head 1.12; access; symbols pkgsrc-2023Q4:1.12.0.4 pkgsrc-2023Q4-base:1.12 pkgsrc-2023Q3:1.12.0.2 pkgsrc-2023Q3-base:1.12 pkgsrc-2023Q2:1.11.0.2 pkgsrc-2023Q2-base:1.11 pkgsrc-2023Q1:1.10.0.2 pkgsrc-2023Q1-base:1.10 pkgsrc-2022Q4:1.9.0.4 pkgsrc-2022Q4-base:1.9 pkgsrc-2022Q3:1.9.0.2 pkgsrc-2022Q3-base:1.9 pkgsrc-2022Q2:1.7.0.4 pkgsrc-2022Q2-base:1.7 pkgsrc-2022Q1:1.7.0.2 pkgsrc-2022Q1-base:1.7 pkgsrc-2021Q4:1.6.0.6 pkgsrc-2021Q4-base:1.6 pkgsrc-2021Q3:1.6.0.4 pkgsrc-2021Q3-base:1.6 pkgsrc-2021Q2:1.6.0.2 pkgsrc-2021Q2-base:1.6 pkgsrc-2021Q1:1.5.0.4 pkgsrc-2021Q1-base:1.5 pkgsrc-2020Q4:1.5.0.2 pkgsrc-2020Q4-base:1.5 pkgsrc-2020Q3:1.4.0.2 pkgsrc-2020Q3-base:1.4 pkgsrc-2020Q2:1.3.0.8 pkgsrc-2020Q2-base:1.3 pkgsrc-2020Q1:1.3.0.4 pkgsrc-2020Q1-base:1.3 pkgsrc-2019Q4:1.3.0.6 pkgsrc-2019Q4-base:1.3 pkgsrc-2019Q3:1.3.0.2 pkgsrc-2019Q3-base:1.3 pkgsrc-2019Q2:1.2.0.2 pkgsrc-2019Q2-base:1.2 pkgsrc-2019Q1:1.1.0.2 pkgsrc-2019Q1-base:1.1; locks; strict; comment @# @; 1.12 date 2023.08.14.05.23.51; author wiz; state Exp; branches; next 1.11; commitid LOSB79OLVxvXjIAE; 1.11 date 2023.05.17.21.55.34; author bacon; state Exp; branches; next 1.10; commitid 27fZ134VGLb3FmpE; 1.10 date 2022.12.28.15.27.16; author bacon; state Exp; branches; next 1.9; commitid MJkRKemaqfXl1l7E; 1.9 date 2022.06.30.11.18.04; author nia; state Exp; branches; next 1.8; commitid AhctUV91Vubws3KD; 1.8 date 2022.06.28.11.31.00; author wiz; state Exp; branches; next 1.7; commitid D2UoJrTHpoHEANJD; 1.7 date 2022.03.17.16.01.11; author bacon; state Exp; branches; next 1.6; commitid Q8UklxdSfTDWnAwD; 1.6 date 2021.05.24.19.49.11; author wiz; state Exp; branches; next 1.5; commitid qokaiStTApGMcrUC; 1.5 date 2020.12.04.20.45.00; author nia; state Exp; branches; next 1.4; commitid FPz71MqRX3WN0tyC; 1.4 date 2020.08.31.18.06.39; author wiz; state Exp; branches; next 1.3; commitid 7zxRbfOkDOoxbfmC; 1.3 date 2019.08.11.13.18.00; author wiz; state Exp; branches; next 1.2; commitid Ifet9Pg6Qt99ZByB; 1.2 date 2019.04.25.07.32.37; author maya; state Exp; branches; next 1.1; commitid 1FEMQBEPb9uTxHkB; 1.1 date 2019.01.15.01.26.29; author bacon; state Exp; branches; next ; commitid BDBV5XMtN1wQKO7B; desc @@ 1.12 log @*: recursive bump for Python 3.11 as new default @ text @# $NetBSD: Makefile,v 1.11 2023/05/17 21:55:34 bacon Exp $ DISTNAME= hisat2-2.2.1 PKGREVISION= 4 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=DaehwanKimLab/} GITHUB_TAG= v${PKGVERSION_NOREV} OWNER= bacon@@NetBSD.org HOMEPAGE= https://ccb.jhu.edu/software/hisat2/index.shtml COMMENT= Alignment program for mapping next-generation sequencing reads LICENSE= gnu-gpl-v3 # 64-bit code, some assembly language ONLY_FOR_PLATFORM= *-*-x86_64 *-*-aarch64 USE_LANGUAGES= c c++ USE_TOOLS+= bash gmake perl REPLACE_BASH= scripts/*.sh REPLACE_PERL= hisat2 scripts/*.sh scripts/*.pl scripts/*.py REPLACE_PYTHON= *.py scripts/*.py hisat2-build hisat2-inspect PTHREAD_AUTO_VARS= yes WRKSRC= ${WRKDIR}/hisat2-2.2.1 # Unbreak #include on case-insensitive file systems post-patch: ${MV} ${WRKSRC}/VERSION ${WRKSRC}/HISAT2_VERSION .include "../../devel/simde/buildlink3.mk" .include "../../lang/python/application.mk" .include "../../mk/pthread.buildlink3.mk" .include "../../mk/bsd.pkg.mk" @ 1.11 log @biology/hisat2: Add SIMDE support SIMDE enables SSE and other x86 intrinsics on other architectures Tested on ARM64, may work on other 64-bit platforms @ text @d1 1 a1 1 # $NetBSD$ d4 1 a4 1 PKGREVISION= 3 @ 1.10 log @Change MAINTAINER= to OWNER= on mission-critical packages @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.9 2022/06/30 11:18:04 nia Exp $ d4 1 a4 1 PKGREVISION= 2 d15 1 a15 1 ONLY_FOR_PLATFORM= *-*-x86_64 d31 1 @ 1.9 log @*: Revbump packages that use Python at runtime without a PKGNAME prefix @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.8 2022/06/28 11:31:00 wiz Exp $ d9 1 a9 1 MAINTAINER= bacon@@NetBSD.org @ 1.8 log @*: recursive bump for perl 5.36 @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.7 2022/03/17 16:01:11 bacon Exp $ d4 1 a4 1 PKGREVISION= 1 @ 1.7 log @biology/hisat2: Update to 2.2.1 pkgsrc fix: Unbreak build on Darwin Add python3 support Several bug fixes and enhancements Changes: https://github.com/DaehwanKimLab/hisat2/tags @ text @d1 1 a1 1 # $NetBSD$ d4 1 @ 1.6 log @*: recursive bump for perl 5.34 @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.5 2020/12/04 20:45:00 nia Exp $ d3 1 a3 2 DISTNAME= hisat2-2.1.0.23 PKGREVISION= 5 d5 2 a6 2 MASTER_SITES= ${MASTER_SITE_GITHUB:=infphilo/} GITHUB_TAG= 20f333e2cfe7ff4d1362b248912893e2644683d7 d19 3 a21 4 REPLACE_BASH= hisatgenotype_scripts/*.sh REPLACE_PERL= hisat2 scripts/*.sh scripts/*.pl REPLACE_PYTHON= *.py hisat2-build hisat2-inspect REPLACE_PYTHON+= hisatgenotype_modules/*.py hisatgenotype_scripts/*.py a22 1 MAKE_FILE= ${FILESDIR}/Makefile.pkg d24 5 @ 1.5 log @Revbump packages with a runtime Python dep but no version prefix. For the Python 3.8 default switch. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.4 2020/08/31 18:06:39 wiz Exp $ d4 1 a4 1 PKGREVISION= 4 @ 1.4 log @*: bump PKGREVISION for perl-5.32. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.3 2019/08/11 13:18:00 wiz Exp $ d4 1 a4 1 PKGREVISION= 3 @ 1.3 log @Bump PKGREVISIONs for perl 5.30.0 @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.2 2019/04/25 07:32:37 maya Exp $ d4 1 a4 1 PKGREVISION= 2 @ 1.2 log @PKGREVISION bump for anything using python without a PYPKGPREFIX. This is a semi-manual PKGREVISION bump. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.1 2019/01/15 01:26:29 bacon Exp $ d4 1 a4 1 PKGREVISION= 1 @ 1.1 log @biology/hisat2: import hisat2-2.1.0.23 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). @ text @d1 1 a1 1 # $NetBSD$ d4 1 @