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freebsd-ports/biology/mummer/Makefile

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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher
2007-12-14 21:54:47 +01:00
PORTNAME= mummer
biology/mummer: Update 3.23 -> 4.0.0beta2-2 Port changes: * Moved to github * It now installs itself * It uses yaggo during build
2018-12-11 08:43:45 +01:00
DISTVERSIONPREFIX= v
DISTVERSION= 4.0.0beta2-2
biology/mummer: fix build on powerpc64 elfv2 and powerpc64le Error: src/tigr/postnuc.cc:174:37: error: non-constant-expression cannot be narrowed from type 'signed char' to 'char' in initializer list [-Wc++11-narrowing] Alignments.push_back({ *Mp, CurrCp->dirB } ); Since it may also fix runtime issues on powerpc64 elfv1, bump PORTREVISION.
2020-10-26 00:03:14 +01:00
PORTREVISION= 3
biology/mummer: Update 3.23 -> 4.0.0beta2-2 Port changes: * Moved to github * It now installs itself * It uses yaggo during build
2018-12-11 08:43:45 +01:00
DISTVERSIONSUFFIX= -g277dac5
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher
2007-12-14 21:54:47 +01:00
CATEGORIES= biology
biology/mummer: Take maintainership
2018-12-11 08:23:54 +01:00
MAINTAINER= yuri@FreeBSD.org
Remove indefinite articles and trailing periods from COMMENT, plus minor COMMENT typos and surrounding whitespace fixes. Categories A-C. CR: D196 Approved by: portmgr (bapt)
2014-06-09 13:21:52 +02:00
COMMENT= Modular system for rapid whole genome alignment
Add WWW entries to port Makefiles It has been common practice to have one or more URLs at the end of the ports' pkg-descr files, one per line and prefixed with "WWW:". These URLs should point at a project website or other relevant resources. Access to these URLs required processing of the pkg-descr files, and they have often become stale over time. If more than one such URL was present in a pkg-descr file, only the first one was tarnsfered into the port INDEX, but for many ports only the last line did contain the port specific URL to further information. There have been several proposals to make a project URL available as a macro in the ports' Makefiles, over time. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner)
2022-09-07 23:06:12 +02:00
WWW= http://mummer.sourceforge.net/
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher
2007-12-14 21:54:47 +01:00
- Fix installing scripts and support binaries - Add LICENSE PR: 223098 Submitted by: mzaki@niid.go.jp
2017-10-30 03:27:23 +01:00
LICENSE= ART10
biology/mummer: Update 3.23 -> 4.0.0beta2-2 Port changes: * Moved to github * It now installs itself * It uses yaggo during build
2018-12-11 08:43:45 +01:00
LICENSE_FILE= ${WRKSRC}/LICENSE.md
- Fix installing scripts and support binaries - Add LICENSE PR: 223098 Submitted by: mzaki@niid.go.jp
2017-10-30 03:27:23 +01:00
biology/mummer: Update 3.23 -> 4.0.0beta2-2 Port changes: * Moved to github * It now installs itself * It uses yaggo during build
2018-12-11 08:43:45 +01:00
BUILD_DEPENDS= yaggo:devel/yaggo
- Fix installing scripts and support binaries - Add LICENSE PR: 223098 Submitted by: mzaki@niid.go.jp
2017-10-30 03:27:23 +01:00
biology/mummer: Add USES=compiler:c++11-lang
2018-12-11 08:48:12 +01:00
USES= autoreconf compiler:c++11-lang gmake libtool perl5 shebangfix
biology/mummer: Update 3.23 -> 4.0.0beta2-2 Port changes: * Moved to github * It now installs itself * It uses yaggo during build
2018-12-11 08:43:45 +01:00
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --disable-static
USE_GITHUB= yes
GH_ACCOUNT= ${PORTNAME}4
USE_LDCONFIG= yes
Fix CONFLICTS entries of multiple ports There have been lots of missing CONFLICTS_INSTALL entries, either because conflicting ports were added without updating existing ports, due to name changes of generated packages, due to mis-understanding the format and semantics of the conflicts entries, or just due to typoes in package names. This patch is the result of a comparison of all files contained in the official packages with each other. This comparison was based on packages built with default options and may therefore have missed further conflicts with optionally installed files. Where possible, version numbers in conflicts entries have been generalized, some times taking advantage of the fact that a port cannot conflict with itself (due to logic in bsd.port.mk that supresses the pattern match result in that case). A few ports that set the conflicts variables depending on complex conditions (e.g. port options), have been left unmodified, despite probably containing outdated package names. These changes should only affect the installation of locally built ports, not the package building with poudriere. They should give an early indication of the install conflict in cases where currently the pkg command aborts an installation when it detects that an existing file would be overwritten, Approved by: portmgr (implicit)
2022-01-10 15:20:12 +01:00
CONFLICTS_INSTALL= ??-libgd libgd
biology/mummer: Update 3.23 -> 4.0.0beta2-2 Port changes: * Moved to github * It now installs itself * It uses yaggo during build
2018-12-11 08:43:45 +01:00
SHEBANG_FILES= scripts/*.pl
- Fix installing scripts and support binaries - Add LICENSE PR: 223098 Submitted by: mzaki@niid.go.jp
2017-10-30 03:27:23 +01:00
perl_OLD_CMD= __PERL_PATH
_SHEBANG_REINPLACE_ARGS+= -e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g"
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher
2007-12-14 21:54:47 +01:00
.include <bsd.port.mk>
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