head 1.6; access; symbols pkgsrc-2023Q4:1.6.0.2 pkgsrc-2023Q4-base:1.6 pkgsrc-2023Q3:1.5.0.6 pkgsrc-2023Q3-base:1.5 pkgsrc-2023Q2:1.5.0.4 pkgsrc-2023Q2-base:1.5 pkgsrc-2023Q1:1.5.0.2 pkgsrc-2023Q1-base:1.5 pkgsrc-2022Q4:1.4.0.8 pkgsrc-2022Q4-base:1.4 pkgsrc-2022Q3:1.4.0.6 pkgsrc-2022Q3-base:1.4 pkgsrc-2022Q2:1.4.0.4 pkgsrc-2022Q2-base:1.4 pkgsrc-2022Q1:1.4.0.2 pkgsrc-2022Q1-base:1.4 pkgsrc-2021Q4:1.3.0.12 pkgsrc-2021Q4-base:1.3 pkgsrc-2021Q3:1.3.0.10 pkgsrc-2021Q3-base:1.3 pkgsrc-2021Q2:1.3.0.8 pkgsrc-2021Q2-base:1.3 pkgsrc-2021Q1:1.3.0.6 pkgsrc-2021Q1-base:1.3 pkgsrc-2020Q4:1.3.0.4 pkgsrc-2020Q4-base:1.3 pkgsrc-2020Q3:1.3.0.2 pkgsrc-2020Q3-base:1.3 pkgsrc-2020Q2:1.2.0.10 pkgsrc-2020Q2-base:1.2 pkgsrc-2020Q1:1.2.0.6 pkgsrc-2020Q1-base:1.2 pkgsrc-2019Q4:1.2.0.8 pkgsrc-2019Q4-base:1.2 pkgsrc-2019Q3:1.2.0.4 pkgsrc-2019Q3-base:1.2 pkgsrc-2019Q2:1.2.0.2 pkgsrc-2019Q2-base:1.2 pkgsrc-2019Q1:1.1.0.4 pkgsrc-2019Q1-base:1.1 pkgsrc-2018Q4:1.1.0.2 pkgsrc-2018Q4-base:1.1; locks; strict; comment @# @; 1.6 date 2023.11.04.14.35.07; author bacon; state Exp; branches; next 1.5; commitid 1gIhLVph3euAJiLE; 1.5 date 2022.12.28.15.27.17; author bacon; state Exp; branches; next 1.4; commitid MJkRKemaqfXl1l7E; 1.4 date 2022.02.27.01.57.27; author bacon; state Exp; branches; next 1.3; commitid 8xLjjdzaBviZicuD; 1.3 date 2020.07.23.19.22.00; author bacon; state Exp; branches; next 1.2; commitid 7lxNBAD1O5kvQehC; 1.2 date 2019.05.01.12.38.54; author bacon; state Exp; branches; next 1.1; commitid YFmmZsJAliz64vlB; 1.1 date 2018.12.21.19.00.56; author bacon; state Exp; branches; next ; commitid fPsZiwOysvbpoH4B; desc @@ 1.6 log @biology/kallisto: Update to 0.50.1 Update kallisto index version to 13 A few other new features Changes: https://github.com/pachterlab/kallisto/releases @ text @# $NetBSD: Makefile,v 1.1 2018/12/21 19:00:56 bacon Exp $ DISTNAME= kallisto-0.50.1 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=pachterlab/} GITHUB_TAG= v${PKGVERSION_NOREV} OWNER= bacon@@NetBSD.org HOMEPAGE= https://pachterlab.github.io/kallisto/ COMMENT= Quantify abundances of transcripts from RNA-Seq data LICENSE= 2-clause-bsd USE_TOOLS+= autoconf gmake pax USE_LANGUAGES= c c++ USE_CMAKE= yes SUBST_CLASSES+= test SUBST_STAGE.test= pre-configure SUBST_FILES.test= kallisto-test SUBST_SED.test= -e 's|/usr/local/share/kallisto|${DATADIR}|g' CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON # Build fails on 8-core Mac M1 MAKE_JOBS_SAFE= no INSTALLATION_DIRS+= ${DATADIR} DATADIR= ${PREFIX}/share/kallisto post-extract: ${CP} ${FILESDIR}/kallisto-test ${WRKSRC} ${RM} -rf ${WRKSRC}/ext/htslib post-install: ${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR} .include "../../devel/hdf5/buildlink3.mk" .include "../../archivers/libaec/buildlink3.mk" .include "../../devel/zlib/buildlink3.mk" .include "../../biology/htslib/buildlink3.mk" .include "../../mk/bsd.pkg.mk" @ 1.5 log @Change MAINTAINER= to OWNER= on mission-critical packages @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.4 2022/02/27 01:57:27 bacon Exp $ d3 1 a3 1 DISTNAME= kallisto-0.48.0 d22 3 a24 1 CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON @ 1.4 log @biology/kallisto: Update to 0.48.0 Long awaited bug fix release Also unbundled htslib Changes: https://github.com/pachterlab/kallisto/tags @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.1 2018/12/21 19:00:56 bacon Exp $ d8 1 a8 1 MAINTAINER= bacon@@NetBSD.org @ 1.3 log @biology/kallisto: Upgrade to 0.46.1 Minor enhancements since 0.45 0.46.2 is available, but has serious regressions. Reverted to bundled htslib 1.4.1, since kallisto source contains modified htslib files that are incompatible with the current 1.10.2 package. @ text @d3 1 a3 1 DISTNAME= kallisto-0.46.1 a22 1 MAKE_JOBS_SAFE= no # Doesn't finished bundled htslib first d29 1 d38 1 @ 1.2 log @biology/kallisto: Switch from archivers/szip to archivers/libaec libaec is a BSD-licensed drop-in replacement for the non-redistributable szip @ text @d3 1 a3 2 DISTNAME= kallisto-${PV} PKGREVISION= 1 d6 1 a6 1 GITHUB_TAG= v${PV} d13 1 a14 1 USE_TOOLS+= pax d18 1 a18 1 SUBST_STAGE.test= post-build d22 3 a24 2 PV= 0.45.0 DATADIR= ${PREFIX}/share/kallisto d26 1 a26 1 INSTALLATION_DIRS= bin ${DATADIR} a34 1 .include "../../biology/htslib/buildlink3.mk" @ 1.1 log @biology/kallisto: import kallisto-0.45.0 Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. @ text @d1 1 a1 1 # $NetBSD$ d4 1 d37 1 a37 1 .include "../../archivers/szip/buildlink3.mk" @