From nobody Sat Feb 25 14:27:48 2023 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4PP8HS63q3z3tDv3; Sat, 25 Feb 2023 14:27:48 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4PP8HS57zCz4dBs; Sat, 25 Feb 2023 14:27:48 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677335268; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=OlM3TwCuaGzZB1qliw1m3BZj+CsIN8irVace1qYjTkI=; b=QEaZP8bXz53DVzb+o1UPfNUNEgi1ot0DnzsVHXL2okYsloFm3cIrSWRZ0faVgwO90miJ+J mtF1H/y4qFqpZ84dG4zwTr0hefEn8p/kq/+6qcMkpyqGr7Hptycr/3wsvXKHn0oJNz//L4 o7dnG8i1ZH80a9fI1VRyMPqnlkeYERciuC2zNHvT0PUpyEqA30aQUM9l4y8aS/3EkcFgpB v2NFU3tI8iZ8jweeQvjPyEHkqRV4P1PJ8faOoAXhNTWEu7Fbbj9dvc3XUAkGdRqxu/yxu1 1nvEzcHDao3zTsMFS8xDbkcfDpTH0IUcOSPT7xyknZJrFUc4fKTM4mDmejm9nQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677335268; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=OlM3TwCuaGzZB1qliw1m3BZj+CsIN8irVace1qYjTkI=; b=XXLbuQyNPXG1qy8qRh/4gRsWxTC3BzPIQWiXFWrXrAibS3FPbt80BMCGSnNufjShhp7pSd 3aGhDn9BkPxw5Te609cDRbv1xPT10HZsxn/51wS4qnlXR5iZsfaUjoyNXY74QzCEKiYpCL mfBOd7EtbLlc3bTxdP3NA2cFkl1WjXveaSGS7hNokP7veVFSU6ocLXVS4k603twDPOdBT2 YSMr5Me21q3Blql8V4P+lx+TorF5xkzzDDBN/8ldvmQaCPT3GQp8mMqX3E8SiTNKXYYtHX 2qPpqGNP6kAQ8BNnCuMYld330Nr7SqUlDcXLTjPez6DiU2sbVA2kYnvi/o2YBQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1677335268; a=rsa-sha256; cv=none; b=WBTjiIb32xTRGSvXO6MBsjuYsn/DF/fbECu6bOx4wy10KzbL8xd75RV0t2AYl//+WcU9Mo EDtSXBOeaXQkMf8BcZPoBxS5lOoCOggp/NSVIwy3IklRYiJjgscjUlQLGLJwA0yrKySBSq M3Kj4S5fsLs6qPu/vBJgLKqIUTPWj9VJZ1ymHUr3NpVQow9khOyLMFSqtl9s2l9kbYk7tl 5OUHlNAke31N/htTCuy2YIj0mwll6hSCLfr6Bch26Wb0CGTlYCPto/65qD8nk5QBUdTfBK ScZxjI0jfbcI+EsOI0QFk0usVQbdjw0CiJFpf/qPsCkGIDQjI4LZmrZ8F6t1jA== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4PP8HS4BPsz176N; Sat, 25 Feb 2023 14:27:48 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 31PERm0T070603; Sat, 25 Feb 2023 14:27:48 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 31PERmmt070602; Sat, 25 Feb 2023 14:27:48 GMT (envelope-from git) Date: Sat, 25 Feb 2023 14:27:48 GMT Message-Id: <202302251427.31PERmmt070602@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 68c12d4ad402 - main - biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics 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: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: 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: 68c12d4ad402d885c078499f05c4a3919276398b Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=68c12d4ad402d885c078499f05c4a3919276398b commit 68c12d4ad402d885c078499f05c4a3919276398b Author: Jason W. Bacon AuthorDate: 2023-02-25 14:27:17 +0000 Commit: Jason W. Bacon 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 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