CVS commit: pkgsrc/biology/bcftools

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/bcftools
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Mon, 27 Jul 2020 00:29:04 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Mon Jul 27 00:29:04 UTC 2020

Modified Files:
        pkgsrc/biology/bcftools: DESCR Makefile PLIST distinfo
Added Files:
        pkgsrc/biology/bcftools/patches: patch-Makefile patch-misc_run-roh.pl

Log Message:
biology/bcftools: Upgrade to 1.10.2

Numerous bug fixes, usability improvements and sanity checks were added since
1.9 to prevent common user errors.


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bcftools/DESCR \
    pkgsrc/biology/bcftools/PLIST pkgsrc/biology/bcftools/distinfo
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/bcftools/Makefile
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bcftools/patches/patch-Makefile \
    pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl

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

Modified files:

Index: pkgsrc/biology/bcftools/DESCR
diff -u pkgsrc/biology/bcftools/DESCR:1.1 pkgsrc/biology/bcftools/DESCR:1.2
--- pkgsrc/biology/bcftools/DESCR:1.1   Thu Nov 15 09:21:24 2018
+++ pkgsrc/biology/bcftools/DESCR       Mon Jul 27 00:29:04 2020
@@ -1,11 +1,4 @@
-BCFtools is a program for variant calling and manipulating files in the Variant
-Call Format (VCF) and its binary counterpart BCF. All commands work
-transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
-In order to avoid tedious repetion, throughout this document we will use "VCF"
-and "BCF" interchangeably, unless specifically noted.
-
-Most commands accept VCF, bgzipped VCF and BCF with filetype detected
-automatically even when streaming from a pipe. Indexed VCF and BCF work in all
-situations. Unindexed VCF and BCF and streams work in most, but not all
-situations. In general, whenever multiple VCFs are read simultaneously, they
-must be indexed and therefore also compressed.
+BCFtools is a set of utilities that manipulate variant calls in the
+Variant Call Format (VCF) and its binary counterpart BCF. All
+commands work transparently with both VCFs and BCFs, both
+uncompressed and BGZF-compressed.
Index: pkgsrc/biology/bcftools/PLIST
diff -u pkgsrc/biology/bcftools/PLIST:1.1 pkgsrc/biology/bcftools/PLIST:1.2
--- pkgsrc/biology/bcftools/PLIST:1.1   Thu Nov 15 09:21:24 2018
+++ pkgsrc/biology/bcftools/PLIST       Mon Jul 27 00:29:04 2020
@@ -1,15 +1,17 @@
-@comment $NetBSD: PLIST,v 1.1 2018/11/15 09:21:24 adam Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/07/27 00:29:04 bacon Exp $
 bin/bcftools
-bin/color-chrs.pl
-bin/guess-ploidy.py
-bin/plot-roh.py
+bin/color-chrs
+bin/guess-ploidy
+bin/plot-roh
 bin/plot-vcfstats
-bin/run-roh.pl
-bin/vcfutils.pl
+bin/run-roh
+bin/vcfutils
 libexec/bcftools/GTisec.so
 libexec/bcftools/GTsubset.so
 libexec/bcftools/ad-bias.so
+libexec/bcftools/add-variantkey.so
 libexec/bcftools/af-dist.so
+libexec/bcftools/allele-length.so
 libexec/bcftools/check-ploidy.so
 libexec/bcftools/check-sparsity.so
 libexec/bcftools/color-chrs.so
@@ -23,15 +25,22 @@ libexec/bcftools/fixploidy.so
 libexec/bcftools/fixref.so
 libexec/bcftools/frameshifts.so
 libexec/bcftools/guess-ploidy.so
+libexec/bcftools/gvcfz.so
 libexec/bcftools/impute-info.so
+libexec/bcftools/indel-stats.so
 libexec/bcftools/isecGT.so
 libexec/bcftools/mendelian.so
 libexec/bcftools/missing2ref.so
+libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so
+libexec/bcftools/remove-overlaps.so
 libexec/bcftools/setGT.so
 libexec/bcftools/smpl-stats.so
+libexec/bcftools/split-vep.so
 libexec/bcftools/split.so
 libexec/bcftools/tag2tag.so
+libexec/bcftools/trio-dnm.so
 libexec/bcftools/trio-stats.so
 libexec/bcftools/trio-switch-rate.so
+libexec/bcftools/variantkey-hex.so
 man/man1/bcftools.1
Index: pkgsrc/biology/bcftools/distinfo
diff -u pkgsrc/biology/bcftools/distinfo:1.1 pkgsrc/biology/bcftools/distinfo:1.2
--- pkgsrc/biology/bcftools/distinfo:1.1        Thu Nov 15 09:21:24 2018
+++ pkgsrc/biology/bcftools/distinfo    Mon Jul 27 00:29:04 2020
@@ -1,6 +1,8 @@
-$NetBSD: distinfo,v 1.1 2018/11/15 09:21:24 adam Exp $
+$NetBSD: distinfo,v 1.2 2020/07/27 00:29:04 bacon Exp $
 
-SHA1 (bcftools-1.9.tar.bz2) = 9b649c3f407528ee193210f68b8e21e8b0aebf31
-RMD160 (bcftools-1.9.tar.bz2) = 59b9997aaa509ba84c41b7e78821f31eca8d90dc
-SHA512 (bcftools-1.9.tar.bz2) = fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c
-Size (bcftools-1.9.tar.bz2) = 3134355 bytes
+SHA1 (bcftools-1.10.2.tar.gz) = b19c9ba06b1c8e8f135c1e0ab0e4ff713a291bf4
+RMD160 (bcftools-1.10.2.tar.gz) = 7713e8c5bd4195eb610544adb26158c16525fdac
+SHA512 (bcftools-1.10.2.tar.gz) = 12c004603db557ac69098e83ad3aaa5762b02b4718b79f3dc259fbcc5c74b8dad3726b5f61efb57f0b8e3d0349577f7934240f36c82bd98849885a5593791995
+Size (bcftools-1.10.2.tar.gz) = 2880994 bytes
+SHA1 (patch-Makefile) = 1f1397e9b0389a7b4fccc9eae87981e7ce1d7980
+SHA1 (patch-misc_run-roh.pl) = 8a29ee7b1001af6670955f174ce4dbab31f05659

Index: pkgsrc/biology/bcftools/Makefile
diff -u pkgsrc/biology/bcftools/Makefile:1.6 pkgsrc/biology/bcftools/Makefile:1.7
--- pkgsrc/biology/bcftools/Makefile:1.6        Sat Jan 18 23:30:08 2020
+++ pkgsrc/biology/bcftools/Makefile    Mon Jul 27 00:29:04 2020
@@ -1,30 +1,55 @@
-# $NetBSD: Makefile,v 1.6 2020/01/18 23:30:08 rillig Exp $
+# $NetBSD: Makefile,v 1.7 2020/07/27 00:29:04 bacon Exp $
 
-DISTNAME=      bcftools-1.9
-PKGREVISION=   2
+DISTNAME=      bcftools-1.10.2
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
-EXTRACT_SUFX=  .tar.bz2
-GITHUB_RELEASE=        ${PKGVERSION_NOREV}
 
 MAINTAINER=    bacon%NetBSD.org@localhost
-HOMEPAGE=      https://samtools.github.io/bcftools/
-COMMENT=       Calling and manipulating files VCF and BCF formats
+HOMEPAGE=      https://www.htslib.org/
+COMMENT=       Tools for manipulating BCF and VCF variant call files
 LICENSE=       mit
 
-USE_TOOLS+=            gmake perl
-GNU_CONFIGURE=         yes
-CONFIGURE_ARGS+=       --with-htslib=system
-TEST_TARGET=           test
+USE_TOOLS+=    autoconf automake autoreconf bash gmake perl
+GNU_CONFIGURE= yes
 
-BUILDLINK_TRANSFORM+=  opt:-ldl:${BUILDLINK_LDADD.dl:M*}
+SUBST_CLASSES+=                version
+SUBST_STAGE.version=   pre-configure
+SUBST_SED.version=     -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=   configure.ac
+
+SUBST_CLASSES+=                bash
+SUBST_STAGE.bash=      pre-configure
+SUBST_SED.bash+=       -e 's|/bin/bash|${TOOLS_PATH.bash}|'
+SUBST_SED.bash+=       -e 's|\\/bin\\/bash|${TOOLS_PATH.bash:S,/,\\\/,g}|'
+SUBST_FILES.bash=      test/test.pl
 
 REPLACE_PERL+=         misc/*.pl
+REPLACE_PERL+=         misc/fix-broken-GATK-Double-vs-Integer
 REPLACE_PERL+=         misc/plot-vcfstats
+REPLACE_PERL+=         test/test.pl
 REPLACE_PYTHON+=       misc/*.py
 
-.include "../../devel/zlib/buildlink3.mk"
+CONFIGURE_ARGS+=       --with-htslib=system
+MAKE_ENV+=             USE_GPL=1
+TEST_TARGET=           test
+
+pre-configure:
+       cd ${WRKSRC} && autoreconf -if
+
+post-install:
+       ${MV} ${DESTDIR}${PREFIX}/bin/color-chrs.pl \
+               ${DESTDIR}${PREFIX}/bin/color-chrs
+       ${MV} ${DESTDIR}${PREFIX}/bin/guess-ploidy.py\
+              ${DESTDIR}${PREFIX}/bin/guess-ploidy
+       ${MV} ${DESTDIR}${PREFIX}/bin/plot-roh.py \
+               ${DESTDIR}${PREFIX}/bin/plot-roh
+       ${MV} ${DESTDIR}${PREFIX}/bin/run-roh.pl \
+               ${DESTDIR}${PREFIX}/bin/run-roh
+       ${MV} ${DESTDIR}${PREFIX}/bin/vcfutils.pl \
+               ${DESTDIR}${PREFIX}/bin/vcfutils
+
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2
 .include "../../biology/htslib/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../lang/python/application.mk"
-.include "../../mk/dlopen.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Added files:

Index: pkgsrc/biology/bcftools/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/bcftools/patches/patch-Makefile:1.1
--- /dev/null   Mon Jul 27 00:29:04 2020
+++ pkgsrc/biology/bcftools/patches/patch-Makefile      Mon Jul 27 00:29:04 2020
@@ -0,0 +1,68 @@
+$NetBSD: patch-Makefile,v 1.1 2020/07/27 00:29:04 bacon Exp $
+
+# Respect pkgsrc env
+
+--- Makefile.orig      2019-12-19 09:57:32.000000000 +0000
++++ Makefile
+@@ -22,12 +22,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC       = gcc
+-AR       = ar
+-RANLIB   = ranlib
+-CPPFLAGS =
+-CFLAGS   = -g -Wall -O2
+-LDFLAGS  =
++CC       ?= gcc
++AR       ?= ar
++RANLIB   ?= ranlib
++# CPPFLAGS =
++CFLAGS   ?= -g -Wall -O2
++# LDFLAGS  =
+ LIBS     =
+ 
+ DYNAMIC_FLAGS = -rdynamic
+@@ -45,12 +45,12 @@ OBJS     = main.o vcfindex.o tabix.o \
+            ccall.o em.o prob1.o kmin.o # the original samtools calling
+ PLUGIN_OBJS = vcfplugin.o
+ 
+-prefix      = /usr/local
+-exec_prefix = $(prefix)
++PREFIX      ?= /usr/local
++exec_prefix = $(PREFIX)
+ bindir      = $(exec_prefix)/bin
+ libdir      = $(exec_prefix)/lib
+ libexecdir  = $(exec_prefix)/libexec
+-mandir      = $(prefix)/share/man
++mandir      = $(PREFIX)/share/man
+ man1dir     = $(mandir)/man1
+ # Installation location for $(PLUGINS)
+ plugindir   = $(libexecdir)/bcftools
+@@ -59,12 +59,11 @@ pluginpath  = $(plugindir)
+ 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 = \
+@@ -78,7 +77,7 @@ TEST_PROGRAMS = test/test-rbuf test/test
+ 
+ ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
+-ALL_LIBS     = -lz $(DL_LIBS) $(LIBS)
++ALL_LIBS     = -lz $(LIBS)
+ 
+ all: $(PROGRAMS) $(TEST_PROGRAMS) plugins
+ 
Index: pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl
diff -u /dev/null pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl:1.1
--- /dev/null   Mon Jul 27 00:29:04 2020
+++ pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl       Mon Jul 27 00:29:04 2020
@@ -0,0 +1,24 @@
+$NetBSD: patch-misc_run-roh.pl,v 1.1 2020/07/27 00:29:04 bacon Exp $
+
+# bash path
+
+--- misc/run-roh.pl.orig       2019-12-19 09:57:32.000000000 +0000
++++ misc/run-roh.pl
+@@ -110,7 +110,7 @@ sub cmd
+ 
+     if ( $args{verbose} ) { print STDERR $cmd,"\n"; }
+ 
+-    # Why not to use backticks? Perl calls /bin/sh, which is often bash. To get the correct
++    # Why not to use backticks? Perl calls bash, which is often bash. To get the correct
+     #   status of failing pipes, it must be called with the pipefail option.
+ 
+     my $kid_io;
+@@ -127,7 +127,7 @@ sub cmd
+     else 
+     {      
+         # child
+-        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
++        exec('bash', '-c', $cmd) or error("Failed to run the command [bash -c $cmd]: $!");
+     }
+ 
+     if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }

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