From nobody Wed Oct 09 22:23:14 2024 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 4XP6pq2WxRz5Z3ss; Wed, 09 Oct 2024 22:23:15 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XP6pq0ZHFz4dMZ; Wed, 9 Oct 2024 22:23:15 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1728512595; 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=bUri6LSeMksiO4XDMg66aqK3HbuqKj+yJvT7zrJj5Y0=; b=OT+55w7knqYP9k5WqrpHNYyp0YRYSWCXe9nflRXr4iOpOwnp8v9t5lksL5VR/52zwRqisE RcMzAOlzyDcDQxiUCyBPfxh9F2qII9NezTry2aB8q+2ndcCHhpJ3zW+60P720/iEdN0pXD tCBV/Do5eJlC+EiaDg8YuqkL6m6vlHh1Z9dgKGaD42yI0DgDE+zAMiUKTMXyisXdYxxLo4 JAS7SnM1SDC7sARwsbpNtB7EoI2bg08XklKDajZSctIAfKQkZyWTysrndQ6UP73At44k+/ rpeS/B8X/0DBLVO5s8GAVXy9BJY1CbECTszhdj+vWDmTJHSwCuTLlLUzTkaQYQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1728512595; 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=bUri6LSeMksiO4XDMg66aqK3HbuqKj+yJvT7zrJj5Y0=; b=cdU7cXskUHF3bfUBCKCDEmWBReaALyQok+iNCdIe7So0NNtGohXEwC4RHAIxFSrhAMzcg4 L8L8nmkOgfM1fC7FXwF5C5Su/S38c+/N1y1UYf91cFZyN2tabZ6ojV4c0jWEI7uwDSK7FJ x8A4GdNPfJ6KYwL+oRbqGoZ4s8/tVyvJLg9FaEbwo5q+eJDzIC71r7PjTG/W0fUBOpLwb2 MhMhvulot8OWfH9WIi3EpUjq1Uul3GyYpw2UIJ72n3z6lgMxyS/SFW5VZ/Rn8xTV1mGtRZ UhdUCd9Mltw/pRupv40F089hahQWcg/GBESBenAUe5nBi6GApq2CsuwF7+bQ/w== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1728512595; a=rsa-sha256; cv=none; b=RKgAJ3J6kMyZTndUAJyvw/ZrUKdZhAEyegU1MEPKcUOb8ZwF2ZRJ5N3iByWAKbvX0z/5h/ tFO0T/lwSSBNZHJRToFGDWDMLE9baAH5Gw9NjzbeVDb6MZHTKygS2oLURnj3g51C2LisrF jdNdhlQGEKkmbGfGmsdBfZ2RO98pb97NRGYr35Fg2ooo5UhVfBt2FDbopS1BhjNZtvEiXR 2ntmF5Tx08LagiM8ZYm91IhKYRwDWHVSO1Esh5v0Ahh+avJDvFMrEzQ8JZEUd+QhieIezC XGWOFKyo0516FRaDU9aEjvTvDIbJjOzQLI48/t2UKqDWMxBRTAoSLvYSwHH6zA== 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 4XP6pq0BNPzXqf; Wed, 9 Oct 2024 22:23:15 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 499MNEvg059828; Wed, 9 Oct 2024 22:23:14 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 499MNEtM059825; Wed, 9 Oct 2024 22:23:14 GMT (envelope-from git) Date: Wed, 9 Oct 2024 22:23:14 GMT Message-Id: <202410092223.499MNEtM059825@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: 384625e2db65 - main - biology/bcf-score: Update to 1.20 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: 384625e2db650bbc95ae66326590e67357126009 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=384625e2db650bbc95ae66326590e67357126009 commit 384625e2db650bbc95ae66326590e67357126009 Author: Jason W. Bacon AuthorDate: 2024-10-09 22:18:18 +0000 Commit: Jason W. Bacon CommitDate: 2024-10-09 22:23:09 +0000 biology/bcf-score: Update to 1.20 Numerous bug fixes and enhancements since 1.16 Reported by: portscout --- biology/bcf-score/Makefile | 31 ++++++++++++++++----------- biology/bcf-score/distinfo | 10 ++++----- biology/bcf-score/files/patch-Makefile | 28 ++++++++++++------------ biology/bcf-score/files/patch-configure.ac | 4 ++-- biology/bcf-score/files/patch-plugins_munge.c | 11 ---------- biology/bcf-score/files/patch-plugins_score.c | 11 ---------- biology/bcf-score/pkg-plist | 3 ++- 7 files changed, 42 insertions(+), 56 deletions(-) diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile index f183641f4a4f..d29f1e583120 100644 --- a/biology/bcf-score/Makefile +++ b/biology/bcf-score/Makefile @@ -1,9 +1,9 @@ PORTNAME= bcf-score -DISTVERSION= 1.16 -PORTREVISION= 1 +DISTVERSION= 1.20 CATEGORIES= biology MASTER_SITES= https://software.broadinstitute.org/software/score/ -DISTFILES+= score_${DISTVERSION}-20221221.tar.gz +# Get this right, or ports will download bcftools in it's place via tuple +DISTFILES+= score_${DISTVERSION}-20240505.tar.gz MAINTAINER= jwb@FreeBSD.org COMMENT= Bcftools plugins for GWAS-VCF summary statistics files @@ -11,9 +11,10 @@ WWW= https://software.broadinstitute.org/software/score/ LICENSE= MIT -LIB_DEPENDS= libhts.so:biology/htslib -BUILD_DEPENDS= bash:shells/bash -RUN_DEPENDS= bcftools>=${PORTVERSION}:biology/bcftools +BUILD_DEPENDS= htslib>=1.21:biology/htslib +LIB_DEPENDS= libhts.so:biology/htslib libcholmod.so:math/suitesparse-cholmod +TEST_DEPENDS= bash:shells/bash +RUN_DEPENDS= bash:shells/bash bcftools>=${PORTVERSION}:biology/bcftools USES= autoreconf gmake localbase perl5 python:env shebangfix USE_GITHUB= yes @@ -21,23 +22,27 @@ USE_PERL5= test GH_ACCOUNT= samtools GH_PROJECT= bcftools -GH_TAGNAME= 1.17 +GH_TAGNAME= 1.21 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 +# From pgs.mk +CFLAGS+= -isystem ${LOCALBASE}/include/suitesparse +LDFLAGS+= -lcholmod pre-configure: @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \ ${WRKSRC}/configure.ac +post-extract: + @${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins + @${MKDIR} ${WRKSRC}/bcf-score + @${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score + # One .so for each .c in the score distfile do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools - ${INSTALL_PROGRAM} ${WRKSRC}/plugins/blupx.so \ + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/blup.so \ ${STAGEDIR}${PREFIX}/libexec/bcftools ${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \ ${STAGEDIR}${PREFIX}/libexec/bcftools @@ -45,6 +50,8 @@ do-install: ${STAGEDIR}${PREFIX}/libexec/bcftools ${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \ ${STAGEDIR}${PREFIX}/libexec/bcftools + ${INSTALL_PROGRAM} ${WRKSRC}/plugins/pgs.so \ + ${STAGEDIR}${PREFIX}/libexec/bcftools ${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \ ${STAGEDIR}${PREFIX}/libexec/bcftools (cd ${WRKSRC}/bcf-score && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) diff --git a/biology/bcf-score/distinfo b/biology/bcf-score/distinfo index d343300fb841..fb0644c4567b 100644 --- a/biology/bcf-score/distinfo +++ b/biology/bcf-score/distinfo @@ -1,5 +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 +TIMESTAMP = 1727475307 +SHA256 (score_1.20-20240505.tar.gz) = c2ac510f0a48e3d2e61d1a9e219e030b1268cdcf3bf987217bbd16740d962d41 +SIZE (score_1.20-20240505.tar.gz) = 96852 +SHA256 (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d +SIZE (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 3665160 diff --git a/biology/bcf-score/files/patch-Makefile b/biology/bcf-score/files/patch-Makefile index 3299954ae45b..55d6f64d426d 100644 --- a/biology/bcf-score/files/patch-Makefile +++ b/biology/bcf-score/files/patch-Makefile @@ -1,6 +1,6 @@ ---- Makefile.orig 2021-03-17 09:16:18 UTC +--- Makefile.orig 2024-09-12 15:06:36 UTC +++ Makefile -@@ -58,13 +58,14 @@ pluginpath = $(plugindir) +@@ -59,13 +59,14 @@ misc_bindir = $(bindir) # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) misc_bindir = $(bindir) @@ -12,22 +12,22 @@ -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 +145,7 @@ 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/bcf-score/files/patch-configure.ac b/biology/bcf-score/files/patch-configure.ac index ca845d2ad85f..31087a94e97f 100644 --- a/biology/bcf-score/files/patch-configure.ac +++ b/biology/bcf-score/files/patch-configure.ac @@ -1,6 +1,6 @@ ---- configure.ac.orig 2018-07-18 08:34:29 UTC +--- configure.ac.orig 2024-09-27 11:57:52 UTC +++ configure.ac -@@ -23,7 +23,7 @@ +@@ -23,7 +23,7 @@ dnl Process this file with autoconf to produce a confi # DEALINGS IN THE SOFTWARE. dnl Process this file with autoconf to produce a configure script diff --git a/biology/bcf-score/files/patch-plugins_munge.c b/biology/bcf-score/files/patch-plugins_munge.c deleted file mode 100644 index 8906f57a0a73..000000000000 --- a/biology/bcf-score/files/patch-plugins_munge.c +++ /dev/null @@ -1,11 +0,0 @@ ---- plugins/munge.c.orig 2023-07-16 07:57:54 UTC -+++ plugins/munge.c -@@ -120,7 +120,7 @@ int tsv_read_string(tsv_t *tsv, bcf1_t *rec, void *usr - return 0; - } - --static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP -+static int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP - tsv_setter_pos_flexible, // BP - tsv_setter_chrom_flexible, // CHR - tsv_read_allele, // A1 diff --git a/biology/bcf-score/files/patch-plugins_score.c b/biology/bcf-score/files/patch-plugins_score.c deleted file mode 100644 index c90a66f313b6..000000000000 --- a/biology/bcf-score/files/patch-plugins_score.c +++ /dev/null @@ -1,11 +0,0 @@ ---- plugins/score.c.orig 2023-07-16 08:04:54 UTC -+++ plugins/score.c -@@ -140,7 +140,7 @@ static int tsv_read_allele(tsv_t *tsv, bcf1_t *rec, vo - return 0; - } - --static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP -+static int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP - tsv_setter_pos_flexible, // BP - tsv_setter_chrom_flexible, // CHR - tsv_read_allele, // A1 diff --git a/biology/bcf-score/pkg-plist b/biology/bcf-score/pkg-plist index 719a907bf251..f9741a4d9fdf 100644 --- a/biology/bcf-score/pkg-plist +++ b/biology/bcf-score/pkg-plist @@ -1,6 +1,7 @@ -libexec/bcftools/blupx.so +libexec/bcftools/blup.so libexec/bcftools/liftover.so libexec/bcftools/metal.so libexec/bcftools/munge.so +libexec/bcftools/pgs.so libexec/bcftools/score.so %%DATADIR%%/assoc_plot.R