CVS commit: pkgsrc/biology/bcf-score

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Oct 11 22:49:06 UTC 2024

Added Files:
        pkgsrc/biology/bcf-score: DESCR Makefile PLIST distinfo
        pkgsrc/biology/bcf-score/patches: patch-Makefile

Log Message:
biology/bcf-score: Bcftools plugin for GWAS 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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bcf-score/DESCR \
    pkgsrc/biology/bcf-score/Makefile pkgsrc/biology/bcf-score/PLIST \
    pkgsrc/biology/bcf-score/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bcf-score/patches/patch-Makefile

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/bcf-score/DESCR
diff -u /dev/null pkgsrc/biology/bcf-score/DESCR:1.1
--- /dev/null   Fri Oct 11 22:49:06 2024
+++ pkgsrc/biology/bcf-score/DESCR      Fri Oct 11 22:49:06 2024
@@ -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.
Index: pkgsrc/biology/bcf-score/Makefile
diff -u /dev/null pkgsrc/biology/bcf-score/Makefile:1.1
--- /dev/null   Fri Oct 11 22:49:06 2024
+++ pkgsrc/biology/bcf-score/Makefile   Fri Oct 11 22:49:06 2024
@@ -0,0 +1,79 @@
+# $NetBSD: Makefile,v 1.1 2024/10/11 22:49:06 bacon Exp $
+
+DISTNAME=      bcf-score-1.20
+CATEGORIES=    biology
+# Can't get ${MASTER_SITE_GITHUB:=samtools/} to work with additional distfile
+MASTER_SITES=  https://software.broadinstitute.org/software/score/
+MASTER_SITES+= https://github.com/samtools/bcftools/releases/download/${GH_TAG}/
+DISTFILES+=    score_1.20-20240505.tar.gz
+DISTFILES+=    bcftools-1.21.tar.bz2
+GH_TAG=                1.21
+
+OWNER=         bacon%NetBSD.org@localhost
+HOMEPAGE=      https://software.broadinstitute.org/software/score/
+COMMENT=       Bcftools plugin for mosaic chromosomal alteration analysis
+LICENSE=       mit
+
+REPLACE_INTERPRETER+=  R
+REPLACE.R.old=         /usr/bin/env Rscript
+REPLACE.R.new=         ${PREFIX}/bin/Rscript
+REPLACE_FILES.R=       bcf-score/*.R
+
+REPLACE_BASH+=         mpileup_bench/compare_vcf_simple.sh
+
+SUBST_CLASSES+=                version
+SUBST_STAGE.version=   pre-configure
+SUBST_SED.version=     -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=   configure.ac
+
+DEPENDS+=      bcftools>=1.16:../../biology/bcftools
+
+USE_TOOLS+=    autoconf automake autoreconf bash gmake perl pax
+GNU_CONFIGURE= yes
+REPLACE_PERL=  misc/* test/test.pl
+
+WRKSRC=                ${WRKDIR}/bcftools-${GH_TAG}
+
+CFLAGS+=       -isystem ${PREFIX}/include/suitesparse
+LDFLAGS+=      -lcholmod
+
+DATADIR=               ${PREFIX}/share/bcf-score
+# FIXME: Why is share/bcf-score only necessary on darwin?
+INSTALLATION_DIRS=     libexec/bcftools share/bcf-score
+
+post-extract:
+       ${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+       ${MKDIR} ${WRKSRC}/bcf-score
+       ${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score
+
+pre-configure:
+       cd ${WRKSRC} && autoreconf -if
+
+# One .so for each .c in the score distfile
+do-install:
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/blup.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/metal.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/pgs.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       ${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \
+               ${DESTDIR}${PREFIX}/libexec/bcftools
+       (cd ${WRKSRC}/bcf-score && pax -rw . ${DESTDIR}${DATADIR})
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../math/gsl/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../biology/htslib/buildlink3.mk"
+.include "../../math/suitesparse/buildlink3.mk"
+.include "../../math/R/buildlink3.mk"
+# Needed on Linux, even though inherited from htslib
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+# Required by cholmod, a not-always-used component of suitesparse
+.include "../../parallel/openmp/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/bcf-score/PLIST
diff -u /dev/null pkgsrc/biology/bcf-score/PLIST:1.1
--- /dev/null   Fri Oct 11 22:49:06 2024
+++ pkgsrc/biology/bcf-score/PLIST      Fri Oct 11 22:49:06 2024
@@ -0,0 +1,8 @@
+@comment $NetBSD: PLIST,v 1.1 2024/10/11 22:49:06 bacon Exp $
+libexec/bcftools/blup.so
+libexec/bcftools/liftover.so
+libexec/bcftools/metal.so
+libexec/bcftools/munge.so
+libexec/bcftools/pgs.so
+libexec/bcftools/score.so
+share/bcf-score/assoc_plot.R
Index: pkgsrc/biology/bcf-score/distinfo
diff -u /dev/null pkgsrc/biology/bcf-score/distinfo:1.1
--- /dev/null   Fri Oct 11 22:49:06 2024
+++ pkgsrc/biology/bcf-score/distinfo   Fri Oct 11 22:49:06 2024
@@ -0,0 +1,9 @@
+$NetBSD: distinfo,v 1.1 2024/10/11 22:49:06 bacon Exp $
+
+BLAKE2s (bcftools-1.21.tar.bz2) = 517b73f84870fa967e6f7f6241c446131cc54229e7ee446110955e39dfbe2563
+SHA512 (bcftools-1.21.tar.bz2) = f8fb2e50a1a9e7a7e8a4f71d71d052f6019d54c60ae060d0abfbd01ab61a2c44e04e069c479ea9f6156513b54a611a9a46930a0ff4454019bb715fdb9558d07d
+Size (bcftools-1.21.tar.bz2) = 7982173 bytes
+BLAKE2s (score_1.20-20240505.tar.gz) = 01791f1c3127f575f34d36fe344b838e4a55b8733791ed4ea44bcf75c2666001
+SHA512 (score_1.20-20240505.tar.gz) = 6e3da79138c83a81d6392a991836c9ba6f92e13fcd1b418647eb83b83952ba79169e6ddc781700f33d9daacbef8731ba0a6f40387bfd93ce0783f78c25d9dd76
+Size (score_1.20-20240505.tar.gz) = 96852 bytes
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731

Index: pkgsrc/biology/bcf-score/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/bcf-score/patches/patch-Makefile:1.1
--- /dev/null   Fri Oct 11 22:49:06 2024
+++ pkgsrc/biology/bcf-score/patches/patch-Makefile     Fri Oct 11 22:49:06 2024
@@ -0,0 +1,23 @@
+$NetBSD: patch-Makefile,v 1.1 2024/10/11 22:49:06 bacon Exp $
+
+# Respect pkgsrc env
+
+--- Makefile.orig      2021-03-19 17:42:33.842623449 +0000
++++ Makefile
+@@ -60,11 +60,11 @@ 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)
++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 = \