Date: Sat, 25 Feb 2023 14:27:48 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 68c12d4ad402 - main - biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics Message-ID: <202302251427.31PERmmt070602@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=68c12d4ad402d885c078499f05c4a3919276398b commit 68c12d4ad402d885c078499f05c4a3919276398b Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-02-25 14:27:17 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2023-02-25 14:27:46 +0000 biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics Score is a set of tools in the form of a bcftools plugin, for handling and converting summary statistics files following the GWAS-VCF specification. --- biology/Makefile | 1 + biology/bcf-score/Makefile | 51 ++++++++++++++++++++++++++++++ biology/bcf-score/distinfo | 5 +++ biology/bcf-score/files/patch-Makefile | 33 +++++++++++++++++++ biology/bcf-score/files/patch-configure.ac | 11 +++++++ biology/bcf-score/pkg-descr | 3 ++ biology/bcf-score/pkg-plist | 6 ++++ 7 files changed, 110 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 43439e1f4a89..927e88c08f00 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -11,6 +11,7 @@ SUBDIR += bamutil SUBDIR += barrnap SUBDIR += bbmap + SUBDIR += bcf-score SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile new file mode 100644 index 000000000000..96207e1f8f84 --- /dev/null +++ b/biology/bcf-score/Makefile @@ -0,0 +1,51 @@ +PORTNAME= bcf-score +DISTVERSION= 1.16 +CATEGORIES= biology +MASTER_SITES= https://software.broadinstitute.org/software/score/ +DISTFILES+= score_${DISTVERSION}-20221221.tar.gz + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Bcftools plugins for GWAS-VCF summary statistics files +WWW= https://software.broadinstitute.org/software/score/ + +LICENSE= MIT + +LIB_DEPENDS= libhts.so:biology/htslib +BUILD_DEPENDS= bash:shells/bash +RUN_DEPENDS= bcftools>=${PORTVERSION}:biology/bcftools + +USES= autoreconf gmake localbase perl5 python:env shebangfix +USE_GITHUB= yes +USE_PERL5= test + +GH_ACCOUNT= samtools +GH_PROJECT= bcftools +GH_TAGNAME= 1.17 +GNU_CONFIGURE= yes +SHEBANG_FILES= misc/* test/test.pl + +post-extract: + @${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins + @${MKDIR} ${WRKSRC}/bcf-score + @${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score + +pre-configure: + @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \ + ${WRKSRC}/configure.ac + +# One .so for each .c in the score distfile +do-install: + ${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/blupx.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/metal.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools + (cd ${WRKSRC}/bcf-score && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) + +.include <bsd.port.mk> diff --git a/biology/bcf-score/distinfo b/biology/bcf-score/distinfo new file mode 100644 index 000000000000..d343300fb841 --- /dev/null +++ b/biology/bcf-score/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1677335027 +SHA256 (score_1.16-20221221.tar.gz) = f5f7331f2f670ea26cbc48a924e1467ac13c69aaf3b2a56599e3decda9375c0b +SIZE (score_1.16-20221221.tar.gz) = 61927 +SHA256 (samtools-bcftools-1.16-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e +SIZE (samtools-bcftools-1.16-1.17_GH0.tar.gz) = 3481344 diff --git a/biology/bcf-score/files/patch-Makefile b/biology/bcf-score/files/patch-Makefile new file mode 100644 index 000000000000..3299954ae45b --- /dev/null +++ b/biology/bcf-score/files/patch-Makefile @@ -0,0 +1,33 @@ +--- Makefile.orig 2021-03-17 09:16:18 UTC ++++ Makefile +@@ -58,13 +58,14 @@ pluginpath = $(plugindir) + # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) + misc_bindir = $(bindir) + +-MKDIR_P = mkdir -p +-INSTALL = install -p +-INSTALL_DATA = $(INSTALL) -m 644 +-INSTALL_DIR = $(MKDIR_P) -m 755 +-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} + + PROGRAMS = bcftools + MISC_SCRIPTS = \ +@@ -142,7 +143,7 @@ print-version: + ifdef USE_GPL + main.o : EXTRA_CPPFLAGS += -DUSE_GPL + OBJS += polysomy.o peakfit.o +- GSL_LIBS ?= -lgsl -lcblas ++ GSL_LIBS ?= -lgslcblas + endif + + print-%: diff --git a/biology/bcf-score/files/patch-configure.ac b/biology/bcf-score/files/patch-configure.ac new file mode 100644 index 000000000000..ca845d2ad85f --- /dev/null +++ b/biology/bcf-score/files/patch-configure.ac @@ -0,0 +1,11 @@ +--- configure.ac.orig 2018-07-18 08:34:29 UTC ++++ configure.ac +@@ -23,7 +23,7 @@ + # DEALINGS IN THE SOFTWARE. + + dnl Process this file with autoconf to produce a configure script +-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]), ++AC_INIT([BCFtools], [@PORTVERSION@], + [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) + AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER + AC_CONFIG_SRCDIR([main.c]) diff --git a/biology/bcf-score/pkg-descr b/biology/bcf-score/pkg-descr new file mode 100644 index 000000000000..2d926613d77b --- /dev/null +++ b/biology/bcf-score/pkg-descr @@ -0,0 +1,3 @@ +Score is a set of tools in the form of a bcftools plugin, for handling +and converting summary statistics files following the GWAS-VCF +specification. diff --git a/biology/bcf-score/pkg-plist b/biology/bcf-score/pkg-plist new file mode 100644 index 000000000000..719a907bf251 --- /dev/null +++ b/biology/bcf-score/pkg-plist @@ -0,0 +1,6 @@ +libexec/bcftools/blupx.so +libexec/bcftools/liftover.so +libexec/bcftools/metal.so +libexec/bcftools/munge.so +libexec/bcftools/score.so +%%DATADIR%%/assoc_plot.R
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