Attachment 155058 Details for Bug 199066 – Unified diff

Unified diff

hmmer-diff.txt (text/plain), 1.87 KB, created by Jason W. Bacon on 2015-03-31 13:58:05 UTC

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Creator: Jason W. Bacon

Created: 2015-03-31 13:58:05 UTC

Size: 1.87 KB

patch

obsolete

>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/hmmer/Makefile /usr/wip/biology/hmmer/Makefile
>--- /usr/ports/biology/hmmer/Makefile	2014-07-15 09:54:54.000000000 -0500
>+++ /usr/wip/biology/hmmer/Makefile	2015-03-31 08:50:02.000000000 -0500
>@@ -7,33 +7,38 @@
> MASTER_SITES=	ftp://selab.janelia.org/pub/software/hmmer3/3.0/ \
> 		http://selab.janelia.org/software/hmmer3/3.0/
> 
>-MAINTAINER=	ports@FreeBSD.org
>+MAINTAINER=	jwbacon@tds.net
> COMMENT=	Profile hidden Markov models for biological sequence analysis
> 
>+LICENSE=	GPLv3
>+
> GNU_CONFIGURE=	yes
> USES=		perl5
>-CONFIGURE_ARGS+=--enable-threads --enable-lfs
>+CONFIGURE_ARGS+=--enable-threads
> 
> DOCFILES=	COPYRIGHT INSTALL LICENSE Userguide.pdf
> EXAMPLES=	7LESS_DROME Pkinase.sto fn3.sto globins4.sto minifam.h3f minifam.h3p \
> 		HBB_HUMAN fn3.hmm globins4.hmm globins45.fa minifam.h3i \
> 		Pkinase.hmm fn3.out globins4.out minifam minifam.h3m
> 
>-OPTIONS_DEFINE=	PVM DOCS EXAMPLES
>-PVM_DESC=	PVM support
>+OPTIONS_DEFINE=	DOCS EXAMPLES
>+
>+.include <bsd.port.options.mk>
> 
>-PVM_CONFIGURE_ENV=	PVM_ROOT="${LOCALBASE}/lib/pvm" PVM_ARCH="FREEBSD"
>-PVM_CONFIGURE_WITH=	pvm
>-PVM_BUILD_DEPENDS=	pvm:${PORTSDIR}/net/pvm
>+# HMMER is useless without SSE and any PC in use today should support it
>+# Should probably also do enable-vmx on Power processors to enable
>+# Altivec/VMX, but I don't have a machine to test this.
>+.if ${ARCH} == "amd64" || ${ARCH} == "ia64" || ${ARCH} == "i386"
>+CONFIGURE_ARGS+=--enable-sse
>+.endif
> 
> post-install:
>+	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*
> 	(cd ${WRKSRC}/documentation/man; for i in *.man; do \
> 		${INSTALL_MAN} $$i ${STAGEDIR}${PREFIX}/man/man1/`echo $$i|${SED} 's/.man/.1/'`; \
> 	done)
>-
> 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
> 	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}
>-
> 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
> 	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR}
>

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