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canu: restore patches to use dependencies from repo (#261)

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Bipin Kumar 2025-02-08 19:37:19 +05:30 • committed by GitHub
parent 5b314c906d
commit ca2031d350
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4 changed files with 61 additions and 18 deletions
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44
BioArchLinux/canu/PKGBUILD
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@ -1,35 +1,49 @@
# 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
pkgver=2.3
pkgrel=0
pkgrel=1
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/"
license=('LicenseRef-canu')
depends=('gcc-libs' 'java-runtime' 'perl')
url="https://canu.readthedocs.io/en/latest/"
license=('GPL-2.0-only AND BSD-3-Clause AND LicenseRef-Public Domain')
makedepends=('git')
depends=('gcc-libs' 'glibc' 'perl' 'mhap' 'zlib' 'xz' 'curl' 'bzip2')
optdepends=('gnuplot')
options=('staticlibs')
source=("$pkgname-$pkgver-src.tar.xz::https://github.com/marbl/canu/releases/download/v$pkgver/canu-$pkgver.tar.xz")
sha256sums=('ecb071943cde722152deb861d4ab897090f00b227fd0b261592e1e3fdd3e3e1a')
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'
)
provides=('meryl')
sha256sums=('ecb071943cde722152deb861d4ab897090f00b227fd0b261592e1e3fdd3e3e1a'
'0c84b28d99a933d04f57726f691d0057b911131b37c008d36670c0c05e1ca2ff'
'dfcb991b8b57fa138f5ecabbc60bdf119de2a5f2484882424f5835e0928e8421')
prepare() {
cp *.patch ${pkgname}-${pkgver}/
cd ${pkgname}-${pkgver}
# create separate file for public domain license to match SPDX license and namcap guidelines
sed -n '80,96p' README.licenses > license-PD
# use mhap provided by Bioarchlinux repo
patch -p1 < use-arch-mhap-at-runtime.patch
patch -p1 < external-mhap.patch
}
build() {
cd "$pkgname-$pkgver"
cd ${pkgname}-${pkgver}/src
CFLAGS="$CFLAGS -ffat-lto-objects" \
CXXFLAGS="$CXXFLAGS -ffat-lto-objects" \
make -C "src"
make
}
package() {
cd "$pkgname-$pkgver"
export perl=$(perl -V:vendorarch | awk -F'/' '{print $4}')
install -Dm755 "build/bin"/* -t "$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/perl5/site_perl/canu"/*.pm -t "$pkgdir"/usr/share/${perl}/vendor_perl/canu
install -Dm644 "build/lib"/*.a -t "$pkgdir/usr/lib"
install -Dm644 "README.licenses" -t "$pkgdir/usr/share/licenses/canu"
install -Dm644 README.licenses "$pkgdir"/usr/share/licenses/$pkgname/license
install -Dm644 license-PD "$pkgdir"/usr/share/licenses/$pkgname/license-PD
}

10
BioArchLinux/canu/external-mhap.patch Normal file
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@ -0,0 +1,10 @@
--- canu-2.3.orig/src/main.mk 2024-12-16 21:53:18.000000000 +0530
+++ canu-2.3/src/main.mk 2025-02-08 15:21:30.531526902 +0530
@@ -267,7 +267,6 @@
pipelines/draw-tig.pl -> bin/draw-tig
FILES += pipelines/canu.defaults -> bin/canu.defaults \
- mhap/mhap-2.1.3.jar -> share/java/classes/mhap-2.1.3.jar \
pipelines/canu/Consensus.pm -> lib/perl5/site_perl/canu/Consensus.pm \
pipelines/canu/CorrectReads.pm -> lib/perl5/site_perl/canu/CorrectReads.pm \
pipelines/canu/HaplotypeReads.pm -> lib/perl5/site_perl/canu/HaplotypeReads.pm \

3
BioArchLinux/canu/lilac.yaml
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@ -13,6 +13,3 @@ update_on:
github: marbl/canu
use_latest_release: true
prefix: 'v'
- source: manual
manual: 1
time_limit_hours: 3

22
BioArchLinux/canu/use-arch-mhap-at-runtime.patch Normal file
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@ -0,0 +1,22 @@
Description: Use mhap jar from mhap package provided by Bioarchlinux repo
=======================================================================================
--- canu-2.3.orig/src/pipelines/canu/OverlapMhap.pm 2024-11-25 23:30:00.000000000 +0530
+++ canu-2.3/src/pipelines/canu/OverlapMhap.pm 2025-02-08 13:35:27.079558823 +0530
@@ -344,7 +344,7 @@
print F "cd ./blocks\n";
print F "\n";
print F "\$je $javaOpt -XX:ParallelGCThreads=", getGlobal("${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);
@@ -467,7 +467,7 @@
print F " # Start up the producer.\n";
print F " \$je $javaOpt -XX:ParallelGCThreads=", getGlobal("${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);