diff options
Diffstat (limited to 'PKGBUILD')
| -rw-r--r-- | PKGBUILD | 72 |
1 files changed, 57 insertions, 15 deletions
@@ -1,27 +1,69 @@ -# Maintainer: Clint Valentine <valentine.clint@gmail.com> +# Maintainer: Bipin Kumar <kbipinkumar@pm.me> +# Previous Maintainer: Clint Valentine <valentine.clint@gmail.com> pkgname=centrifuge pkgver=1.0.4 -pkgrel=1 -pkgdesc="Bioinformatics taxonomic classifier for microbial classification" +pkgrel=2 +pkgdesc="Rapid and memory-efficient tool for classification of metagenomic sequences" arch=('x86_64') url=https://ccb.jhu.edu/software/centrifuge/ license=('GPL3') -depends=('libpthread-stubs' 'zlib') -source=("${pkgname}"-"${pkgver}".tar.gz::https://github.com/infphilo/"${pkgname}"/archive/v"${pkgver}"-beta.tar.gz) -sha256sums=('64eb3aa3461d27462357811832f39a8f85702eb536482f1e67344761ad8ca757') +depends=( + 'glibc' + 'gcc-libs' + 'python' + 'perl' + 'bash' + 'jellyfish' + 'hisat2' + ) +makedepends=('git' 'inetutils' 'pandoc-cli') +source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v${pkgver}.tar.gz" + 'alphabet.cpp.patch' + 'alphabet.h.patch' + 'centrifuge-build.patch' + 'centrifuge_evaluate_mason.py.patch' + 'centrifuge_evaluate.py.patch' + 'centrifuge-inspect.patch' + 'centrifuge_simulate_reads.py.patch' + 'Makefile.patch' + ) +sha256sums=('929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc' + 'ae9334ddd0cb9b09811969c151350c4e5ee73452fe5d00f01fd7cf23d6573d78' + 'f681bd2fd89429245ff092b689d53c7e119a5f1270a414b8629896fd5ced90f5' + '12be02a7c3b63679703874b45b6491c81402bac7159859936fe4c78a47632ded' + 'ee6e4c8d8b3d12c141bfeff1aa8c7afd027259d8aa0d1380f6854d4619d868ad' + 'ad05064999c0da91866c82063e42ef60107142acc878fde0342bd629d26d3e68' + 'bf19a2b9e4ef745227eb593d93543020d31726e38d000c6a0091aeb0c3931ffc' + 'f4268c3aa84fc1e14281470251217c1a4a36317c6ad93fc772ea4a46218a3a67' + 'e523ba32ad8163db09fd516a51756f726434dbbe2a2dd9697a5e6a6d606097c1') + +prepare() { + cp *.py.patch ${pkgname}-${pkgver}/evaluation + cp *.patch ${pkgname}-${pkgver}/ + cp ${pkgname}-${pkgver}/evaluation/centrifuge_evaluate_mason.py.patch ${pkgname}-${pkgver}/evaluation/test + cd "${pkgname}-${pkgver}" + # patch Makefile to be inline with archlinux build guidelines + patch -p1 < Makefile.patch + # patch for arm compatibility (not tested fully) + patch -p1 < alphabet.cpp.patch + patch -p1 < alphabet.h.patch + # patch scripts for python3 compatibility + patch -p1 < centrifuge-build.patch + patch -p1 < centrifuge-inspect.patch + cd evaluation + patch -p1 < centrifuge_evaluate.py.patch + patch -p1 < centrifuge_simulate_reads.py.patch + cd test + patch -p1 < centrifuge_evaluate_mason.py.patch +} build() { - cd "${srcdir}"/"${pkgname}"-"${pkgver}"-beta - make + cd "${pkgname}-${pkgver}" + make prefix="/usr" } package() { - cd "${srcdir}"/"${pkgname}"-"${pkgver}"-beta - make install prefix="${pkgdir}"/usr/bin - - install -Dm644 MANUAL "${pkgdir}"/usr/share/doc/"${pkgname}"/MANUAL - install -Dm644 MANUAL.markdown "${pkgdir}"/usr/share/doc/"${pkgname}"/MANUAL.markdown - install -Dm644 AUTHORS "${pkgdir}"/usr/share/doc/"${pkgname}"/AUTHORS - install -Dm644 NEWS "${pkgdir}"/usr/share/doc/"${pkgname}"/NEWS + cd "${pkgname}-${pkgver}" + make DESTDIR=${pkgdir} install } |