canu: rm patch to fix

BioArchLinux/canu/PKGBUILD

@@ -1,56 +1,35 @@
 # Maintainer: Chocobo1 <chocobo1 AT archlinux DOT net>
 # Previous maintainer: Roberto Rossini ("robymetallo") <roberto.rossini.9533@student.uu.se>
-# Contributor: Bipin Kumar <kbipinkumar@pm.me>
+
-pkgname=canu 
+pkgname=canu
-pkgver=2.2
+pkgver=2.3
-pkgrel=5
+pkgrel=0
 pkgdesc="A single molecule sequence assembler for large and small genomes. https://doi.org/10.1101/gr.215087.116"
 arch=('i686' 'x86_64')
-url="https://canu.readthedocs.io/en/latest/"
+url="https://canu.readthedocs.io/"
-license=('custom')
+license=('LicenseRef-canu')
-makedepends=('git')
+depends=('gcc-libs' 'java-runtime' 'perl')
-depends=('gcc-libs' 'glibc' 'perl' 'mhap')
 optdepends=('gnuplot')
 options=('staticlibs')
-source=("${pkgname}.${pkgver}.tar.xz::https://github.com/marbl/canu/releases/download/v${pkgver}/canu-${pkgver}.tar.xz"
+source=("$pkgname-$pkgver-src.tar.xz::https://github.com/marbl/canu/releases/download/v$pkgver/canu-$pkgver.tar.xz")
-        'use-arch-mhap-at-runtime.patch'
+sha256sums=('ecb071943cde722152deb861d4ab897090f00b227fd0b261592e1e3fdd3e3e1a')
-'external-mhap.patch'
-'canu_version.patch'
-)
-provides=('meryl')
-sha256sums=('e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'
-            'd94a1f933d34448a94d43b300bf7ac9294898a6a7dac4b47fb4f6c6e76762e4d'
-            'efcfa7aab0752eba85c7c9a56048b838e44076221bc6f4b37377ca16f347788f'
-            '04f84c399232d5433fcec2e62294f0d767608ae39a0bff937a50356bd44b2660')
 
-prepare() {
-  cp *.patch ${pkgname}-${pkgver}/
-  cd ${pkgname}-${pkgver}
-  patch -p1 < use-arch-mhap-at-runtime.patch
-  patch -p1 < external-mhap.patch
-  patch -p1 < canu_version.patch
-}
 
 build() {
-  cd ${pkgname}-${pkgver}/src
+  cd "$pkgname-$pkgver"
-  make
+
+  CFLAGS="$CFLAGS -ffat-lto-objects" \
+  CXXFLAGS="$CXXFLAGS -ffat-lto-objects" \
+  make -C "src"
 }
 
 package() {
-  cd ${pkgname}-${pkgver}/build  
+  cd "$pkgname-$pkgver"
-  install -d $pkgdir/usr/bin
+
-  for bin in bin/*
+  install -Dm755 "build/bin"/* -t "$pkgdir/usr/bin"
-  do [ -f "$bin" ] || continue
+  install -Dm644 "build/lib/site_perl/canu"/*.pm -t "$pkgdir/usr/lib/site_perl/canu"
-  install -Dm755 ${bin} $pkgdir/usr/${bin}
+  install -Dm644 "build/share/java/classes"/*.jar -t "$pkgdir/usr/share/java/classes"
-  done
+  install -Dm644 "build/lib"/*.a -t "$pkgdir/usr/lib"
-  install -d $pkgdir/usr/lib
+
-  for file in lib/*
+  install -Dm644 "README.licenses" -t "$pkgdir/usr/share/licenses/canu"
-  do [ -f "$file" ] || continue
-  install -Dm644 ${file} $pkgdir/usr/${file}
-  done
-  for file in lib/site_perl/canu/*
-  do [ -f "$file" ] || continue
-  install -Dm644 ${file} $pkgdir/usr/${file}
-  done
-  install -Dm644 ../README.licenses -t "$pkgdir/usr/share/licenses/canu"
 }

BioArchLinux/canu/canu_version.patch

@@ -1,12 +0,0 @@
---- canu-2.2.orig/scripts/version_update.pl	2021-08-27 01:27:04.000000000 +0530
-+++ canu-2.2.new/scripts/version_update.pl	2023-06-24 11:43:58.925026735 +0530
-@@ -61,7 +61,8 @@
- 
- #  If in a git repo, we can get the actual values.
- 
--if (-d "../.git") {
-+#if (-d "../.git") {
-+if (0) {
-     $label = "snapshot";
- 
-     #  Count the number of changes since the last release.

BioArchLinux/canu/external-mhap.patch

@@ -1,12 +0,0 @@
-Description: remove bundled mhap from being installed.
-===================================================================
---- canu-2.2.orig/src/Makefile	2021-08-27 01:27:04.000000000 +0530
-+++ canu-2.2.new/src/Makefile	2023-06-24 11:49:01.274587478 +0530
-@@ -679,7 +679,6 @@
-      ${TARGET_DIR}/bin/canu-time \
-      ${TARGET_DIR}/bin/draw-tig \
-      ${TARGET_DIR}/bin/canu.defaults \
--     ${TARGET_DIR}/share/java/classes/mhap-2.1.3.jar \
-      ${TARGET_DIR}/lib/site_perl/canu/Consensus.pm \
-      ${TARGET_DIR}/lib/site_perl/canu/CorrectReads.pm \
-      ${TARGET_DIR}/lib/site_perl/canu/HaplotypeReads.pm \

BioArchLinux/canu/use-arch-mhap-at-runtime.patch

@@ -1,22 +0,0 @@
-Description: Use mhap jar from mhap package provided by Bioarchlinux repo
-===================================================================
---- canu-2.2.orig/src/pipelines/canu/OverlapMhap.pm	2021-08-27 01:27:04.000000000 +0530
-+++ canu-2.2.new/src/pipelines/canu/OverlapMhap.pm	2023-06-24 11:58:23.382864802 +0530
-@@ -345,7 +345,7 @@
-     print F "cd ./blocks\n";
-     print F "\n";
-     print F "$javaPath $javaOpt -XX:ParallelGCThreads=",  getGlobal("${tag}mhapThreads"), " -server -Xms", $javaMemory, "m -Xmx", $javaMemory, "m \\\n";
--    print F "  -jar $cygA \$bin/../share/java/classes/mhap-" . getGlobal("${tag}MhapVersion") . ".jar $cygB \\\n";
-+    print F "  -jar $cygA /usr/share/mhap/mhap.jar $cygB \\\n";
-     print F "  --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
-     print F "  --supress-noise 2 \\\n"  if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
-     print F "  --no-tf \\\n"            if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);
-@@ -464,7 +464,7 @@
- 
-     print F "  #  Start up the producer.\n";
-     print F "  $javaPath $javaOpt -XX:ParallelGCThreads=",  getGlobal("${tag}mhapThreads"), " -server -Xms", $javaMemory, "m -Xmx", $javaMemory, "m \\\n";
--    print F "    -jar $cygA \$bin/../share/java/classes/mhap-" . getGlobal("${tag}MhapVersion") . ".jar $cygB \\\n";
-+    print F "    -jar $cygA /usr/share/mhap/mhap.jar $cygB \\\n";
-     print F "    --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
-     print F "    --supress-noise 2 \\\n"  if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
-     print F "    --no-tf \\\n"            if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);