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canu: rm patch to fix
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parent
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commit
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4 changed files with 22 additions and 89 deletions
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@ -1,56 +1,35 @@
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# Maintainer: Chocobo1 <chocobo1 AT archlinux DOT net>
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# Previous maintainer: Roberto Rossini ("robymetallo") <roberto.rossini.9533@student.uu.se>
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# Contributor: Bipin Kumar <kbipinkumar@pm.me>
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pkgname=canu
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pkgver=2.2
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pkgrel=5
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pkgname=canu
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pkgver=2.3
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pkgrel=0
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pkgdesc="A single molecule sequence assembler for large and small genomes. https://doi.org/10.1101/gr.215087.116"
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arch=('i686' 'x86_64')
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url="https://canu.readthedocs.io/en/latest/"
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license=('custom')
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makedepends=('git')
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depends=('gcc-libs' 'glibc' 'perl' 'mhap')
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url="https://canu.readthedocs.io/"
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license=('LicenseRef-canu')
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depends=('gcc-libs' 'java-runtime' 'perl')
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optdepends=('gnuplot')
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options=('staticlibs')
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source=("${pkgname}.${pkgver}.tar.xz::https://github.com/marbl/canu/releases/download/v${pkgver}/canu-${pkgver}.tar.xz"
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'use-arch-mhap-at-runtime.patch'
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'external-mhap.patch'
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'canu_version.patch'
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)
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provides=('meryl')
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sha256sums=('e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'
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'd94a1f933d34448a94d43b300bf7ac9294898a6a7dac4b47fb4f6c6e76762e4d'
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'efcfa7aab0752eba85c7c9a56048b838e44076221bc6f4b37377ca16f347788f'
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'04f84c399232d5433fcec2e62294f0d767608ae39a0bff937a50356bd44b2660')
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source=("$pkgname-$pkgver-src.tar.xz::https://github.com/marbl/canu/releases/download/v$pkgver/canu-$pkgver.tar.xz")
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sha256sums=('ecb071943cde722152deb861d4ab897090f00b227fd0b261592e1e3fdd3e3e1a')
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prepare() {
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cp *.patch ${pkgname}-${pkgver}/
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cd ${pkgname}-${pkgver}
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patch -p1 < use-arch-mhap-at-runtime.patch
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patch -p1 < external-mhap.patch
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patch -p1 < canu_version.patch
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}
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build() {
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cd ${pkgname}-${pkgver}/src
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make
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cd "$pkgname-$pkgver"
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CFLAGS="$CFLAGS -ffat-lto-objects" \
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CXXFLAGS="$CXXFLAGS -ffat-lto-objects" \
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make -C "src"
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}
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package() {
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cd ${pkgname}-${pkgver}/build
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install -d $pkgdir/usr/bin
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for bin in bin/*
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do [ -f "$bin" ] || continue
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install -Dm755 ${bin} $pkgdir/usr/${bin}
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done
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install -d $pkgdir/usr/lib
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for file in lib/*
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do [ -f "$file" ] || continue
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install -Dm644 ${file} $pkgdir/usr/${file}
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done
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for file in lib/site_perl/canu/*
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do [ -f "$file" ] || continue
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install -Dm644 ${file} $pkgdir/usr/${file}
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done
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install -Dm644 ../README.licenses -t "$pkgdir/usr/share/licenses/canu"
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cd "$pkgname-$pkgver"
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install -Dm755 "build/bin"/* -t "$pkgdir/usr/bin"
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install -Dm644 "build/lib/site_perl/canu"/*.pm -t "$pkgdir/usr/lib/site_perl/canu"
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install -Dm644 "build/share/java/classes"/*.jar -t "$pkgdir/usr/share/java/classes"
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install -Dm644 "build/lib"/*.a -t "$pkgdir/usr/lib"
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install -Dm644 "README.licenses" -t "$pkgdir/usr/share/licenses/canu"
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}
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@ -1,12 +0,0 @@
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--- canu-2.2.orig/scripts/version_update.pl 2021-08-27 01:27:04.000000000 +0530
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+++ canu-2.2.new/scripts/version_update.pl 2023-06-24 11:43:58.925026735 +0530
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@@ -61,7 +61,8 @@
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# If in a git repo, we can get the actual values.
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-if (-d "../.git") {
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+#if (-d "../.git") {
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+if (0) {
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$label = "snapshot";
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# Count the number of changes since the last release.
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@ -1,12 +0,0 @@
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Description: remove bundled mhap from being installed.
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===================================================================
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--- canu-2.2.orig/src/Makefile 2021-08-27 01:27:04.000000000 +0530
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+++ canu-2.2.new/src/Makefile 2023-06-24 11:49:01.274587478 +0530
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@@ -679,7 +679,6 @@
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${TARGET_DIR}/bin/canu-time \
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${TARGET_DIR}/bin/draw-tig \
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${TARGET_DIR}/bin/canu.defaults \
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- ${TARGET_DIR}/share/java/classes/mhap-2.1.3.jar \
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${TARGET_DIR}/lib/site_perl/canu/Consensus.pm \
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${TARGET_DIR}/lib/site_perl/canu/CorrectReads.pm \
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${TARGET_DIR}/lib/site_perl/canu/HaplotypeReads.pm \
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@ -1,22 +0,0 @@
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Description: Use mhap jar from mhap package provided by Bioarchlinux repo
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===================================================================
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--- canu-2.2.orig/src/pipelines/canu/OverlapMhap.pm 2021-08-27 01:27:04.000000000 +0530
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+++ canu-2.2.new/src/pipelines/canu/OverlapMhap.pm 2023-06-24 11:58:23.382864802 +0530
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@@ -345,7 +345,7 @@
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print F "cd ./blocks\n";
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print F "\n";
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print F "$javaPath $javaOpt -XX:ParallelGCThreads=", getGlobal("${tag}mhapThreads"), " -server -Xms", $javaMemory, "m -Xmx", $javaMemory, "m \\\n";
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- print F " -jar $cygA \$bin/../share/java/classes/mhap-" . getGlobal("${tag}MhapVersion") . ".jar $cygB \\\n";
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+ print F " -jar $cygA /usr/share/mhap/mhap.jar $cygB \\\n";
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print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
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print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
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print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);
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@@ -464,7 +464,7 @@
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print F " # Start up the producer.\n";
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print F " $javaPath $javaOpt -XX:ParallelGCThreads=", getGlobal("${tag}mhapThreads"), " -server -Xms", $javaMemory, "m -Xmx", $javaMemory, "m \\\n";
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- print F " -jar $cygA \$bin/../share/java/classes/mhap-" . getGlobal("${tag}MhapVersion") . ".jar $cygB \\\n";
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+ print F " -jar $cygA /usr/share/mhap/mhap.jar $cygB \\\n";
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print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
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print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
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print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);
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