3 files changed, 46 insertions, 32 deletions

diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index ecbd3fc18926..18c873e337ee 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -2,41 +2,51 @@
 # $FreeBSD$
 
 PORTNAME=	hmmer
-PORTVERSION=	2.3.2
+PORTVERSION=	3.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://selab.janelia.org/pub/software/hmmer/CURRENT/
+MASTER_SITES=	ftp://selab.janelia.org/pub/software/hmmer3/3.0/ \
+		http://selab.janelia.org/software/hmmer3/3.0/
 
-MAINTAINER=	wen@FreeBSD.org
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Profile hidden Markov models for biological sequence analysis
 
 GNU_CONFIGURE=	yes
 USE_PERL5=	yes
 CONFIGURE_ARGS+=--enable-threads --enable-lfs
 
-DOCFILES=	00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf
-EXAMPLES=	7LES_DROME amino.null globins50.msf nucleic.pri rrm.sto \
-		Artemia.fa amino.pri globins630.fa pkinase.sto RU1A_HUMAN \
-		fn3.sto nucleic.null rrm.hmm
-MAN1=		hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 \
-		hmmer.1 hmmfetch.1 hmmindex.1 hmmpfam.1 hmmsearch.1
+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
+#MAN1=		hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 \
+#		hmmer.1 hmmfetch.1 hmmindex.1 hmmpfam.1 hmmsearch.1
 
-.if defined(WITH_PVM)
+OPTIONS_DEFINE=	PVM
+PVM_DESC=	PVM support
+
+.include <bsd.port.options.mk>
+
+.if ${PORT_OPTIONS:MPVM}
 CONFIGURE_ENV+=		PVM_ROOT="${LOCALBASE}/lib/pvm" PVM_ARCH="FREEBSD"
 CONFIGURE_ARGS+=	--with-pvm
 BUILD_DEPENDS+=		pvm:${PORTSDIR}/net/pvm
 .endif
 
 post-install:
-.if !defined(NOPORTDOCS)
+.if ${PORT_OPTIONS:MDOCS}
 	@ ${MKDIR} ${DOCSDIR}
 .for docfile in ${DOCFILES}
 	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
 .endfor
 .endif
+
+.if ${PORT_OPTIONS:MEXAMPLES}
 	@ ${MKDIR} ${EXAMPLESDIR}
 .for example in ${EXAMPLES}
 	@ ${INSTALL_DATA} ${WRKSRC}/tutorial/${example} ${EXAMPLESDIR}
 .endfor
+.endif
+
 .if !defined(BATCH)
 	@ ${CAT} ${PKGMESSAGE}
 .endif
diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
index 8b88529fa328..13d961a4bbee 100644
--- a/biology/hmmer/distinfo
+++ b/biology/hmmer/distinfo
@@ -1,2 +1,2 @@
-SHA256 (hmmer-2.3.2.tar.gz) = d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4
-SIZE (hmmer-2.3.2.tar.gz) = 1024933
+SHA256 (hmmer-3.0.tar.gz) = 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83
+SIZE (hmmer-3.0.tar.gz) = 3952015
diff --git a/biology/hmmer/pkg-plist b/biology/hmmer/pkg-plist
index 27a07b38ee15..69fc094f12b5 100644
--- a/biology/hmmer/pkg-plist
+++ b/biology/hmmer/pkg-plist
@@ -1,30 +1,34 @@
 bin/hmmalign
 bin/hmmbuild
-bin/hmmcalibrate
 bin/hmmconvert
 bin/hmmemit
 bin/hmmfetch
-bin/hmmindex
-bin/hmmpfam
+bin/hmmpress
+bin/hmmscan
 bin/hmmsearch
-%%PORTDOCS%%%%DOCSDIR%%/00README
+bin/hmmsim
+bin/hmmstat
+bin/jackhmmer
+bin/phmmer
 %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
 %%PORTDOCS%%%%DOCSDIR%%/INSTALL
 %%PORTDOCS%%%%DOCSDIR%%/LICENSE
-%%PORTDOCS%%%%DOCSDIR%%/NOTES
 %%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
-%%EXAMPLESDIR%%/7LES_DROME
-%%EXAMPLESDIR%%/amino.null
-%%EXAMPLESDIR%%/globins50.msf
-%%EXAMPLESDIR%%/nucleic.pri
-%%EXAMPLESDIR%%/rrm.sto
-%%EXAMPLESDIR%%/Artemia.fa
-%%EXAMPLESDIR%%/amino.pri
-%%EXAMPLESDIR%%/globins630.fa
-%%EXAMPLESDIR%%/pkinase.sto
-%%EXAMPLESDIR%%/RU1A_HUMAN
-%%EXAMPLESDIR%%/fn3.sto
-%%EXAMPLESDIR%%/nucleic.null
-%%EXAMPLESDIR%%/rrm.hmm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%EXAMPLESDIR%%
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%