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biology/mummer: Update 3.23 -> 4.0.0beta2-2

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Port changes:
* Moved to github
* It now installs itself
* It uses yaggo during build
This commit is contained in:
Yuri Victorovich
2018-12-11 07:43:45 +00:00
parent 5054438501
commit da87b8a1d5
3 changed files with 61 additions and 47 deletions
Download Patch File Download Diff File Expand all files Collapse all files
biology/mummer/Makefile
+13 -31
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@@ -2,46 +2,28 @@
# $FreeBSD$
PORTNAME= mummer
PORTVERSION= 3.23
PORTREVISION= 2
DISTVERSIONPREFIX= v
DISTVERSION= 4.0.0beta2-2
DISTVERSIONSUFFIX= -g277dac5
CATEGORIES= biology
MASTER_SITES= SF
DISTNAME= MUMmer${PORTVERSION}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Modular system for rapid whole genome alignment
LICENSE= ART10
LICENSE_FILE= ${WRKSRC}/LICENSE
LICENSE_FILE= ${WRKSRC}/LICENSE.md
USES= gmake perl5 shebangfix
BUILD_DEPENDS= yaggo:devel/yaggo
SHEBANG_FILES= scripts/*.csh scripts/*.pl
SHEBANG_LANG= csh
USES= autoreconf gmake libtool perl5 shebangfix
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --disable-static
USE_GITHUB= yes
GH_ACCOUNT= ${PORTNAME}4
USE_LDCONFIG= yes
SHEBANG_FILES= scripts/*.pl
perl_OLD_CMD= __PERL_PATH
csh_OLD_CMD= __CSH_PATH
csh_CMD= /bin/csh
_SHEBANG_REINPLACE_ARGS+= -e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g"
PROGRAMS= annotate combineMUMs delta-filter gaps \
mgaps mummer repeat-match show-aligns \
show-coords show-diff show-snps show-tiling
SCRIPTS= dnadiff.pl exact-tandems.csh mapview.pl mummerplot.pl nucmer.pl \
nucmer2xfig.pl promer.pl run-mummer1.csh run-mummer3.csh
LIBEXEC= Foundation.pm tandem-repeat.awk
DOCUMENTS= COPYRIGHT INSTALL LICENSE README
OPTIONS_DEFINE= DOCS
do-install:
${INSTALL_PROGRAM} ${PROGRAMS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
.for file in ${SCRIPTS}
${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${STAGEDIR}${PREFIX}/bin/${file:R}
.endfor
@${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/* ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
${INSTALL_DATA} ${LIBEXEC:S|^|${WRKSRC}/scripts/|} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
@${MKDIR} ${STAGEDIR}${DOCSDIR}
${INSTALL_DATA} ${DOCUMENTS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}
.include <bsd.port.mk>
biology/mummer/distinfo
+3 -3
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@@ -1,3 +1,3 @@
TIMESTAMP = 1509357521
SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f
SIZE (MUMmer3.23.tar.gz) = 3160143
TIMESTAMP = 1544513160
SHA256 (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 4b77fb57f0e7994ed0cb9886de23ce620b89cb16734df82ba492dbc750e387f1
SIZE (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 18369428
biology/mummer/pkg-plist
+45 -13
View File
@@ -3,29 +3,61 @@ bin/combineMUMs
bin/delta-filter
bin/dnadiff
bin/exact-tandems
bin/gaps
bin/mapview
bin/mgaps
bin/mummer
bin/mummerplot
bin/nucmer
bin/nucmer2xfig
bin/promer
bin/repeat-match
bin/run-mummer1
bin/run-mummer3
bin/show-aligns
bin/show-coords
bin/show-diff
bin/show-snps
bin/show-tiling
libexec/mummer/Foundation.pm
include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort.hpp
include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort_imp.hpp
include/mummer-4.0.0beta2/include/compactsufsort/const_iterator_traits.hpp
include/mummer-4.0.0beta2/include/compactsufsort/divsufsort_private.h
include/mummer-4.0.0beta2/include/compactsufsort/said_traits.hpp
include/mummer-4.0.0beta2/include/compactsufsort/sssort_imp.hpp
include/mummer-4.0.0beta2/include/compactsufsort/trsort_imp.hpp
include/mummer-4.0.0beta2/include/jellyfish/circular_buffer.hpp
include/mummer-4.0.0beta2/include/jellyfish/cooperative_pool2.hpp
include/mummer-4.0.0beta2/include/jellyfish/cpp_array.hpp
include/mummer-4.0.0beta2/include/jellyfish/divisor.hpp
include/mummer-4.0.0beta2/include/jellyfish/stream_manager.hpp
include/mummer-4.0.0beta2/include/jellyfish/whole_sequence_parser.hpp
include/mummer-4.0.0beta2/include/mt_skip_list/common.hpp
include/mummer-4.0.0beta2/include/mt_skip_list/set.hpp
include/mummer-4.0.0beta2/include/mummer/48bit_index.hpp
include/mummer-4.0.0beta2/include/mummer/48bit_iterator.hpp
include/mummer-4.0.0beta2/include/mummer/const_iterator_traits.hpp
include/mummer-4.0.0beta2/include/mummer/delta.hh
include/mummer-4.0.0beta2/include/mummer/dset.hpp
include/mummer-4.0.0beta2/include/mummer/fasta.hpp
include/mummer-4.0.0beta2/include/mummer/mgaps.hh
include/mummer-4.0.0beta2/include/mummer/nucmer.hpp
include/mummer-4.0.0beta2/include/mummer/openmp_qsort.hpp
include/mummer-4.0.0beta2/include/mummer/postnuc.hh
include/mummer-4.0.0beta2/include/mummer/redirect_to_pager.hpp
include/mummer-4.0.0beta2/include/mummer/sparseSA.hpp
include/mummer-4.0.0beta2/include/mummer/sparseSA_imp.hpp
include/mummer-4.0.0beta2/include/mummer/sw_align.hh
include/mummer-4.0.0beta2/include/mummer/sw_alignscore.hh
include/mummer-4.0.0beta2/include/mummer/tigrinc.hh
include/mummer-4.0.0beta2/include/mummer/timer.hpp
include/mummer-4.0.0beta2/include/mummer/translate.hh
include/mummer-4.0.0beta2/include/thread_pipe.hpp
include/mummer-4.0.0beta2/include/thread_pipe/circular_buffer.hpp
include/mummer-4.0.0beta2/include/thread_pipe/cooperative_pool2.hpp
include/mummer-4.0.0beta2/include/thread_pipe/divisor.hpp
include/mummer-4.0.0beta2/include/thread_pipe/traits.hpp
lib/libumdmummer.so
lib/libumdmummer.so.0
lib/libumdmummer.so.0.0.0
lib/mummer/Foundation.pm
lib/mummer/tandem-repeat.awk
libdata/pkgconfig/mummer.pc
libexec/mummer/mgaps
libexec/mummer/postnuc
libexec/mummer/postpro
libexec/mummer/prenuc
libexec/mummer/prepro
libexec/mummer/tandem-repeat.awk
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%%%DOCSDIR%%/INSTALL
%%PORTDOCS%%%%DOCSDIR%%/LICENSE
%%PORTDOCS%%%%DOCSDIR%%/README