diff --git a/BioArchLinux/canu/PKGBUILD b/BioArchLinux/canu/PKGBUILD index 0daca99e12..76fbcb247b 100644 --- a/BioArchLinux/canu/PKGBUILD +++ b/BioArchLinux/canu/PKGBUILD @@ -1,56 +1,35 @@ # Maintainer: Chocobo1 # Previous maintainer: Roberto Rossini ("robymetallo") -# Contributor: Bipin Kumar -pkgname=canu -pkgver=2.2 -pkgrel=5 + +pkgname=canu +pkgver=2.3 +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/" -license=('custom') -makedepends=('git') -depends=('gcc-libs' 'glibc' 'perl' 'mhap') +url="https://canu.readthedocs.io/" +license=('LicenseRef-canu') +depends=('gcc-libs' 'java-runtime' 'perl') optdepends=('gnuplot') options=('staticlibs') -source=("${pkgname}.${pkgver}.tar.xz::https://github.com/marbl/canu/releases/download/v${pkgver}/canu-${pkgver}.tar.xz" - 'use-arch-mhap-at-runtime.patch' -'external-mhap.patch' -'canu_version.patch' -) -provides=('meryl') -sha256sums=('e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404' - 'd94a1f933d34448a94d43b300bf7ac9294898a6a7dac4b47fb4f6c6e76762e4d' - 'efcfa7aab0752eba85c7c9a56048b838e44076221bc6f4b37377ca16f347788f' - '04f84c399232d5433fcec2e62294f0d767608ae39a0bff937a50356bd44b2660') +source=("$pkgname-$pkgver-src.tar.xz::https://github.com/marbl/canu/releases/download/v$pkgver/canu-$pkgver.tar.xz") +sha256sums=('ecb071943cde722152deb861d4ab897090f00b227fd0b261592e1e3fdd3e3e1a') -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 - make + cd "$pkgname-$pkgver" + + CFLAGS="$CFLAGS -ffat-lto-objects" \ + CXXFLAGS="$CXXFLAGS -ffat-lto-objects" \ + make -C "src" } package() { - cd ${pkgname}-${pkgver}/build - install -d $pkgdir/usr/bin - for bin in bin/* - do [ -f "$bin" ] || continue - install -Dm755 ${bin} $pkgdir/usr/${bin} - done - install -d $pkgdir/usr/lib - for file in lib/* - do [ -f "$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 "$pkgdir/usr/share/licenses/canu" + cd "$pkgname-$pkgver" + + install -Dm755 "build/bin"/* -t "$pkgdir/usr/bin" + install -Dm644 "build/lib/site_perl/canu"/*.pm -t "$pkgdir/usr/lib/site_perl/canu" + install -Dm644 "build/share/java/classes"/*.jar -t "$pkgdir/usr/share/java/classes" + install -Dm644 "build/lib"/*.a -t "$pkgdir/usr/lib" + + install -Dm644 "README.licenses" -t "$pkgdir/usr/share/licenses/canu" } diff --git a/BioArchLinux/canu/canu_version.patch b/BioArchLinux/canu/canu_version.patch deleted file mode 100644 index 6d85cb8874..0000000000 --- a/BioArchLinux/canu/canu_version.patch +++ /dev/null @@ -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. diff --git a/BioArchLinux/canu/external-mhap.patch b/BioArchLinux/canu/external-mhap.patch deleted file mode 100644 index 92e8836c65..0000000000 --- a/BioArchLinux/canu/external-mhap.patch +++ /dev/null @@ -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 \ - ${TARGET_DIR}/lib/site_perl/canu/HaplotypeReads.pm \ diff --git a/BioArchLinux/canu/use-arch-mhap-at-runtime.patch b/BioArchLinux/canu/use-arch-mhap-at-runtime.patch deleted file mode 100644 index dcf711ca9c..0000000000 --- a/BioArchLinux/canu/use-arch-mhap-at-runtime.patch +++ /dev/null @@ -1,22 +0,0 @@ -Description: Use mhap jar from mhap package provided by Bioarchlinux repo -=================================================================== ---- canu-2.2.orig/src/pipelines/canu/OverlapMhap.pm 2021-08-27 01:27:04.000000000 +0530 -+++ canu-2.2.new/src/pipelines/canu/OverlapMhap.pm 2023-06-24 11:58:23.382864802 +0530 -@@ -345,7 +345,7 @@ - print F "cd ./blocks\n"; - print F "\n"; - print F "$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);