Date: Thu, 2 Aug 2018 19:30:57 +0000 (UTC) From: =?UTF-8?Q?Fernando_Apestegu=c3=ada?= <fernape@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r476247 - in head/biology/bcftools: . files Message-ID: <201808021930.w72JUvqd087935@repo.freebsd.org>
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Author: fernape Date: Thu Aug 2 19:30:57 2018 New Revision: 476247 URL: https://svnweb.freebsd.org/changeset/ports/476247 Log: biology/bcftools: update to 1.9 While here: * Update LICENSE handling * Move all commands to bin/ PR: 230169 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16543 Modified: head/biology/bcftools/Makefile head/biology/bcftools/distinfo head/biology/bcftools/files/patch-Makefile head/biology/bcftools/files/patch-configure.ac head/biology/bcftools/pkg-plist Modified: head/biology/bcftools/Makefile ============================================================================== --- head/biology/bcftools/Makefile Thu Aug 2 19:28:36 2018 (r476246) +++ head/biology/bcftools/Makefile Thu Aug 2 19:30:57 2018 (r476247) @@ -2,15 +2,14 @@ # $FreeBSD$ PORTNAME= bcftools -PORTVERSION= 1.6 -PORTREVISION= 1 +PORTVERSION= 1.9 CATEGORIES= biology MAINTAINER= cartwright@asu.edu COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT -# LICENSE_FILE= ${WRKSRC}/LICENSE +LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= htslib>=1.6:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib @@ -18,13 +17,15 @@ TEST_DEPENDS= bash:shells/bash CONFLICTS_BUILD=openssl +USES= autoreconf gmake localbase \ + perl5 python:env shebangfix + USE_GITHUB= yes GH_ACCOUNT= samtools -USES= autoreconf gmake perl5 python:env shebangfix +USE_LDCONFIG= ${PREFIX}/libexec/${PORTNAME} USE_PERL5= test GNU_CONFIGURE= yes -SUB_FILES= pkg-message SHEBANG_FILES= misc/* test/test.pl OPTIONS_DEFINE= GPL @@ -35,18 +36,30 @@ GPL_LIB_DEPENDS= libgsl.so:math/gsl .include <bsd.port.options.mk> -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib - .if ${PORT_OPTIONS:MGPL} MAKE_ENV+= USE_GPL=1 -LICENSE= GPLv3 +LICENSE+= GPLv3 +LICENSE_COMB= multi .endif TEST_TARGET= test post-patch: - @${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1) @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac + +post-install: + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \ + ${STAGEDIR}${PREFIX}/bin/color-chrs + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\ + ${STAGEDIR}${PREFIX}/bin/guess-ploidy + ${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \ + ${STAGEDIR}${PREFIX}/bin/plot-roh + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \ + ${STAGEDIR}${PREFIX}/bin/run-roh + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \ + ${STAGEDIR}${PREFIX}/bin/vcfutils + ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \ + ${STAGEDIR}${PREFIX}/bin/ + ${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/ .include <bsd.port.mk> Modified: head/biology/bcftools/distinfo ============================================================================== --- head/biology/bcftools/distinfo Thu Aug 2 19:28:36 2018 (r476246) +++ head/biology/bcftools/distinfo Thu Aug 2 19:30:57 2018 (r476247) @@ -1,3 +1,3 @@ -TIMESTAMP = 1508307708 -SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025 -SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330 +TIMESTAMP = 1532903716 +SHA256 (samtools-bcftools-1.9_GH0.tar.gz) = 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e +SIZE (samtools-bcftools-1.9_GH0.tar.gz) = 2394968 Modified: head/biology/bcftools/files/patch-Makefile ============================================================================== --- head/biology/bcftools/files/patch-Makefile Thu Aug 2 19:28:36 2018 (r476246) +++ head/biology/bcftools/files/patch-Makefile Thu Aug 2 19:30:57 2018 (r476247) @@ -1,4 +1,4 @@ ---- Makefile.orig 2017-09-28 11:22:48 UTC +--- Makefile.orig 2018-07-18 08:34:29 UTC +++ Makefile @@ -22,10 +22,10 @@ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER @@ -68,10 +68,10 @@ endif bcftools: $(OBJS) $(HTSLIB) -@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html +@@ -278,7 +277,7 @@ docs: doc/bcftools.1 doc/bcftools.html # Since there is no make dependency, bcftools.1 can be out-of-date and # make docs can be run to update if asciidoc is available - install: $(PROG) $(PLUGINS) + install: $(PROGRAMS) $(PLUGINS) - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) Modified: head/biology/bcftools/files/patch-configure.ac ============================================================================== --- head/biology/bcftools/files/patch-configure.ac Thu Aug 2 19:28:36 2018 (r476246) +++ head/biology/bcftools/files/patch-configure.ac Thu Aug 2 19:30:57 2018 (r476247) @@ -1,10 +1,10 @@ ---- configure.ac.orig 2017-09-28 11:22:48 UTC +--- configure.ac.orig 2018-07-18 08:34:29 UTC +++ configure.ac @@ -23,7 +23,7 @@ # DEALINGS IN THE SOFTWARE. dnl Process this file with autoconf to produce a configure script --AC_INIT([BCFtools], m4_esyscmd_s([make print-version]), +-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]), +AC_INIT([BCFtools], [@PORTVERSION@], [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER Modified: head/biology/bcftools/pkg-plist ============================================================================== --- head/biology/bcftools/pkg-plist Thu Aug 2 19:28:36 2018 (r476246) +++ head/biology/bcftools/pkg-plist Thu Aug 2 19:30:57 2018 (r476247) @@ -1,10 +1,10 @@ bin/bcftools -bin/samtools_misc/color-chrs.pl -bin/samtools_misc/guess-ploidy.py -bin/samtools_misc/plot-roh.py -bin/samtools_misc/plot-vcfstats -bin/samtools_misc/run-roh.pl -bin/samtools_misc/vcfutils.pl +bin/color-chrs +bin/guess-ploidy +bin/plot-roh +bin/plot-vcfstats +bin/run-roh +bin/vcfutils libexec/bcftools/GTisec.so libexec/bcftools/GTsubset.so libexec/bcftools/ad-bias.so @@ -12,6 +12,7 @@ libexec/bcftools/af-dist.so libexec/bcftools/check-ploidy.so libexec/bcftools/check-sparsity.so libexec/bcftools/color-chrs.so +libexec/bcftools/contrast.so libexec/bcftools/counts.so libexec/bcftools/dosage.so libexec/bcftools/fill-AN-AC.so @@ -27,6 +28,9 @@ libexec/bcftools/mendelian.so libexec/bcftools/missing2ref.so libexec/bcftools/prune.so libexec/bcftools/setGT.so +libexec/bcftools/smpl-stats.so +libexec/bcftools/split.so libexec/bcftools/tag2tag.so +libexec/bcftools/trio-stats.so libexec/bcftools/trio-switch-rate.so man/man1/bcftools.1.gz
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