diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/hmmer/Makefile | 32 | ||||
| -rw-r--r-- | biology/hmmer/distinfo | 4 | ||||
| -rw-r--r-- | biology/hmmer/pkg-plist | 42 |
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%% |