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amrfinderplus: update to version 3.12.8

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bipin kumar 2024-03-03 22:49:56 +05:30
parent 02901307bd
commit 2e1f85b14d
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GPG key ID: C67233497C15E476
1 changed files with 8 additions and 17 deletions
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BioArchLinux/amrfinderplus/PKGBUILD
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@ -1,12 +1,13 @@
# Maintianer: Bipin Kumar <bipin@ccmb.res.in>
# Maintainer: Bipin Kumar <kbipinkumar@pm.me>
pkgname=amrfinderplus
pkgver=3.11.26
pkgrel=2
pkgver=3.12.8
pkgrel=1
pkgdesc="Identify Antimicrobial resistance genes in assembled bacterial nucleotide and protein sequence. https://doi.org/10.1038/s41598-021-91456-0"
arch=('x86_64' 'i686')
url="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/"
license=('custom: Public Domain')
license=('LicenseRef-Public Domain')
depends=(
'glibc'
'gcc-libs'
@ -14,28 +15,18 @@ depends=(
'blast+'
'hmmer'
)
source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ncbi/amr/archive/refs/tags/amrfinder_v${pkgver}.tar.gz"
"LDFLAG.patch::https://patch-diff.githubusercontent.com/raw/ncbi/amr/pull/132.patch"
"destdir.patch::https://patch-diff.githubusercontent.com/raw/ncbi/amr/pull/131.patch"
)
sha256sums=('49d98d0f66e121d3ed5a3d9a817089ee69399b0bd06af52f79d796bfe8b2d8b2'
'efa5f955d235e739b5e282f87d4a25ec0b6acc26d99487c816e6753924ecfa09'
'94a47bc95906ce5da028a7fa869c1120a7b0165d4ed90078978fe041c5d424dd')
source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ncbi/amr/archive/refs/tags/amrfinder_v${pkgver}.tar.gz")
sha256sums=('a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0')
prepare() {
cp *.patch amr-amrfinder_v${pkgver}
cd amr-amrfinder_v${pkgver}
# patch Makefile to use $(LDFLAGS)
patch -p1 < LDFLAG.patch
# patch Makefile to use gnu make's destdir variable
patch -p1 < destdir.patch
# set optimisation flag to archlinux recommended -O2
sed -i '76s/-O3/-O2/' Makefile
}
build() {
cd amr-amrfinder_v${pkgver}
export LDFLAGS="-Wl,-O2,--sort-common,--as-needed,-z,relro,-z,now"
export LDFLAGS="-Wl,-O2,--sort-common,--as-needed,-z,shstk,-z,relro,-z,now"
export PREFIX="/usr"
export DEFAULT_DB_DIR="/usr/share/amrfinderplus/data"
make