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Bacon" Subject: git: 6a3ed7c42449 - main - biology/bcftools: Update to 1.21 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 6a3ed7c424497df7ed9b3d7b1ff977d25012e25f Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=6a3ed7c424497df7ed9b3d7b1ff977d25012e25f commit 6a3ed7c424497df7ed9b3d7b1ff977d25012e25f Author: Jason W. Bacon AuthorDate: 2024-10-09 22:12:12 +0000 Commit: Jason W. Bacon CommitDate: 2024-10-09 22:23:09 +0000 biology/bcftools: Update to 1.21 Numerous bug fixes and enhancements since 1.17 Changes: https://github.com/samtools/bcftools/releases Reported by: portscout --- biology/bcftools/Makefile | 5 ++--- biology/bcftools/distinfo | 6 +++--- biology/bcftools/files/patch-Makefile | 29 ++++++++++++++--------------- biology/bcftools/pkg-plist | 1 - 4 files changed, 19 insertions(+), 22 deletions(-) diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile index 9525d7fd3450..f04c0777bc27 100644 --- a/biology/bcftools/Makefile +++ b/biology/bcftools/Makefile @@ -1,6 +1,5 @@ PORTNAME= bcftools -PORTVERSION= 1.17 -PORTREVISION= 1 +PORTVERSION= 1.21 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -10,6 +9,7 @@ WWW= https://www.htslib.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE +BUILD_DEPENDS= htslib>=1.21:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash RUN_DEPENDS= bash:shells/bash @@ -17,7 +17,6 @@ RUN_DEPENDS= bash:shells/bash USES= autoreconf gmake localbase perl5 python:env shebangfix USE_GITHUB= yes -USE_PERL5= test GH_ACCOUNT= samtools GNU_CONFIGURE= yes diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo index e485c96d9038..a39dbc0e3ca0 100644 --- a/biology/bcftools/distinfo +++ b/biology/bcftools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1677246068 -SHA256 (samtools-bcftools-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e -SIZE (samtools-bcftools-1.17_GH0.tar.gz) = 3481344 +TIMESTAMP = 1727437561 +SHA256 (samtools-bcftools-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d +SIZE (samtools-bcftools-1.21_GH0.tar.gz) = 3665160 diff --git a/biology/bcftools/files/patch-Makefile b/biology/bcftools/files/patch-Makefile index 3299954ae45b..a00ca91d18cb 100644 --- a/biology/bcftools/files/patch-Makefile +++ b/biology/bcftools/files/patch-Makefile @@ -1,6 +1,6 @@ ---- Makefile.orig 2021-03-17 09:16:18 UTC +--- Makefile.orig 2024-09-27 11:44:03 UTC +++ Makefile -@@ -58,13 +58,14 @@ pluginpath = $(plugindir) +@@ -59,13 +59,13 @@ misc_bindir = $(bindir) # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) misc_bindir = $(bindir) @@ -11,23 +11,22 @@ -INSTALL_MAN = $(INSTALL_DATA) -INSTALL_PROGRAM = $(INSTALL) -INSTALL_SCRIPT = $(INSTALL_PROGRAM) -+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set -+MKDIR_P = mkdir -p -+INSTALL = install -p -+INSTALL_DATA = ${BSD_INSTALL_DATA} -+INSTALL_DIR = $(MKDIR_P) -+INSTALL_MAN = ${BSD_INSTALL_MAN} -+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} -+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} ++MKDIR_P = mkdir -p ++INSTALL = install -p ++INSTALL_DATA = ${BSD_INSTALL_DATA} ++INSTALL_DIR = $(MKDIR_P) ++INSTALL_MAN = ${BSD_INSTALL_MAN} ++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} ++INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} PROGRAMS = bcftools MISC_SCRIPTS = \ -@@ -142,7 +143,7 @@ print-version: - ifdef USE_GPL +@@ -144,7 +144,7 @@ ifdef USE_GPL main.o : EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o -- GSL_LIBS ?= -lgsl -lcblas -+ GSL_LIBS ?= -lgslcblas + ifndef GSL_LIBS +- GSL_LIBS += -lgsl -lcblas ++ GSL_LIBS += -lgslcblas + endif endif - print-%: diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist index 6f40c8532f31..6aa7a6d9f73e 100644 --- a/biology/bcftools/pkg-plist +++ b/biology/bcftools/pkg-plist @@ -29,7 +29,6 @@ libexec/bcftools/gvcfz.so libexec/bcftools/impute-info.so libexec/bcftools/indel-stats.so libexec/bcftools/isecGT.so -libexec/bcftools/mendelian.so libexec/bcftools/mendelian2.so libexec/bcftools/missing2ref.so libexec/bcftools/parental-origin.so