++ recipes/rdeval/meta.yaml | 1 + 2 files changed, 14 insertions(+) create mode 100644 recipes/rdeval/libs.patch diff --git a/recipes/rdeval/libs.patch b/recipes/rdeval/libs.patch new file mode 100644 index 0000000000000..15ed067146411 --- /dev/null +++ b/recipes/rdeval/libs.patch @@ -0,0 +1,13 @@ +diff --git a/Makefile b/Makefile +index 5823f28..19d1be3 100644 +--- a/Makefile ++++ b/Makefile +@@ -13,7 +13,7 @@ INCLUDE = include + BINDIR := $(BUILD)/.o + + LDFLAGS := -pthread +-LIBS = -lz ++LIBS := -lz + + OBJS := main input reads + BINS := $(addprefix $(BINDIR)/, $(OBJS)) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 08ccf16e35704..ff63e17dfc107 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -10,6 +10,7 @@ source: sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - quote.patch + - libs.patch requirements: build: From a401dab7db394cc5b13c1678b33aad708f7cd72b Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 14:47:57 -0500 Subject: [PATCH 13/55] a --- recipes/rdeval/quote.patch | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/recipes/rdeval/quote.patch b/recipes/rdeval/quote.patch index 42944e0ada46e..979ef6e4c0356 100644 --- a/recipes/rdeval/quote.patch +++ b/recipes/rdeval/quote.patch @@ -1,15 +1,3 @@ -diff --git a/Makefile b/Makefile -index 5823f28..7e1295c 100644 ---- a/Makefile -+++ b/Makefile -@@ -14,6 +14,7 @@ BINDIR := $(BUILD)/.o - - LDFLAGS := -pthread - LIBS = -lz -+-L/usr/lib/x86_64-linux-gnu -lz - - OBJS := main input reads - BINS := $(addprefix $(BINDIR)/, $(OBJS)) diff --git a/src/reads.cpp b/src/reads.cpp index 866f49b..ac714cf 100644 --- a/src/reads.cpp From 5e8732657ee3431526f451c707cdbb0432f39d16 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 15:02:52 -0500 Subject: [PATCH 14/55] patch --- recipes/rdeval/quote.patch | 13 ---------- recipes/rdeval/zlib.patch | 52 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 52 insertions(+), 13 deletions(-) delete mode 100644 recipes/rdeval/quote.patch create mode 100644 recipes/rdeval/zlib.patch diff --git a/recipes/rdeval/quote.patch b/recipes/rdeval/quote.patch deleted file mode 100644 index 979ef6e4c0356..0000000000000 --- a/recipes/rdeval/quote.patch +++ /dev/null @@ -1,13 +0,0 @@ -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 - #include "zstream/zstream_common.hpp" - #include "zstream/ozstream.hpp" - #include "zstream/ozstream_impl.hpp" diff --git a/recipes/rdeval/zlib.patch b/recipes/rdeval/zlib.patch new file mode 100644 index 0000000000000..d1e9639bb43c4 --- /dev/null +++ b/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 + #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 +-#include "zlib.h" ++#include + + 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 + #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 + #include "zstream/zstream_common.hpp" + #include "zstream/ozstream.hpp" + #include "zstream/ozstream_impl.hpp" From de1a4fb8193513e9437f0ff391d7e09ab5320ccc Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 15:03:12 -0500 Subject: [PATCH 15/55] zlib --- recipes/rdeval/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index ff63e17dfc107..fbfddbc3a7dc9 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -9,7 +9,7 @@ source: url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - - quote.patch + - zlib.patch - libs.patch requirements: From 2c7164a371cc075c53c8e4a7fc12373a02cbe04b Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 15:18:23 -0500 Subject: [PATCH 16/55] zlib --- recipes/rdeval/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index fbfddbc3a7dc9..1ae135fe8f7ca 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -11,6 +11,7 @@ source: patches: - zlib.patch - libs.patch + - foo.patch requirements: build: From 9ce5806a918e9bb2ffb8cc9a2b445c938b8dacf4 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Tue, 12 Nov 2024 15:27:48 -0500 Subject: [PATCH 17/55] foo --- recipes/rdeval/foo.patch | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 recipes/rdeval/foo.patch diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch new file mode 100644 index 0000000000000..ec4427aa0e3d5 --- /dev/null +++ b/recipes/rdeval/foo.patch @@ -0,0 +1,26 @@ +diff --git a/Makefile b/Makefile +index de9ab9b..f291529 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,4 +1,3 @@ +-CXX = g++ + INCLUDE_DIR = -I./include + WARNINGS = -Wall -Wextra + +@@ -9,6 +8,7 @@ BUILD = build/bin + SOURCE = src + INCLUDE = include + LDFLAGS := ++LIBS := -lz + + 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) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ $(LIBS) + + clean: + $(RM) *.o From b5372a1f75ee48003812d093c3fbab817137e179 Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 12 Nov 2024 18:22:36 -0600 Subject: [PATCH 18/55] clean up recipe --- recipes/rdeval/build.sh | 4 ++-- recipes/rdeval/foo.patch | 42 ++++++++++++++++++++++------------------ recipes/rdeval/meta.yaml | 15 ++++++++------ 3 files changed, 34 insertions(+), 27 deletions(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 189f8cbba1b77..7721abc3520f2 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -6,8 +6,8 @@ set -o xtrace cd "$SRC_DIR" -export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" +export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -make +make -j"${CPU_COUNT}" install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index ec4427aa0e3d5..370493544ec90 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -1,26 +1,30 @@ -diff --git a/Makefile b/Makefile -index de9ab9b..f291529 100644 +diff --git a/Makefile b/Makefile2 +index 5823f28..41cdab3 100644 --- a/Makefile -+++ b/Makefile -@@ -1,4 +1,3 @@ --CXX = g++ - INCLUDE_DIR = -I./include ++++ b/Makefile2 +@@ -1,5 +1,5 @@ +-CXX ?= g++ +-INCLUDE_DIR = -I./include -I./gfalibs/include ++CXX ?= ${CXX} ++INCLUDE_DIR = -I./include -I./gfalibs/include -I${PREFIX}/include WARNINGS = -Wall -Wextra -@@ -9,6 +8,7 @@ BUILD = build/bin - SOURCE = src + CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) +@@ -12,7 +12,7 @@ SOURCE = src INCLUDE = include - LDFLAGS := -+LIBS := -lz + BINDIR := $(BUILD)/.o - SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) +-LDFLAGS := -pthread ++LDFLAGS := -pthread -L${PREFIX}/lib + LIBS = -lz -@@ -16,7 +16,7 @@ all: $(SOURCES) - @ + OBJS := main input reads +@@ -27,7 +27,7 @@ head: $(BINS) gfalibs | $(BUILD) + all: head validate regenerate - %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h -- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ $(LIBS) - - clean: - $(RM) *.o + $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) +- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) + + .PHONY: gfalibs + gfalibs: diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 1ae135fe8f7ca..05e79c13df944 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -13,24 +13,27 @@ source: - libs.patch - foo.patch +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} + requirements: build: - {{ compiler('cxx') }} - make + host: - zlib -build: - number: 0 - run_exports: - - {{ pin_subpackage(name|lower, max_pin="x.x") }} - test: commands: - - ${PREFIX}/bin/rdeval --help + - 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 license_url: https://github.com/vgl-hub/{{ name }}/blob/main/LICENSE + dev_url: https://github.com/vgl-hub/{{ name }} From b061c2d32240e4f57525e65226b918c27ba654ae Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 12 Nov 2024 18:39:56 -0600 Subject: [PATCH 19/55] clean up patches --- recipes/rdeval/foo.patch | 12 +++++++----- recipes/rdeval/libs.patch | 13 ------------- recipes/rdeval/meta.yaml | 2 +- 3 files changed, 8 insertions(+), 19 deletions(-) delete mode 100644 recipes/rdeval/libs.patch diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index 370493544ec90..2e00c643294ce 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -1,7 +1,7 @@ -diff --git a/Makefile b/Makefile2 -index 5823f28..41cdab3 100644 +diff --git a/Makefile b/Makefile +index 5823f28..cb3efa1 100644 --- a/Makefile -+++ b/Makefile2 ++++ b/Makefile @@ -1,5 +1,5 @@ -CXX ?= g++ -INCLUDE_DIR = -I./include -I./gfalibs/include @@ -10,15 +10,17 @@ index 5823f28..41cdab3 100644 WARNINGS = -Wall -Wextra CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) -@@ -12,7 +12,7 @@ SOURCE = src +@@ -12,8 +12,8 @@ SOURCE = src INCLUDE = include BINDIR := $(BUILD)/.o -LDFLAGS := -pthread +-LIBS = -lz +LDFLAGS := -pthread -L${PREFIX}/lib - LIBS = -lz ++LIBS := -lz OBJS := main input reads + BINS := $(addprefix $(BINDIR)/, $(OBJS)) @@ -27,7 +27,7 @@ head: $(BINS) gfalibs | $(BUILD) all: head validate regenerate diff --git a/recipes/rdeval/libs.patch b/recipes/rdeval/libs.patch deleted file mode 100644 index 15ed067146411..0000000000000 --- a/recipes/rdeval/libs.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/Makefile b/Makefile -index 5823f28..19d1be3 100644 ---- a/Makefile -+++ b/Makefile -@@ -13,7 +13,7 @@ INCLUDE = include - BINDIR := $(BUILD)/.o - - LDFLAGS := -pthread --LIBS = -lz -+LIBS := -lz - - OBJS := main input reads - BINS := $(addprefix $(BINDIR)/, $(OBJS)) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 05e79c13df944..07859fe9894ce 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -10,7 +10,6 @@ source: sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - zlib.patch - - libs.patch - foo.patch build: @@ -37,3 +36,4 @@ about: license_file: LICENSE license_url: https://github.com/vgl-hub/{{ name }}/blob/main/LICENSE dev_url: https://github.com/vgl-hub/{{ name }} + doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md From 7a51e11f730925a69afa790ba4566ad7b4e49d83 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 18:49:12 -0600 Subject: [PATCH 20/55] Update build.sh --- recipes/rdeval/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 7721abc3520f2..76dd3ffe4d28a 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -9,5 +9,5 @@ cd "$SRC_DIR" export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -make -j"${CPU_COUNT}" +make -j"${CPU_COUNT}" CXX="${CXX}" install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" From 5155d5ca72690febe1f94d4304fd8a4d626e06ed Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 12 Nov 2024 21:03:12 -0600 Subject: [PATCH 21/55] add gfalibs patch --- recipes/rdeval/build.sh | 2 +- recipes/rdeval/gfalibs.patch | 21 +++++++++++++++++++++ recipes/rdeval/meta.yaml | 1 + 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 recipes/rdeval/gfalibs.patch diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 76dd3ffe4d28a..66ee84b573957 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -9,5 +9,5 @@ cd "$SRC_DIR" export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -make -j"${CPU_COUNT}" CXX="${CXX}" +make -j"${CPU_COUNT}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch new file mode 100644 index 0000000000000..a91ff832d0c78 --- /dev/null +++ b/recipes/rdeval/gfalibs.patch @@ -0,0 +1,21 @@ +diff --git a/gfalibs/Makefile b/gfalibs/Makefile +index de9ab9b..912802e 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 + 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 -lz + + SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) + diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 07859fe9894ce..6746354c643ef 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -11,6 +11,7 @@ source: patches: - zlib.patch - foo.patch + - gfalibs.patch build: number: 0 From 68a3123b3a04b55d2d7778830c314ef92288eaff Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 21:04:32 -0600 Subject: [PATCH 22/55] Update meta.yaml --- recipes/rdeval/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 6746354c643ef..5725a6aa08ebc 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -35,6 +35,10 @@ about: license: MIT license_family: MIT license_file: LICENSE - license_url: https://github.com/vgl-hub/{{ name }}/blob/main/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 From a32a8b4c3c0dcc17c5e278e9926e78596274d2a3 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 21:21:18 -0600 Subject: [PATCH 23/55] Update meta.yaml --- recipes/rdeval/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 5725a6aa08ebc..a50dc5293e59a 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -23,6 +23,7 @@ requirements: - {{ compiler('cxx') }} - make host: + - parallel-hashmap - zlib test: From 165854e62386b5176a37cc9692a83448ca7f8918 Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 12 Nov 2024 21:32:54 -0600 Subject: [PATCH 24/55] add gfalibs patch --- recipes/rdeval/gfalibs.patch | 15 ++++++++++++--- recipes/rdeval/meta.yaml | 1 - 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index a91ff832d0c78..36415a7eff9c2 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,12 +1,12 @@ diff --git a/gfalibs/Makefile b/gfalibs/Makefile -index de9ab9b..912802e 100644 +index de9ab9b..c1766ae 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 ++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap WARNINGS = -Wall -Wextra CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) @@ -15,7 +15,16 @@ index de9ab9b..912802e 100644 SOURCE = src INCLUDE = include -LDFLAGS := -+LDFLAGS := -L${PREFIX}/lib -lz ++LDFLAGS := -L${PREFIX}/lib 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 + + clean: + $(RM) *.o diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index a50dc5293e59a..5725a6aa08ebc 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -23,7 +23,6 @@ requirements: - {{ compiler('cxx') }} - make host: - - parallel-hashmap - zlib test: From 9557f454e4cb212a9544d23cd8699962058c7ab9 Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 12 Nov 2024 21:41:29 -0600 Subject: [PATCH 25/55] edit foo.patch --- recipes/rdeval/foo.patch | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index 2e00c643294ce..55604f55442a8 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -1,12 +1,12 @@ diff --git a/Makefile b/Makefile -index 5823f28..cb3efa1 100644 +index 5823f28..0472d19 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ -CXX ?= g++ -INCLUDE_DIR = -I./include -I./gfalibs/include +CXX ?= ${CXX} -+INCLUDE_DIR = -I./include -I./gfalibs/include -I${PREFIX}/include ++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include WARNINGS = -Wall -Wextra CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) @@ -21,7 +21,13 @@ index 5823f28..cb3efa1 100644 OBJS := main input reads BINS := $(addprefix $(BINDIR)/, $(OBJS)) -@@ -27,7 +27,7 @@ head: $(BINS) gfalibs | $(BUILD) +@@ -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) From e758cf81acf6ce8daf6864e00ab5882737a12b88 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 21:42:12 -0600 Subject: [PATCH 26/55] Update foo.patch --- recipes/rdeval/foo.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index 55604f55442a8..de7b50834a478 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -32,7 +32,7 @@ index 5823f28..0472d19 100644 $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) ++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) .PHONY: gfalibs gfalibs: From 7b3e88834124009e6011c67c9a24dce1f13e1453 Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 12 Nov 2024 21:57:17 -0600 Subject: [PATCH 27/55] edit foo.patch --- recipes/rdeval/foo.patch | 6 +++--- recipes/rdeval/gfalibs.patch | 6 +++--- recipes/rdeval/meta.yaml | 1 + 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index de7b50834a478..6e9ea5665c480 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -1,5 +1,5 @@ diff --git a/Makefile b/Makefile -index 5823f28..0472d19 100644 +index 5823f28..6d448f3 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ @@ -17,7 +17,7 @@ index 5823f28..0472d19 100644 -LDFLAGS := -pthread -LIBS = -lz +LDFLAGS := -pthread -L${PREFIX}/lib -+LIBS := -lz ++LIBS := -lz -lpthread OBJS := main input reads BINS := $(addprefix $(BINDIR)/, $(OBJS)) @@ -32,7 +32,7 @@ index 5823f28..0472d19 100644 $(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) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) .PHONY: gfalibs gfalibs: diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index 36415a7eff9c2..e6cc8439bf6c2 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,5 +1,5 @@ diff --git a/gfalibs/Makefile b/gfalibs/Makefile -index de9ab9b..c1766ae 100644 +index de9ab9b..90a703c 100644 --- a/gfalibs/Makefile +++ b/gfalibs/Makefile @@ -1,5 +1,5 @@ @@ -15,7 +15,7 @@ index de9ab9b..c1766ae 100644 SOURCE = src INCLUDE = include -LDFLAGS := -+LDFLAGS := -L${PREFIX}/lib ++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) @@ -24,7 +24,7 @@ index de9ab9b..c1766ae 100644 %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -+ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz ++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz -lpthread clean: $(RM) *.o diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 5725a6aa08ebc..ce1571a5436bd 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -23,6 +23,7 @@ requirements: - {{ compiler('cxx') }} - make host: + - pthread-stubs - zlib test: From 8e8c1f142f926c477180e088a23b4cb56751231b Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 12 Nov 2024 22:04:20 -0600 Subject: [PATCH 28/55] edit foo.patch --- recipes/rdeval/foo.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index 6e9ea5665c480..417701560725a 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -1,5 +1,5 @@ diff --git a/Makefile b/Makefile -index 5823f28..6d448f3 100644 +index 5823f28..6f4a60f 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ @@ -32,7 +32,7 @@ index 5823f28..6d448f3 100644 $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) ++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) .PHONY: gfalibs gfalibs: From 843478268d4ec2198f7166f294a6bce85ef4c0be Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 22:14:02 -0600 Subject: [PATCH 29/55] Update build.sh --- recipes/rdeval/build.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 66ee84b573957..0082bc9545c6a 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -9,5 +9,6 @@ cd "$SRC_DIR" export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -make -j"${CPU_COUNT}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" -install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" +make -j"${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/" From d4830681549b23e03d62adceaae004023e75a43d Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Wed, 13 Nov 2024 10:48:47 -0500 Subject: [PATCH 30/55] makefile --- recipes/rdeval/foo.patch | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index ec4427aa0e3d5..22f7dea291e5e 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -1,7 +1,7 @@ -diff --git a/Makefile b/Makefile +diff --git a/gfalibs/Makefile b/gfalibs/Makefile index de9ab9b..f291529 100644 ---- a/Makefile -+++ b/Makefile +--- a/gfalibs/Makefile ++++ b/gfalibs/Makefile @@ -1,4 +1,3 @@ -CXX = g++ INCLUDE_DIR = -I./include From 44a2f68e7ba982d4f6b0097bb04d1acdce712349 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Wed, 13 Nov 2024 10:53:11 -0500 Subject: [PATCH 31/55] makefile --- recipes/rdeval/foo.patch | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch index d356364ff7094..f50f0b45951af 100644 --- a/recipes/rdeval/foo.patch +++ b/recipes/rdeval/foo.patch @@ -1,4 +1,3 @@ -<<<<<<< HEAD diff --git a/gfalibs/Makefile b/gfalibs/Makefile index de9ab9b..f291529 100644 --- a/gfalibs/Makefile @@ -6,17 +5,6 @@ index de9ab9b..f291529 100644 @@ -1,4 +1,3 @@ -CXX = g++ INCLUDE_DIR = -I./include -======= -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 ->>>>>>> 843478268d4ec2198f7166f294a6bce85ef4c0be WARNINGS = -Wall -Wextra CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) From 1dc56cd773d5adab3a26419a22f7f9352be62d33 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Wed, 13 Nov 2024 11:03:12 -0500 Subject: [PATCH 32/55] updating submodule makefile --- recipes/rdeval/foo.patch | 36 ------------------------------------ recipes/rdeval/gfalibs.patch | 22 +++++++++------------- recipes/rdeval/meta.yaml | 1 - 3 files changed, 9 insertions(+), 50 deletions(-) delete mode 100644 recipes/rdeval/foo.patch diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch deleted file mode 100644 index f50f0b45951af..0000000000000 --- a/recipes/rdeval/foo.patch +++ /dev/null @@ -1,36 +0,0 @@ -diff --git a/gfalibs/Makefile b/gfalibs/Makefile -index de9ab9b..f291529 100644 ---- a/gfalibs/Makefile -+++ b/gfalibs/Makefile -@@ -1,4 +1,3 @@ --CXX = g++ - INCLUDE_DIR = -I./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: diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index e6cc8439bf6c2..531f38fa99ab3 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,30 +1,26 @@ -diff --git a/gfalibs/Makefile b/gfalibs/Makefile -index de9ab9b..90a703c 100644 ---- a/gfalibs/Makefile -+++ b/gfalibs/Makefile -@@ -1,5 +1,5 @@ +--- a/gfalibs/Makefile 2024-11-13 10:59:02.777393016 -0500 ++++ b/gfalibs/Makefile 2024-11-13 11:00:47.981938010 -0500 +@@ -1,4 +1,4 @@ -CXX = g++ --INCLUDE_DIR = -I./include -+CXX = $(CXX) -+INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap ++CXX ?= g++ + INCLUDE_DIR = -I./include WARNINGS = -Wall -Wextra - CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) -@@ -8,7 +8,7 @@ TARGET = gfalibs +@@ -8,7 +8,7 @@ BUILD = build/bin SOURCE = src INCLUDE = include -LDFLAGS := -+LDFLAGS := -L${PREFIX}/lib -pthread ++LIBS := -lz 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) +@@ -16,7 +16,7 @@ @ %.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 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ $(LIBS) clean: $(RM) *.o diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index ce1571a5436bd..0c8e120e53e8f 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -10,7 +10,6 @@ source: sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - zlib.patch - - foo.patch - gfalibs.patch build: From 5af9fd4bd19f426230c3e7cca0b7ab3a8eb1c4c9 Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Wed, 13 Nov 2024 11:12:53 -0500 Subject: [PATCH 33/55] bumping build version --- recipes/rdeval/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 0c8e120e53e8f..4fc313cb7b3ed 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -13,7 +13,7 @@ source: - gfalibs.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} From 55f449b204756ee482ea40449dd87ef49ae520df Mon Sep 17 00:00:00 2001 From: "Richard C. Burhans" Date: Wed, 13 Nov 2024 11:34:19 -0500 Subject: [PATCH 34/55] includes --- recipes/rdeval/meta.yaml | 1 + recipes/rdeval/parallel-hashmap.patch | 66 +++++++++++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 recipes/rdeval/parallel-hashmap.patch diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 4fc313cb7b3ed..0fb6b8006cd56 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -11,6 +11,7 @@ source: patches: - zlib.patch - gfalibs.patch + - parallel-hashmap.patch build: number: 1 diff --git a/recipes/rdeval/parallel-hashmap.patch b/recipes/rdeval/parallel-hashmap.patch new file mode 100644 index 0000000000000..86593fda7c360 --- /dev/null +++ b/recipes/rdeval/parallel-hashmap.patch @@ -0,0 +1,66 @@ +--- gfalibs.orig/include/functions.h 2024-11-12 16:11:22.000000000 -0500 ++++ gfalibs/include/functions.h 2024-11-13 11:26:47.585980869 -0500 +@@ -31,7 +31,7 @@ + #include + #endif + +-#include ++#include "parallel-hashmap/phmap.h" + #include "global.h" + #include "bed.h" + #include "struct.h" +--- gfalibs.orig/include/kmer.h 2024-11-12 16:11:22.000000000 -0500 ++++ gfalibs/include/kmer.h 2024-11-13 11:27:01.022050240 -0500 +@@ -2,7 +2,7 @@ + #define KMER_H + + #include +-#include ++#include "parallel-hashmap/phmap.h" + #include "parallel-hashmap/phmap_dump.h" + + #include +--- gfalibs.orig/src/gfa.cpp 2024-11-12 16:11:22.000000000 -0500 ++++ gfalibs/src/gfa.cpp 2024-11-13 11:27:44.086272576 -0500 +@@ -2,7 +2,7 @@ + #include + #include + +-#include ++#include "parallel-hashmap/phmap.h" + + #include "log.h" + #include "global.h" +--- gfalibs.orig/src/input-agp.cpp 2024-11-12 16:11:22.000000000 -0500 ++++ gfalibs/src/input-agp.cpp 2024-11-13 11:27:10.734100380 -0500 +@@ -2,7 +2,7 @@ + #include + #include + +-#include ++#include "parallel-hashmap/phmap.h" + + #include "bed.h" + #include "struct.h" +--- gfalibs.orig/src/input-gfa.cpp 2024-11-12 16:11:22.000000000 -0500 ++++ gfalibs/src/input-gfa.cpp 2024-11-13 11:27:25.134174730 -0500 +@@ -5,7 +5,7 @@ + #include + #include + +-#include ++#include "parallel-hashmap/phmap.h" + + #include "bed.h" + #include "struct.h" +--- gfalibs.orig/src/output.cpp 2024-11-12 16:11:22.000000000 -0500 ++++ gfalibs/src/output.cpp 2024-11-13 11:27:35.606228804 -0500 +@@ -5,7 +5,7 @@ + #include + #include + +-#include ++#include "parallel-hashmap/phmap.h" + + #include "bed.h" + #include "struct.h" From 2857c8df94e2db573072d757f645e3ba60398052 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 14:17:54 -0500 Subject: [PATCH 35/55] testing makefile changrs --- recipes/rdeval/gfalibs.patch | 17 +++++++++++------ recipes/rdeval/meta.yaml | 2 -- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index 531f38fa99ab3..4578ad4ebc060 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,26 +1,31 @@ ---- a/gfalibs/Makefile 2024-11-13 10:59:02.777393016 -0500 -+++ b/gfalibs/Makefile 2024-11-13 11:00:47.981938010 -0500 -@@ -1,4 +1,4 @@ +--- code/old/gfalibs/Makefile 2024-11-12 16:11:22 ++++ code/new/gfalibs/Makefile 2024-11-14 14:16:03 +@@ -1,5 +1,5 @@ -CXX = g++ +-INCLUDE_DIR = -I./include +CXX ?= g++ - INCLUDE_DIR = -I./include ++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap WARNINGS = -Wall -Wextra -@@ -8,7 +8,7 @@ + CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) +@@ -8,7 +8,8 @@ BUILD = build/bin SOURCE = src INCLUDE = include -LDFLAGS := ++LDFLAGS := -L${PREFIX}/lib -pthread +LIBS := -lz SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) -@@ -16,7 +16,7 @@ +@@ -16,7 +17,9 @@ @ %.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 + $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ $(LIBS) clean: $(RM) *.o ++ diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 0fb6b8006cd56..f9fdca0eac30a 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -9,9 +9,7 @@ source: url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - - zlib.patch - gfalibs.patch - - parallel-hashmap.patch build: number: 1 From 5b96de8377d4ab1f9976829e6407f8ee578a42c1 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 14:28:56 -0500 Subject: [PATCH 36/55] make --- recipes/rdeval/gfalibs.patch | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index 4578ad4ebc060..a732db27b4054 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,5 +1,5 @@ --- code/old/gfalibs/Makefile 2024-11-12 16:11:22 -+++ code/new/gfalibs/Makefile 2024-11-14 14:16:03 ++++ code/new/gfalibs/Makefile 2024-11-14 14:28:06 @@ -1,5 +1,5 @@ -CXX = g++ -INCLUDE_DIR = -I./include @@ -8,23 +8,22 @@ WARNINGS = -Wall -Wextra CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) -@@ -8,7 +8,8 @@ +@@ -8,15 +8,17 @@ BUILD = build/bin SOURCE = src INCLUDE = include -LDFLAGS := -+LDFLAGS := -L${PREFIX}/lib -pthread +LIBS := -lz SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) -@@ -16,7 +17,9 @@ + all: $(SOURCES) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o $@ $(LIBS) @ %.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 -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ $(LIBS) ++ $(CXX) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ clean: $(RM) *.o From 46b5350141140694af9dcf80efc1c9379d822bdd Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 15:06:10 -0500 Subject: [PATCH 37/55] patches --- recipes/rdeval/gfalibs.patch | 4 +- recipes/rdeval/meta.yaml | 1 + recipes/rdeval/parallel-hashmap.patch | 61 ++++++++++++++++----------- 3 files changed, 39 insertions(+), 27 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index a732db27b4054..9796f096c527c 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,5 +1,5 @@ ---- code/old/gfalibs/Makefile 2024-11-12 16:11:22 -+++ code/new/gfalibs/Makefile 2024-11-14 14:28:06 +--- code/old/gfalibs/Makefile ++++ code/new/gfalibs/Makefile @@ -1,5 +1,5 @@ -CXX = g++ -INCLUDE_DIR = -I./include diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index f9fdca0eac30a..a96fc0b9f3d6c 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -10,6 +10,7 @@ source: sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - gfalibs.patch + - parallel-hashmap.patch build: number: 1 diff --git a/recipes/rdeval/parallel-hashmap.patch b/recipes/rdeval/parallel-hashmap.patch index 86593fda7c360..ac8e55e07206a 100644 --- a/recipes/rdeval/parallel-hashmap.patch +++ b/recipes/rdeval/parallel-hashmap.patch @@ -1,5 +1,16 @@ ---- gfalibs.orig/include/functions.h 2024-11-12 16:11:22.000000000 -0500 -+++ gfalibs/include/functions.h 2024-11-13 11:26:47.585980869 -0500 +--- old/gfalibs/include/kmer.h ++++ new/gfalibs/include/kmer.h +@@ -2,7 +2,7 @@ + #define KMER_H + + #include +-#include ++#include "parallel-hashmap/phmap.h" + #include "parallel-hashmap/phmap_dump.h" + + #include +--- old/gfalibs/include/functions.h ++++ new/gfalibs/include/functions.h @@ -31,7 +31,7 @@ #include #endif @@ -9,30 +20,30 @@ #include "global.h" #include "bed.h" #include "struct.h" ---- gfalibs.orig/include/kmer.h 2024-11-12 16:11:22.000000000 -0500 -+++ gfalibs/include/kmer.h 2024-11-13 11:27:01.022050240 -0500 +--- old/gfalibs/src/gfa.cpp ++++ new/gfalibs/src/gfa.cpp @@ -2,7 +2,7 @@ - #define KMER_H + #include + #include - #include -#include +#include "parallel-hashmap/phmap.h" - #include "parallel-hashmap/phmap_dump.h" - #include ---- gfalibs.orig/src/gfa.cpp 2024-11-12 16:11:22.000000000 -0500 -+++ gfalibs/src/gfa.cpp 2024-11-13 11:27:44.086272576 -0500 -@@ -2,7 +2,7 @@ - #include + #include "log.h" + #include "global.h" +--- old/gfalibs/src/input-gfa.cpp ++++ new/gfalibs/src/input-gfa.cpp +@@ -5,7 +5,7 @@ #include + #include -#include +#include "parallel-hashmap/phmap.h" - #include "log.h" - #include "global.h" ---- gfalibs.orig/src/input-agp.cpp 2024-11-12 16:11:22.000000000 -0500 -+++ gfalibs/src/input-agp.cpp 2024-11-13 11:27:10.734100380 -0500 + #include "bed.h" + #include "struct.h" +--- old/gfalibs/src/input-agp.cpp ++++ new/gfalibs/src/input-agp.cpp @@ -2,7 +2,7 @@ #include #include @@ -42,22 +53,22 @@ #include "bed.h" #include "struct.h" ---- gfalibs.orig/src/input-gfa.cpp 2024-11-12 16:11:22.000000000 -0500 -+++ gfalibs/src/input-gfa.cpp 2024-11-13 11:27:25.134174730 -0500 +--- old/gfalibs/src/output.cpp ++++ new/gfalibs/src/output.cpp @@ -5,7 +5,7 @@ - #include - #include + #include + #include -#include +#include "parallel-hashmap/phmap.h" #include "bed.h" #include "struct.h" ---- gfalibs.orig/src/output.cpp 2024-11-12 16:11:22.000000000 -0500 -+++ gfalibs/src/output.cpp 2024-11-13 11:27:35.606228804 -0500 -@@ -5,7 +5,7 @@ - #include - #include +--- old/gfalibs/src/input-filters.cpp ++++ new/gfalibs/src/input-filters.cpp +@@ -2,7 +2,7 @@ + #include + #include -#include +#include "parallel-hashmap/phmap.h" From 46e896f543b386d33ae9b0dbfd5faf80ac07967e Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 15:17:04 -0500 Subject: [PATCH 38/55] patches --- recipes/rdeval/gfalibs.patch | 10 ++++------ recipes/rdeval/parallel-hashmap.patch | 28 +++++++++++++-------------- 2 files changed, 18 insertions(+), 20 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index 9796f096c527c..7ac815ea3ef89 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,13 +1,11 @@ ---- code/old/gfalibs/Makefile -+++ code/new/gfalibs/Makefile -@@ -1,5 +1,5 @@ +--- a/gfalibs/Makefile ++++ b/gfalibs/Makefil +@@ -1,4 +1,4 @@ -CXX = g++ --INCLUDE_DIR = -I./include +CXX ?= g++ -+INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap + INCLUDE_DIR = -I./include WARNINGS = -Wall -Wextra - CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) @@ -8,15 +8,17 @@ BUILD = build/bin SOURCE = src diff --git a/recipes/rdeval/parallel-hashmap.patch b/recipes/rdeval/parallel-hashmap.patch index ac8e55e07206a..a2df850f130ec 100644 --- a/recipes/rdeval/parallel-hashmap.patch +++ b/recipes/rdeval/parallel-hashmap.patch @@ -1,5 +1,5 @@ ---- old/gfalibs/include/kmer.h -+++ new/gfalibs/include/kmer.h +--- a/gfalibs/include/kmer.h ++++ b/gfalibs/include/kmer.h @@ -2,7 +2,7 @@ #define KMER_H @@ -9,8 +9,8 @@ #include "parallel-hashmap/phmap_dump.h" #include ---- old/gfalibs/include/functions.h -+++ new/gfalibs/include/functions.h +--- a/gfalibs/include/functions.h ++++ b/gfalibs/include/functions.h @@ -31,7 +31,7 @@ #include #endif @@ -20,8 +20,8 @@ #include "global.h" #include "bed.h" #include "struct.h" ---- old/gfalibs/src/gfa.cpp -+++ new/gfalibs/src/gfa.cpp +--- a/gfalibs/src/gfa.cpp ++++ b/gfalibs/src/gfa.cpp @@ -2,7 +2,7 @@ #include #include @@ -31,8 +31,8 @@ #include "log.h" #include "global.h" ---- old/gfalibs/src/input-gfa.cpp -+++ new/gfalibs/src/input-gfa.cpp +--- a/gfalibs/src/input-gfa.cpp ++++ b/gfalibs/src/input-gfa.cpp @@ -5,7 +5,7 @@ #include #include @@ -42,8 +42,8 @@ #include "bed.h" #include "struct.h" ---- old/gfalibs/src/input-agp.cpp -+++ new/gfalibs/src/input-agp.cpp +--- a/gfalibs/src/input-agp.cpp ++++ b/gfalibs/src/input-agp.cpp @@ -2,7 +2,7 @@ #include #include @@ -53,8 +53,8 @@ #include "bed.h" #include "struct.h" ---- old/gfalibs/src/output.cpp -+++ new/gfalibs/src/output.cpp +--- a/gfalibs/src/output.cpp ++++ b/gfalibs/src/output.cpp @@ -5,7 +5,7 @@ #include #include @@ -64,8 +64,8 @@ #include "bed.h" #include "struct.h" ---- old/gfalibs/src/input-filters.cpp -+++ new/gfalibs/src/input-filters.cpp +--- a/gfalibs/src/input-filters.cpp ++++ b/gfalibs/src/input-filters.cpp @@ -2,7 +2,7 @@ #include #include From 4b25f44e9520ed316214b842d18c8b885eea576a Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 16:18:17 -0500 Subject: [PATCH 39/55] patches --- recipes/rdeval/gfalibs.patch | 17 +++++++++-------- recipes/rdeval/meta.yaml | 1 - 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index 7ac815ea3ef89..35543b14f1634 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,23 +1,25 @@ --- a/gfalibs/Makefile -+++ b/gfalibs/Makefil -@@ -1,4 +1,4 @@ ++++ b/gfalibs/Makefile +@@ -1,5 +1,5 @@ -CXX = g++ +-INCLUDE_DIR = -I./include +CXX ?= g++ - INCLUDE_DIR = -I./include ++INCLUDE_DIR = -I./include -I./include/parallel-hashmap WARNINGS = -Wall -Wextra -@@ -8,15 +8,17 @@ + CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) +@@ -8,15 +8,14 @@ BUILD = build/bin SOURCE = src INCLUDE = include -LDFLAGS := +LIBS := -lz - SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) +-SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) ++SOURCES= $(addsuffix .o, gfa gfa-lines input-agp input-filters input-gfa log memory output stream-obj struct uid-generator) all: $(SOURCES) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o $@ $(LIBS) - @ +- @ %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ @@ -25,4 +27,3 @@ clean: $(RM) *.o -+ diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index a96fc0b9f3d6c..f9fdca0eac30a 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -10,7 +10,6 @@ source: sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - gfalibs.patch - - parallel-hashmap.patch build: number: 1 From 890c1bb42de6c481160769bc601c5cdcb2b2ce90 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 17:09:33 -0500 Subject: [PATCH 40/55] patches --- recipes/rdeval/gfalibs.patch | 9 +++------ recipes/rdeval/meta.yaml | 1 + 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index 35543b14f1634..b6fc3eee3ce94 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -1,13 +1,11 @@ --- a/gfalibs/Makefile +++ b/gfalibs/Makefile -@@ -1,5 +1,5 @@ +@@ -1,4 +1,4 @@ -CXX = g++ --INCLUDE_DIR = -I./include +CXX ?= g++ -+INCLUDE_DIR = -I./include -I./include/parallel-hashmap + INCLUDE_DIR = -I./include WARNINGS = -Wall -Wextra - CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) @@ -8,15 +8,14 @@ BUILD = build/bin SOURCE = src @@ -15,8 +13,7 @@ -LDFLAGS := +LIBS := -lz --SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) -+SOURCES= $(addsuffix .o, gfa gfa-lines input-agp input-filters input-gfa log memory output stream-obj struct uid-generator) + SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) all: $(SOURCES) - @ diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index f9fdca0eac30a..a96fc0b9f3d6c 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -10,6 +10,7 @@ source: sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - gfalibs.patch + - parallel-hashmap.patch build: number: 1 From 43f531e36b7437b26280f6fca39f332f7d2f9e96 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 17:37:51 -0500 Subject: [PATCH 41/55] patches --- recipes/rdeval/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index a96fc0b9f3d6c..5fac80f760034 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -11,6 +11,7 @@ source: patches: - gfalibs.patch - parallel-hashmap.patch + - reads.patch build: number: 1 From 2798153bb37981838aa2a9225300e77539640ae1 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 18:37:58 -0500 Subject: [PATCH 42/55] forgot reads.patch --- recipes/rdeval/reads.patch | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 recipes/rdeval/reads.patch diff --git a/recipes/rdeval/reads.patch b/recipes/rdeval/reads.patch new file mode 100644 index 0000000000000..f9019dfc6d8f2 --- /dev/null +++ b/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)) { + From 3b136ab1223524ee808ccb0c2cf5e1478553c38d Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 19:02:24 -0500 Subject: [PATCH 43/55] upp --- recipes/rdeval/build.sh | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 0082bc9545c6a..4c2fc868d496a 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -6,9 +6,6 @@ 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}" +make -j "$CPU_COUNT" install -d "$PREFIX/bin" install -v -m 0755 build/bin/rdeval "$PREFIX/bin/" From f87fa82d9cbb7583ac09e0181d633e470bed1703 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Thu, 14 Nov 2024 19:22:15 -0500 Subject: [PATCH 44/55] zlib --- recipes/rdeval/meta.yaml | 1 + recipes/rdeval/zlib.patch | 8 -------- 2 files changed, 1 insertion(+), 8 deletions(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 5fac80f760034..3b13a99f3f451 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -12,6 +12,7 @@ source: - gfalibs.patch - parallel-hashmap.patch - reads.patch + - zlib.patch build: number: 1 diff --git a/recipes/rdeval/zlib.patch b/recipes/rdeval/zlib.patch index d1e9639bb43c4..09eb17bfb0dac 100644 --- a/recipes/rdeval/zlib.patch +++ b/recipes/rdeval/zlib.patch @@ -1,5 +1,3 @@ -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 @@ @@ -11,8 +9,6 @@ index aabbec0..20f0dc1 100644 #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 @@ @@ -24,8 +20,6 @@ index 1faa4df..8e28bf6 100644 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 @@ @@ -37,8 +31,6 @@ index e9694ee..c6eca26 100644 #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 @@ From f1eb31e0e0eae8f282ae000e2f9e4b685e9e7493 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 12:23:04 -0500 Subject: [PATCH 45/55] zlib --- recipes/rdeval/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 3b13a99f3f451..19992f8b46301 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -23,6 +23,7 @@ requirements: build: - {{ compiler('cxx') }} - make + - zlib host: - pthread-stubs - zlib From a25ff6446f76ac695bc25e2c801ae809b3ca6bd2 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 12:33:31 -0500 Subject: [PATCH 46/55] patch --- recipes/rdeval/gfalibs.patch | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index b6fc3eee3ce94..bfd550318a1c1 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -6,12 +6,11 @@ INCLUDE_DIR = -I./include WARNINGS = -Wall -Wextra -@@ -8,15 +8,14 @@ +@@ -8,15 +8,13 @@ BUILD = build/bin SOURCE = src INCLUDE = include -LDFLAGS := -+LIBS := -lz SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) From 9b35d02a0f41f71c35fdb38e5d922096f75021b9 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 12:45:27 -0500 Subject: [PATCH 47/55] patches --- recipes/rdeval/meta.yaml | 2 - recipes/rdeval/parallel-hashmap.patch | 77 --------------------------- recipes/rdeval/zlib.patch | 44 --------------- 3 files changed, 123 deletions(-) delete mode 100644 recipes/rdeval/parallel-hashmap.patch delete mode 100644 recipes/rdeval/zlib.patch diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 19992f8b46301..7ac445f99745f 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -10,9 +10,7 @@ source: sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - gfalibs.patch - - parallel-hashmap.patch - reads.patch - - zlib.patch build: number: 1 diff --git a/recipes/rdeval/parallel-hashmap.patch b/recipes/rdeval/parallel-hashmap.patch deleted file mode 100644 index a2df850f130ec..0000000000000 --- a/recipes/rdeval/parallel-hashmap.patch +++ /dev/null @@ -1,77 +0,0 @@ ---- a/gfalibs/include/kmer.h -+++ b/gfalibs/include/kmer.h -@@ -2,7 +2,7 @@ - #define KMER_H - - #include --#include -+#include "parallel-hashmap/phmap.h" - #include "parallel-hashmap/phmap_dump.h" - - #include ---- a/gfalibs/include/functions.h -+++ b/gfalibs/include/functions.h -@@ -31,7 +31,7 @@ - #include - #endif - --#include -+#include "parallel-hashmap/phmap.h" - #include "global.h" - #include "bed.h" - #include "struct.h" ---- a/gfalibs/src/gfa.cpp -+++ b/gfalibs/src/gfa.cpp -@@ -2,7 +2,7 @@ - #include - #include - --#include -+#include "parallel-hashmap/phmap.h" - - #include "log.h" - #include "global.h" ---- a/gfalibs/src/input-gfa.cpp -+++ b/gfalibs/src/input-gfa.cpp -@@ -5,7 +5,7 @@ - #include - #include - --#include -+#include "parallel-hashmap/phmap.h" - - #include "bed.h" - #include "struct.h" ---- a/gfalibs/src/input-agp.cpp -+++ b/gfalibs/src/input-agp.cpp -@@ -2,7 +2,7 @@ - #include - #include - --#include -+#include "parallel-hashmap/phmap.h" - - #include "bed.h" - #include "struct.h" ---- a/gfalibs/src/output.cpp -+++ b/gfalibs/src/output.cpp -@@ -5,7 +5,7 @@ - #include - #include - --#include -+#include "parallel-hashmap/phmap.h" - - #include "bed.h" - #include "struct.h" ---- a/gfalibs/src/input-filters.cpp -+++ b/gfalibs/src/input-filters.cpp -@@ -2,7 +2,7 @@ - #include - #include - --#include -+#include "parallel-hashmap/phmap.h" - - #include "bed.h" - #include "struct.h" diff --git a/recipes/rdeval/zlib.patch b/recipes/rdeval/zlib.patch deleted file mode 100644 index 09eb17bfb0dac..0000000000000 --- a/recipes/rdeval/zlib.patch +++ /dev/null @@ -1,44 +0,0 @@ ---- 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 - #include "zstream/zstream_common.hpp" - #include "zstream/ozstream.hpp" - #include "zstream/ozstream_impl.hpp" ---- a/gfalibs/include/stream-obj.h -+++ b/gfalibs/include/stream-obj.h -@@ -2,7 +2,7 @@ - #define STREAM_OBJ_H - - #include --#include "zlib.h" -+#include - - class membuf : public std::streambuf { - ---- 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 - #include "global.h" - #include "log.h" - #include "threadpool.h" ---- 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 - #include "zstream/zstream_common.hpp" - #include "zstream/ozstream.hpp" - #include "zstream/ozstream_impl.hpp" From 95f5fe842414f4b4c16dd997c0d692a55dc6ba3f Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 12:51:40 -0500 Subject: [PATCH 48/55] requirememts --- recipes/rdeval/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 7ac445f99745f..0892ab1d6c2e9 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -21,7 +21,6 @@ requirements: build: - {{ compiler('cxx') }} - make - - zlib host: - pthread-stubs - zlib From 4e0433de68939eb1943c138a8526c81fc4d883fe Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 13:29:04 -0500 Subject: [PATCH 49/55] zlib --- recipes/rdeval/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 0892ab1d6c2e9..f792a66d35dc1 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -22,8 +22,10 @@ requirements: - {{ compiler('cxx') }} - make host: - - pthread-stubs - - zlib + - libzlib + +# - pthread-stubs +# - zlib test: commands: From 48e074c3229cf35bf6da6d2b3bff4c3bb6fa4a6a Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 13:39:06 -0500 Subject: [PATCH 50/55] zlib --- recipes/rdeval/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index f792a66d35dc1..8b9403f91e1f9 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -23,9 +23,9 @@ requirements: - make host: - libzlib + - zlib # - pthread-stubs -# - zlib test: commands: From 5b306882338e712604e3ee0ee870987b1d0fcdd0 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 13:49:40 -0500 Subject: [PATCH 51/55] zlib --- recipes/rdeval/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 8b9403f91e1f9..f0745003a7a15 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -22,7 +22,6 @@ requirements: - {{ compiler('cxx') }} - make host: - - libzlib - zlib # - pthread-stubs From 921aea785cc5f354119a93ee044cc57608b371fd Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 14:38:51 -0500 Subject: [PATCH 52/55] zlib --- recipes/rdeval/build.sh | 16 ++++++++++++++++ recipes/rdeval/gfalibs.patch | 2 +- recipes/rdeval/makefile.patch | 25 +++++++++++++++++++++++++ recipes/rdeval/meta.yaml | 1 + 4 files changed, 43 insertions(+), 1 deletion(-) create mode 100644 recipes/rdeval/makefile.patch diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 4c2fc868d496a..71cca44d1d28a 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -4,8 +4,24 @@ 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" make -j "$CPU_COUNT" install -d "$PREFIX/bin" install -v -m 0755 build/bin/rdeval "$PREFIX/bin/" + + + +# Compiling C++ programs +# n.o is made automatically from n.cc, n.cpp, or n.C with a recipe of the form ‘$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c’. We encourage you to use the suffix ‘.cc’ or ‘.cpp’ for C++ source files instead of ‘.C’ to better support case-insensitive file systems. diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch index bfd550318a1c1..d43d6346dadaa 100644 --- a/recipes/rdeval/gfalibs.patch +++ b/recipes/rdeval/gfalibs.patch @@ -19,7 +19,7 @@ %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -+ $(CXX) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ clean: $(RM) *.o diff --git a/recipes/rdeval/makefile.patch b/recipes/rdeval/makefile.patch new file mode 100644 index 0000000000000..b9243d5f94b5d --- /dev/null +++ b/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 $@ + + .PHONY: gfalibs + gfalibs: diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index f0745003a7a15..11b11b55a0cda 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -9,6 +9,7 @@ source: url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: + - makefile.patch - gfalibs.patch - reads.patch From 83bc1de9e91df7e3880059d4fcfea1353d6da0ac Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 15:32:33 -0500 Subject: [PATCH 53/55] reads --- recipes/rdeval/build.sh | 9 ++------- recipes/rdeval/meta.yaml | 3 --- 2 files changed, 2 insertions(+), 10 deletions(-) diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh index 71cca44d1d28a..3f30b2376ac7a 100644 --- a/recipes/rdeval/build.sh +++ b/recipes/rdeval/build.sh @@ -2,7 +2,6 @@ set -o errexit set -o nounset -set -o xtrace if [ -e "$PREFIX/include" ]; then export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I$PREFIX/include" @@ -17,11 +16,7 @@ echo "LDFLAGS=\"$LDFLAGS\"" cd "$SRC_DIR" -make -j "$CPU_COUNT" +make + install -d "$PREFIX/bin" install -v -m 0755 build/bin/rdeval "$PREFIX/bin/" - - - -# Compiling C++ programs -# n.o is made automatically from n.cc, n.cpp, or n.C with a recipe of the form ‘$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c’. We encourage you to use the suffix ‘.cc’ or ‘.cpp’ for C++ source files instead of ‘.C’ to better support case-insensitive file systems. diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 11b11b55a0cda..9e26a13eaee9b 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -11,7 +11,6 @@ source: patches: - makefile.patch - gfalibs.patch - - reads.patch build: number: 1 @@ -25,8 +24,6 @@ requirements: host: - zlib -# - pthread-stubs - test: commands: - rdeval --help From 6ab51c58c8b60f001b402ef62be9d132496bbe02 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 16:08:17 -0500 Subject: [PATCH 54/55] rename patch files --- recipes/rdeval/{makefile.patch => Makefile.patch} | 0 recipes/rdeval/{gfalibs.patch => gfalibs-Makefile.patch} | 0 recipes/rdeval/meta.yaml | 4 ++-- 3 files changed, 2 insertions(+), 2 deletions(-) rename recipes/rdeval/{makefile.patch => Makefile.patch} (100%) rename recipes/rdeval/{gfalibs.patch => gfalibs-Makefile.patch} (100%) diff --git a/recipes/rdeval/makefile.patch b/recipes/rdeval/Makefile.patch similarity index 100% rename from recipes/rdeval/makefile.patch rename to recipes/rdeval/Makefile.patch diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs-Makefile.patch similarity index 100% rename from recipes/rdeval/gfalibs.patch rename to recipes/rdeval/gfalibs-Makefile.patch diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml index 9e26a13eaee9b..a495d435df647 100644 --- a/recipes/rdeval/meta.yaml +++ b/recipes/rdeval/meta.yaml @@ -9,8 +9,8 @@ source: url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d patches: - - makefile.patch - - gfalibs.patch + - Makefile.patch + - gfalibs-Makefile.patch build: number: 1 From 168d50a2259dee9fffaff5ae30615774798981da Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Fri, 15 Nov 2024 16:48:21 -0500 Subject: [PATCH 55/55] removed patches --- recipes/rdeval/reads.patch | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 recipes/rdeval/reads.patch diff --git a/recipes/rdeval/reads.patch b/recipes/rdeval/reads.patch deleted file mode 100644 index f9019dfc6d8f2..0000000000000 --- a/recipes/rdeval/reads.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- 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)) { -