mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2024-11-18 00:10:04 +00:00
Code Issues Releases Activity

biology/bcf-score: Update to 1.20

Browse Source 
Numerous bug fixes and enhancements since 1.16

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2024-10-09 17:18:18 -05:00
parent 6a3ed7c424
commit 384625e2db
7 changed files with 42 additions and 56 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

31
biology/bcf-score/Makefile
View File

@ -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
# 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 ${WRKSRC}/bcf-score
pre-configure:
@${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 \
${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})

10
biology/bcf-score/distinfo
View File

@ -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

28
biology/bcf-score/files/patch-Makefile
View File

@ -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-%:

4
biology/bcf-score/files/patch-configure.ac
View File

@ -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

11
biology/bcf-score/files/patch-plugins_munge.c
View File

@ -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

11
biology/bcf-score/files/patch-plugins_score.c
View File

@ -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

3
biology/bcf-score/pkg-plist
View File

@ -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