From a3c5df66461de8bc9d0706e148030bd9b6a6f3ee Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Mon, 3 Feb 2025 11:02:41 +0200 Subject: [PATCH 01/17] fastx_toolkit: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov --- recipes/fastx_toolkit/build.sh | 4 +++- recipes/fastx_toolkit/meta.yaml | 18 +++++++++++++----- 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 1db7194d8dfd4..ce6b37f3f8954 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -xe + export GTEXTUTILS_CFLAGS="-I $PREFIX/include/gtextutils" export GTEXTUTILS_LIBS="$PREFIX/lib/libgtextutils.a" export CXXFLAGS="${CXXFLAGS} -std=c++11 -Wall -Wno-implicit-fallthrough" @@ -12,5 +14,5 @@ if [ "$(uname)" == "Darwin" ]; then fi ./configure --prefix=$PREFIX -make +make -j"${CPU_COUNT}" make install diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index a24945a75d1ec..731631ed9570d 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -1,16 +1,21 @@ +{% set name = "fastx_toolkit" %} +{% set version = "0.0.14" %} + package: - name: fastx_toolkit - version: 0.0.14 + name: {{ name }} + version: {{ version }} source: - url: https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 - md5: bf1993c898626bb147de3d6695c20b40 + url: https://github.com/agordon/fastx_toolkit/releases/download/{{ version }}/fastx_toolkit-{{ version }}.tar.bz2 + sha256: 9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806 patches: - fastx.patch build: preserve_egg_dir: True - number: 12 + number: 13 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x.x") }} requirements: build: @@ -37,6 +42,7 @@ test: about: home: https://github.com/agordon/fastx_toolkit license: AGPL + license_file: COPYING summary: | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. @@ -57,6 +63,8 @@ about: The FASTX-Toolkit tools perform some of these preprocessing tasks.' extra: + additional-platforms: + - linux-aarch64 container: # gnuplot fails without libGL.so.1 extended-base: true From 936795e5af7f3cc0d198d82dc1bd15efa079ecce Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Mon, 3 Feb 2025 19:00:51 +0200 Subject: [PATCH 02/17] Use newer config.sub/.guess for aarch64 support Signed-off-by: Martin Tzvetanov Grigorov --- recipes/fastx_toolkit/build.sh | 2 ++ recipes/fastx_toolkit/meta.yaml | 1 + 2 files changed, 3 insertions(+) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index ce6b37f3f8954..3c323d0985b3b 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -2,6 +2,8 @@ set -xe +cp $BUILD_PREFIX/share/gnuconfig/config.* config/ + export GTEXTUTILS_CFLAGS="-I $PREFIX/include/gtextutils" export GTEXTUTILS_LIBS="$PREFIX/lib/libgtextutils.a" export CXXFLAGS="${CXXFLAGS} -std=c++11 -Wall -Wno-implicit-fallthrough" diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index 731631ed9570d..42afdb2173784 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -23,6 +23,7 @@ requirements: - {{ compiler('cxx') }} - {{ compiler('c') }} - pkg-config # [osx] + - gnuconfig host: - cython - nose From 0d3aeae3f593f992d88cec99cea2847c1107a5e8 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 20:49:35 -0600 Subject: [PATCH 03/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 3c323d0985b3b..55108e9e08e16 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -2,19 +2,21 @@ set -xe -cp $BUILD_PREFIX/share/gnuconfig/config.* config/ +cp -rf $BUILD_PREFIX/share/gnuconfig/config.* config/ export GTEXTUTILS_CFLAGS="-I $PREFIX/include/gtextutils" export GTEXTUTILS_LIBS="$PREFIX/lib/libgtextutils.a" -export CXXFLAGS="${CXXFLAGS} -std=c++11 -Wall -Wno-implicit-fallthrough" +export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" sed -i.bak 's/#pragma pack(1)//g' src/libfastx/fastx.h -if [ "$(uname)" == "Darwin" ]; then +if [[ "$(uname)" == "Darwin" ]]; then export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib" - MACOSX_DEPLOYMENT_TARGET=10.7 - CXXFLAGS="${CXXFLAGS} -std=c++11 -stdlib=libc++" + MACOSX_DEPLOYMENT_TARGET=10.15 + CXXFLAGS="${CXXFLAGS} -std=c++14 -stdlib=libc++" fi -./configure --prefix=$PREFIX +autoreconf -if + +./configure --prefix="$PREFIX" CC="$CC" CXX="$CXX" CXXFLAGS="$CXXFLAGS" LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" make -j"${CPU_COUNT}" make install From 8d4ec882281261b0de87256cd8278cc09a28fcc7 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 20:53:22 -0600 Subject: [PATCH 04/17] Update meta.yaml --- recipes/fastx_toolkit/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index 42afdb2173784..a06907546970a 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -24,6 +24,9 @@ requirements: - {{ compiler('c') }} - pkg-config # [osx] - gnuconfig + - autoconf + - automake + - libtool host: - cython - nose @@ -42,6 +45,7 @@ test: about: home: https://github.com/agordon/fastx_toolkit + dev_url: https://github.com/agordon/fastx_toolkit license: AGPL license_file: COPYING summary: | From 2f898398df41afe540af1dc85273721372d1bf1c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 22:47:02 -0600 Subject: [PATCH 05/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 55108e9e08e16..00d5bffc076a3 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -4,19 +4,23 @@ set -xe cp -rf $BUILD_PREFIX/share/gnuconfig/config.* config/ -export GTEXTUTILS_CFLAGS="-I $PREFIX/include/gtextutils" -export GTEXTUTILS_LIBS="$PREFIX/lib/libgtextutils.a" -export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" +export GTEXTUTILS_CFLAGS="-I${PREFIX}/include/gtextutils" +export GTEXTUTILS_LIBS="${PREFIX}/lib/libgtextutils.a" +export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 --disable-dependency-tracking --enable-silent-rules -I${PREFIX}/include -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" +export CFLAGS="${CFLAGS} -O3" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXCPP="${CXX}" sed -i.bak 's/#pragma pack(1)//g' src/libfastx/fastx.h +rm -rf src/libfastx/*.bak if [[ "$(uname)" == "Darwin" ]]; then export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib" - MACOSX_DEPLOYMENT_TARGET=10.15 - CXXFLAGS="${CXXFLAGS} -std=c++14 -stdlib=libc++" + export MACOSX_DEPLOYMENT_TARGET="10.15" + export CXXFLAGS="${CXXFLAGS} -std=c++14 -stdlib=libc++" fi autoreconf -if -./configure --prefix="$PREFIX" CC="$CC" CXX="$CXX" CXXFLAGS="$CXXFLAGS" LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" +./configure --prefix="${PREFIX}" make -j"${CPU_COUNT}" make install From f85d6c2ff36f5ff088b70537f165e4f226b6b55f Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 23:12:12 -0600 Subject: [PATCH 06/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 00d5bffc076a3..3262fb89728e0 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -9,7 +9,6 @@ export GTEXTUTILS_LIBS="${PREFIX}/lib/libgtextutils.a" export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 --disable-dependency-tracking --enable-silent-rules -I${PREFIX}/include -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" export CFLAGS="${CFLAGS} -O3" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CXXCPP="${CXX}" sed -i.bak 's/#pragma pack(1)//g' src/libfastx/fastx.h rm -rf src/libfastx/*.bak From 629ef47ca78714a2cb455cb3827a072953b21cf8 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 23:19:14 -0600 Subject: [PATCH 07/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 3262fb89728e0..4e93d8779d4d1 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -4,7 +4,7 @@ set -xe cp -rf $BUILD_PREFIX/share/gnuconfig/config.* config/ -export GTEXTUTILS_CFLAGS="-I${PREFIX}/include/gtextutils" +export GTEXTUTILS_CFLAGS="-I ${PREFIX}/include/gtextutils" export GTEXTUTILS_LIBS="${PREFIX}/lib/libgtextutils.a" export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 --disable-dependency-tracking --enable-silent-rules -I${PREFIX}/include -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" export CFLAGS="${CFLAGS} -O3" From 5fbbe3b7ecef7a7a2168383b320b7e12dcee95e7 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 23:19:43 -0600 Subject: [PATCH 08/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 4e93d8779d4d1..aa42977cb61df 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -18,8 +18,6 @@ if [[ "$(uname)" == "Darwin" ]]; then export CXXFLAGS="${CXXFLAGS} -std=c++14 -stdlib=libc++" fi -autoreconf -if - ./configure --prefix="${PREFIX}" make -j"${CPU_COUNT}" make install From 8cc8c7deeb74c2367d41e1a50f6551c59f0243a5 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 23:33:05 -0600 Subject: [PATCH 09/17] Update meta.yaml --- recipes/fastx_toolkit/meta.yaml | 23 ++++++++++------------- 1 file changed, 10 insertions(+), 13 deletions(-) diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index a06907546970a..b27bbffda8892 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -12,7 +12,6 @@ source: - fastx.patch build: - preserve_egg_dir: True number: 13 run_exports: - {{ pin_subpackage(name, max_pin="x.x.x") }} @@ -24,32 +23,30 @@ requirements: - {{ compiler('c') }} - pkg-config # [osx] - gnuconfig - - autoconf - - automake - - libtool host: - - cython - - nose - libgtextutils run: - - gnuplot >=5.0.5 + - gnuplot >=5.4.10 - perl - perl-perlio-gzip - perl-gd - perl-gdgraph-histogram + - libgtextutils test: commands: - - fasta_clipping_histogram.pl + - 'fasta_clipping_histogram.pl' - 'fastx_trimmer -h | grep "Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)"' about: - home: https://github.com/agordon/fastx_toolkit - dev_url: https://github.com/agordon/fastx_toolkit - license: AGPL + home: "https://github.com/agordon/fastx_toolkit" + dev_url: "https://github.com/agordon/fastx_toolkit" + doc_url: "https://github.com/agordon/fastx_toolkit/blob/{{ version }}/README" + license: "AGPL-3.0-or-later" + license_family: AGPL license_file: COPYING summary: | - The FASTX-Toolkit is a collection of command line tools for + 'The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, @@ -72,4 +69,4 @@ extra: - linux-aarch64 container: # gnuplot fails without libGL.so.1 - extended-base: true + extended-base: True From bca963cc2001512944c65f294f39c69c7bc82b4a Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 3 Feb 2025 23:59:15 -0600 Subject: [PATCH 10/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index aa42977cb61df..9ce1a1716e999 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -6,8 +6,8 @@ cp -rf $BUILD_PREFIX/share/gnuconfig/config.* config/ export GTEXTUTILS_CFLAGS="-I ${PREFIX}/include/gtextutils" export GTEXTUTILS_LIBS="${PREFIX}/lib/libgtextutils.a" +export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 --disable-dependency-tracking --enable-silent-rules -I${PREFIX}/include -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" -export CFLAGS="${CFLAGS} -O3" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" sed -i.bak 's/#pragma pack(1)//g' src/libfastx/fastx.h rm -rf src/libfastx/*.bak @@ -15,7 +15,12 @@ rm -rf src/libfastx/*.bak if [[ "$(uname)" == "Darwin" ]]; then export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib" export MACOSX_DEPLOYMENT_TARGET="10.15" - export CXXFLAGS="${CXXFLAGS} -std=c++14 -stdlib=libc++" + export CXXFLAGS="${CXXFLAGS} -stdlib=libc++" + sed -i.bak '' '88,90d;58d' src/fastx_artifacts_filter/fastx_artifacts_filter.c + sed -i.bak '' 's/-Werror//' configure.ac +else + sed -i.bak '88,90d;58d' src/fastx_artifacts_filter/fastx_artifacts_filter.c + sed -i.bak 's/-Werror//' configure.ac fi ./configure --prefix="${PREFIX}" From e04c352ae405d12cea198b0a40051cd5e108506a Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 4 Feb 2025 00:07:48 -0600 Subject: [PATCH 11/17] Update meta.yaml --- recipes/fastx_toolkit/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index b27bbffda8892..86533f0c9d8e0 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -1,5 +1,6 @@ {% set name = "fastx_toolkit" %} {% set version = "0.0.14" %} +{% set sha256 = "9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806" %} package: name: {{ name }} @@ -7,7 +8,7 @@ package: source: url: https://github.com/agordon/fastx_toolkit/releases/download/{{ version }}/fastx_toolkit-{{ version }}.tar.bz2 - sha256: 9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806 + sha256: {{ sha256 }} patches: - fastx.patch @@ -23,6 +24,9 @@ requirements: - {{ compiler('c') }} - pkg-config # [osx] - gnuconfig + - autoconf + - automake + - libtool host: - libgtextutils run: From 493a70ce802e494e3e88c94148d6a7c7705ee85b Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 4 Feb 2025 00:09:15 -0600 Subject: [PATCH 12/17] Update fastx.patch --- recipes/fastx_toolkit/fastx.patch | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/recipes/fastx_toolkit/fastx.patch b/recipes/fastx_toolkit/fastx.patch index ea248f28e1e06..b7e290aee574f 100644 --- a/recipes/fastx_toolkit/fastx.patch +++ b/recipes/fastx_toolkit/fastx.patch @@ -1,24 +1,24 @@ -diff -Naur scripts/fasta_clipping_histogram.pl scripts/fasta_clipping_histogram.pl ---- scripts/fasta_clipping_histogram.pl 2014-01-05 16:10:49.000000000 -0500 -+++ scripts/fasta_clipping_histogram.pl 2018-04-24 14:55:17.509357447 -0400 +diff -Naur a/scripts/fasta_clipping_histogram.pl b/scripts/fasta_clipping_histogram.pl +--- a/scripts/fasta_clipping_histogram.pl 2014-01-05 16:10:49.000000000 -0500 ++++ b/scripts/fasta_clipping_histogram.pl 2018-04-24 14:55:17.509357447 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) -diff -Naur scripts/fastx_barcode_splitter.pl scripts/fastx_barcode_splitter.pl ---- scripts/fastx_barcode_splitter.pl 2014-01-05 16:10:49.000000000 -0500 -+++ scripts/fastx_barcode_splitter.pl 2018-04-24 14:55:07.909304624 -0400 +diff -Naur a/scripts/fastx_barcode_splitter.pl b/scripts/fastx_barcode_splitter.pl +--- a/scripts/fastx_barcode_splitter.pl 2014-01-05 16:10:49.000000000 -0500 ++++ b/scripts/fastx_barcode_splitter.pl 2018-04-24 14:55:07.909304624 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/env perl # FASTX-toolkit - FASTA/FASTQ preprocessing tools. # Copyright (C) 2009-2013 A. Gordon (assafgordon@gmail.com) -diff -Naur src/libfastx/fastx.c src/libfastx/fastx.c ---- src/libfastx/fastx.c 2014-01-05 16:10:49.000000000 -0500 -+++ src/libfastx/fastx.c 2018-04-24 14:53:55.188903629 -0400 +diff -Naur a/src/libfastx/fastx.c b/src/libfastx/fastx.c +--- a/src/libfastx/fastx.c 2014-01-05 16:10:49.000000000 -0500 ++++ b/src/libfastx/fastx.c 2018-04-24 14:53:55.188903629 -0400 @@ -126,7 +126,7 @@ for (i=0; iquality[i], pFASTX->input_line_number ); -diff -Naur src/libfastx/fastx.h src/libfastx/fastx.h ---- src/libfastx/fastx.h 2014-01-05 16:10:49.000000000 -0500 -+++ src/libfastx/fastx.h 2018-04-24 14:53:55.188903629 -0400 +diff -Naur a/src/libfastx/fastx.h b/src/libfastx/fastx.h +--- a/src/libfastx/fastx.h 2014-01-05 16:10:49.000000000 -0500 ++++ b/src/libfastx/fastx.h 2018-04-24 14:53:55.188903629 -0400 @@ -25,8 +25,8 @@ /* for PATH_MAX */ #include From fb32b23892eb6177a7b553bed0d4e9deca6b7520 Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 4 Feb 2025 00:59:36 -0600 Subject: [PATCH 13/17] add patch --- recipes/fastx_toolkit/build.sh | 21 ++-- .../fastx_toolkit/build_failure.osx-64.yaml | 106 ------------------ .../fastx_toolkit/fastx-toolkit-gcc7.patch | 28 +++++ recipes/fastx_toolkit/meta.yaml | 1 + 4 files changed, 40 insertions(+), 116 deletions(-) delete mode 100644 recipes/fastx_toolkit/build_failure.osx-64.yaml create mode 100644 recipes/fastx_toolkit/fastx-toolkit-gcc7.patch diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 9ce1a1716e999..f47b5e01d4d57 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -4,25 +4,26 @@ set -xe cp -rf $BUILD_PREFIX/share/gnuconfig/config.* config/ +export M4="${BUILD_PREFIX}/bin/m4" export GTEXTUTILS_CFLAGS="-I ${PREFIX}/include/gtextutils" export GTEXTUTILS_LIBS="${PREFIX}/lib/libgtextutils.a" export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" -export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 --disable-dependency-tracking --enable-silent-rules -I${PREFIX}/include -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" +export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include -Wall -Wno-implicit-fallthrough -Wno-unused-but-set-variable" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" sed -i.bak 's/#pragma pack(1)//g' src/libfastx/fastx.h +sed -i.bak '88,90d;58d' src/fastx_artifacts_filter/fastx_artifacts_filter.c +sed -i.bak 's/ -Werror//' configure.ac rm -rf src/libfastx/*.bak +rm -rf src/fastx_artifacts_filter/*.bak +rm -rf *.bak if [[ "$(uname)" == "Darwin" ]]; then - export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib" - export MACOSX_DEPLOYMENT_TARGET="10.15" - export CXXFLAGS="${CXXFLAGS} -stdlib=libc++" - sed -i.bak '' '88,90d;58d' src/fastx_artifacts_filter/fastx_artifacts_filter.c - sed -i.bak '' 's/-Werror//' configure.ac -else - sed -i.bak '88,90d;58d' src/fastx_artifacts_filter/fastx_artifacts_filter.c - sed -i.bak 's/-Werror//' configure.ac + export DYLD_FALLBACK_LIBRARY_PATH="${PREFIX}/lib" + export MACOSX_DEPLOYMENT_TARGET="10.15" + export CXXFLAGS="${CXXFLAGS} -stdlib=libc++" fi -./configure --prefix="${PREFIX}" +./reconf +./configure --prefix="${PREFIX}" --disable-option-checking make -j"${CPU_COUNT}" make install diff --git a/recipes/fastx_toolkit/build_failure.osx-64.yaml b/recipes/fastx_toolkit/build_failure.osx-64.yaml deleted file mode 100644 index 0c41cf70e0d09..0000000000000 --- a/recipes/fastx_toolkit/build_failure.osx-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 5e8a4c7c910b810953593f2f8fa55c95e04344cfb040dd50d51e2dd63bf6921f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - config.status: creating build_scripts/Makefile - config.status: creating config.h - config.status: executing depfiles commands - config.status: executing libtool commands - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - make all-recursive - make[1]: Entering directory '$SRC_DIR' - Making all in m4 - make[2]: Entering directory '$SRC_DIR/m4' - make[2]: Nothing to be done for 'all'. - make[2]: Leaving directory '$SRC_DIR/m4' - Making all in src - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - make[2]: Entering directory '$SRC_DIR/src' - Making all in libfastx - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastx_toolkit_1734563654197/work/conda_build.sh']' returned non-zero exit status 2. - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - make[3]: Entering directory '$SRC_DIR/src/libfastx' - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build - raise BuildScriptException(str(exc), caused_by=exc) from exc - conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastx_toolkit_1734563654197/work/conda_build.sh']' returned non-zero exit status 2. - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT chomp.o -MD -MP -MF .deps/chomp.Tpo -c -o chomp.o chomp.c - mv -f .deps/chomp.Tpo .deps/chomp.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx.o -MD -MP -MF .deps/fastx.Tpo -c -o fastx.o fastx.c - mv -f .deps/fastx.Tpo .deps/fastx.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_args.o -MD -MP -MF .deps/fastx_args.Tpo -c -o fastx_args.o fastx_args.c - mv -f .deps/fastx_args.Tpo .deps/fastx_args.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT sequence_alignment.o -MD -MP -MF .deps/sequence_alignment.Tpo -c -o sequence_alignment.o sequence_alignment.cpp - mv -f .deps/sequence_alignment.Tpo .deps/sequence_alignment.Po - rm -f libfastx.a - x86_64-apple-darwin13.4.0-ar cru libfastx.a chomp.o fastx.o fastx_args.o sequence_alignment.o - x86_64-apple-darwin13.4.0-ranlib libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/libfastx' - Making all in fastx_clipper - make[3]: Entering directory '$SRC_DIR/src/fastx_clipper' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_clipper.o -MD -MP -MF .deps/fastx_clipper.Tpo -c -o fastx_clipper.o fastx_clipper.cpp - mv -f .deps/fastx_clipper.Tpo .deps/fastx_clipper.Po - /bin/sh ../../libtool --tag=CXX --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_clipper fastx_clipper.o -L$PREFIX/lib ../libfastx/libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/fastx_clipper' - Making all in fastx_trimmer - make[3]: Entering directory '$SRC_DIR/src/fastx_trimmer' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_trimmer.o -MD -MP -MF .deps/fastx_trimmer.Tpo -c -o fastx_trimmer.o fastx_trimmer.c - mv -f .deps/fastx_trimmer.Tpo .deps/fastx_trimmer.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_trimmer fastx_trimmer.o -L$PREFIX/lib ../libfastx/libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/fastx_trimmer' - Making all in fastx_quality_stats - make[3]: Entering directory '$SRC_DIR/src/fastx_quality_stats' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_quality_stats.o -MD -MP -MF .deps/fastx_quality_stats.Tpo -c -o fastx_quality_stats.o fastx_quality_stats.c - mv -f .deps/fastx_quality_stats.Tpo .deps/fastx_quality_stats.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_quality_stats fastx_quality_stats.o -L$PREFIX/lib ../libfastx/libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/fastx_quality_stats' - Making all in fastq_quality_converter - make[3]: Entering directory '$SRC_DIR/src/fastq_quality_converter' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_converter.o -MD -MP -MF .deps/fastq_quality_converter.Tpo -c -o fastq_quality_converter.o fastq_quality_converter.c - mv -f .deps/fastq_quality_converter.Tpo .deps/fastq_quality_converter.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_converter fastq_quality_converter.o -L$PREFIX/lib ../libfastx/libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/fastq_quality_converter' - Making all in fastq_to_fasta - make[3]: Entering directory '$SRC_DIR/src/fastq_to_fasta' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_to_fasta.o -MD -MP -MF .deps/fastq_to_fasta.Tpo -c -o fastq_to_fasta.o fastq_to_fasta.c - mv -f .deps/fastq_to_fasta.Tpo .deps/fastq_to_fasta.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_to_fasta fastq_to_fasta.o -L$PREFIX/lib ../libfastx/libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/fastq_to_fasta' - Making all in fastq_quality_filter - make[3]: Entering directory '$SRC_DIR/src/fastq_quality_filter' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_filter.o -MD -MP -MF .deps/fastq_quality_filter.Tpo -c -o fastq_quality_filter.o fastq_quality_filter.c - mv -f .deps/fastq_quality_filter.Tpo .deps/fastq_quality_filter.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_filter fastq_quality_filter.o -L$PREFIX/lib ../libfastx/libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/fastq_quality_filter' - Making all in fastq_quality_trimmer - make[3]: Entering directory '$SRC_DIR/src/fastq_quality_trimmer' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_trimmer.o -MD -MP -MF .deps/fastq_quality_trimmer.Tpo -c -o fastq_quality_trimmer.o fastq_quality_trimmer.c - mv -f .deps/fastq_quality_trimmer.Tpo .deps/fastq_quality_trimmer.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_trimmer fastq_quality_trimmer.o -L$PREFIX/lib ../libfastx/libfastx.a - make[3]: Leaving directory '$SRC_DIR/src/fastq_quality_trimmer' - Making all in fastx_artifacts_filter - make[3]: Entering directory '$SRC_DIR/src/fastx_artifacts_filter' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_artifacts_filter.o -MD -MP -MF .deps/fastx_artifacts_filter.Tpo -c -o fastx_artifacts_filter.o fastx_artifacts_filter.c - make[3]: Leaving directory '$SRC_DIR/src/fastx_artifacts_filter' - make[2]: Leaving directory '$SRC_DIR/src' - make[1]: Leaving directory '$SRC_DIR' -# Last 100 lines of the build log. -category: |- - compiler error diff --git a/recipes/fastx_toolkit/fastx-toolkit-gcc7.patch b/recipes/fastx_toolkit/fastx-toolkit-gcc7.patch new file mode 100644 index 0000000000000..5970e70875df5 --- /dev/null +++ b/recipes/fastx_toolkit/fastx-toolkit-gcc7.patch @@ -0,0 +1,28 @@ +diff -Naur a/src/fasta_formatter/fasta_formatter.cpp b/src/fasta_formatter/fasta_formatter.cpp +--- a/src/fasta_formatter/fasta_formatter.cpp 2014-01-05 21:10:49.038563296 +0000 ++++ b/src/fasta_formatter/fasta_formatter.cpp 2017-07-28 10:52:17.568172280 +0100 +@@ -87,12 +87,6 @@ + "\n" \ + "\n"; + +-void usage() +-{ +- printf("%s",usage_string); +- exit(0); +-} +- + void parse_command_line(int argc, char* argv[]) + { + int opt; +@@ -102,8 +96,9 @@ + //Parse the default options + switch(opt) { + case 'h': +- usage(); +- ++ printf("%s",usage_string); ++ exit(0); ++ + case 'i': + input_filename = optarg; + break; diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index 86533f0c9d8e0..f4e619611b3c7 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} patches: - fastx.patch + - fastx-toolkit-gcc7.patch build: number: 13 From 79e98b17db16acbbe81d4a647476f9835a5ec5df Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 4 Feb 2025 01:13:00 -0600 Subject: [PATCH 14/17] Update meta.yaml --- recipes/fastx_toolkit/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index f4e619611b3c7..485b083ad9bfa 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -23,7 +23,7 @@ requirements: - make - {{ compiler('cxx') }} - {{ compiler('c') }} - - pkg-config # [osx] + - pkg-config - gnuconfig - autoconf - automake From 11474c45d68ca67622c280174282bc4c403c71fa Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 4 Feb 2025 01:45:48 -0600 Subject: [PATCH 15/17] add macos patch --- recipes/fastx_toolkit/build.sh | 3 ++- recipes/fastx_toolkit/fastx.patch | 26 ++++++++++++++++++++++---- 2 files changed, 24 insertions(+), 5 deletions(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index f47b5e01d4d57..62e77aa31a90f 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -24,6 +24,7 @@ if [[ "$(uname)" == "Darwin" ]]; then fi ./reconf -./configure --prefix="${PREFIX}" --disable-option-checking +./configure --prefix="${PREFIX}" CXXFLAGS="${CXXFLAGS}" \ + CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" --disable-option-checking make -j"${CPU_COUNT}" make install diff --git a/recipes/fastx_toolkit/fastx.patch b/recipes/fastx_toolkit/fastx.patch index b7e290aee574f..a9f7c23d61eec 100644 --- a/recipes/fastx_toolkit/fastx.patch +++ b/recipes/fastx_toolkit/fastx.patch @@ -28,10 +28,11 @@ diff -Naur a/src/libfastx/fastx.c b/src/libfastx/fastx.c errx(1, "Invalid quality score value (char '%c' ord %d quality value %d) on line %lld", ascii_quality_scores[i], ascii_quality_scores[i], pFASTX->quality[i], pFASTX->input_line_number ); -diff -Naur a/src/libfastx/fastx.h b/src/libfastx/fastx.h ---- a/src/libfastx/fastx.h 2014-01-05 16:10:49.000000000 -0500 -+++ b/src/libfastx/fastx.h 2018-04-24 14:53:55.188903629 -0400 -@@ -25,8 +25,8 @@ +diff --git a/src/libfastx/fastx.h b/src/libfastx/fastx.h +index 5a8639d..ed9c81d 100644 +--- a/src/libfastx/fastx.h ++++ b/src/libfastx/fastx.h +@@ -25,8 +25,8 @@ extern "C" { /* for PATH_MAX */ #include @@ -42,3 +43,20 @@ diff -Naur a/src/libfastx/fastx.h b/src/libfastx/fastx.h #define QUALITY_VALUES_RANGE (MAX_QUALITY_VALUE-MIN_QUALITY_VALUE) +@@ -58,7 +58,7 @@ typedef enum { + OUTPUT_SAME_AS_INPUT=3 + } OUTPUT_FILE_TYPE; + +-#pragma pack(1) ++#pragma pack(push,1) + typedef struct + { + /* Record data - common for FASTA/FASTQ */ +@@ -115,6 +115,7 @@ typedef struct + FILE* input; + FILE* output; + } FASTX ; ++#pragma pack(pop) + + + void fastx_init_reader(FASTX *pFASTX, const char* filename, From 66cb9ab46b1ff51ac6abcc32963982c9e04fc487 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 4 Feb 2025 01:55:22 -0600 Subject: [PATCH 16/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 62e77aa31a90f..92baadeca8188 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -25,6 +25,7 @@ fi ./reconf ./configure --prefix="${PREFIX}" CXXFLAGS="${CXXFLAGS}" \ - CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" --disable-option-checking + CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \ + --enable-debug=no --enable-all-static --disable-option-checking make -j"${CPU_COUNT}" make install From 00c4c5f5e9a7d17075f075d0227f166b69fdca53 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 4 Feb 2025 02:07:26 -0600 Subject: [PATCH 17/17] Update build.sh --- recipes/fastx_toolkit/build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/fastx_toolkit/build.sh b/recipes/fastx_toolkit/build.sh index 92baadeca8188..71c40e89d393f 100755 --- a/recipes/fastx_toolkit/build.sh +++ b/recipes/fastx_toolkit/build.sh @@ -26,6 +26,7 @@ fi ./reconf ./configure --prefix="${PREFIX}" CXXFLAGS="${CXXFLAGS}" \ CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \ - --enable-debug=no --enable-all-static --disable-option-checking + --enable-debug=no --enable-static --enable-all-static \ + --disable-shared --disable-option-checking make -j"${CPU_COUNT}" make install