git: 384625e2db65 - main - biology/bcf-score: Update to 1.20
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Date: Wed, 09 Oct 2024 22:23:14 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=384625e2db650bbc95ae66326590e67357126009
commit 384625e2db650bbc95ae66326590e67357126009
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-10-09 22:18:18 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
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