diff --git a/biology/Makefile b/biology/Makefile index fee70f22165f..1e9c12638370 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -18,6 +18,7 @@ SUBDIR += deft SUBDIR += distribfold SUBDIR += dna-qc + SUBDIR += embassy SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile new file mode 100644 index 000000000000..9580b205cfcc --- /dev/null +++ b/biology/embassy/Makefile @@ -0,0 +1,96 @@ +# New ports collection makefile for: embassy +# Date created: 1.November.2004 +# Whom: Fernan Aguero +# +# $FreeBSD$ +# + +PORTNAME= embassy +PORTVERSION= 2.9.0 +CATEGORIES= biology +MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ + ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ + ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ +DIST_SUBDIR= ${PORTNAME} + +MAINTAINER= fernan@iib.unsam.edu.ar +COMMENT= A collection of contributed EMBOSS applications + +BUILD_DEPENDS= ${LOCALBASE}/include/emboss.h:${PORTSDIR}/biology/emboss +LIB_DEPENDS= nucleus.1:${PORTSDIR}/biology/emboss:install + +USE_SUBMAKE= yes +USE_GMAKE= yes +GNU_CONFIGURE= yes +USE_XLIB= yes +USE_MOTIF= yes + +OPTIONS= DOMAINATRIX "Protein structure and domain apps" on \ + EMNU "EMBOSS simple menu" on \ + ESIM4 "Align cDNA/EST to genome" on \ + HMMER "HMM alignment and searches" on \ + MEME "Motif detection" on \ + MSE "Sequence editor" on \ + PHYLIP "Phylogeny inference" on \ + TOPO "Transmembrane display" on + +CONFIGURE_ENV+= CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \ + LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib" + +EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY +DOMAINATRIX_VERSION= 1.0.0 +EMNU_VERSION= 1.05 +ESIM4_VERSION= 1.0.0 +HMMER_VERSION= 2.1.1 +MEME_VERSION= 2.3.1 +MSE_VERSION= 1.0.0 +TOPO_VERSION= 1.0.0 +PHYLIP_VERSION= 3.57c +EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO + +.include + +.for app in ${EMBASSY_APPS} +.if defined(WITH_${app}) +APPLIST+= ${app} +${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION} +${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX} +DISTFILES+= ${${app}_DISTFILE} +PLIST_${app}= "" +.else +PLIST_${app}= "@comment " +.endif +PLIST_SUB+= PLIST_${app}=${PLIST_${app}} +.endfor + +do-extract: +.for app in ${APPLIST} + @ ${MKDIR} ${EMBASSY_WRKDIR} + @ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \ + ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS} + @ if [ `id -u` = 0 ]; then \ + ${CHMOD} -R ug-s ${${app}_WRKSRC}; \ + ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \ + fi +.endfor + +do-configure: +.for app in ${APPLIST} + @ cd ${${app}_WRKSRC} && \ + ${SETENV} ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} +.endfor + +do-build: +.for app in ${APPLIST} + @ cd ${${app}_WRKSRC} && \ + ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} +.endfor + +do-install: +.for app in ${APPLIST} + @ cd ${${app}_WRKSRC} && \ + ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ + ${MAKE_ARGS} ${INSTALL_TARGET} +.endfor + +.include diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo new file mode 100644 index 000000000000..b84869ad3c93 --- /dev/null +++ b/biology/embassy/distinfo @@ -0,0 +1,16 @@ +MD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 78e1145851073a277e568ee3a691d999 +SIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 551090 +MD5 (embassy/EMNU-1.05.tar.gz) = b091db115506ef89157b1cfb92a964b3 +SIZE (embassy/EMNU-1.05.tar.gz) = 341879 +MD5 (embassy/ESIM4-1.0.0.tar.gz) = 3fa1de555365d79bdc38490e09683632 +SIZE (embassy/ESIM4-1.0.0.tar.gz) = 377821 +MD5 (embassy/HMMER-2.1.1.tar.gz) = e7762beca88f2748cb7449e7f89ca068 +SIZE (embassy/HMMER-2.1.1.tar.gz) = 555504 +MD5 (embassy/MEME-2.3.1.tar.gz) = 014237836443382b767efb4b315c2b6d +SIZE (embassy/MEME-2.3.1.tar.gz) = 417514 +MD5 (embassy/MSE-1.0.0.tar.gz) = f55522c9f474319f56227e6a63c91dad +SIZE (embassy/MSE-1.0.0.tar.gz) = 407726 +MD5 (embassy/PHYLIP-3.57c.tar.gz) = bd242c3382a82d1a842e0a82778a40c2 +SIZE (embassy/PHYLIP-3.57c.tar.gz) = 856814 +MD5 (embassy/TOPO-1.0.0.tar.gz) = 18409cc3ce6a402690b14a73535ebe07 +SIZE (embassy/TOPO-1.0.0.tar.gz) = 345281 diff --git a/biology/embassy/pkg-descr b/biology/embassy/pkg-descr new file mode 100644 index 000000000000..8a04b6c0ec88 --- /dev/null +++ b/biology/embassy/pkg-descr @@ -0,0 +1,14 @@ +EMBASSY is a collection of contributed EMBOSS software. From the web +pages: + + "EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL). + Programs which have been included from third parties who have their own + licencing terms are kept apart under the EMBASSY grouping. + + This allows the EMBOSS libraries to link to other software, and only + requires that software to have an LGPL-compatible licence. Phylip, for + example, fits this model. + + But, to the user they do look exactly like EMBOSS aplications." + +WWW: http://emboss.sourceforge.net/apps/#Embassy diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist new file mode 100644 index 000000000000..9f368de07280 --- /dev/null +++ b/biology/embassy/pkg-plist @@ -0,0 +1,144 @@ +%%PLIST_DOMAINATRIX%%bin/contacts +%%PLIST_DOMAINATRIX%%bin/domainer +%%PLIST_DOMAINATRIX%%bin/fraggle +%%PLIST_DOMAINATRIX%%bin/hetparse +%%PLIST_DOMAINATRIX%%bin/hmmgen +%%PLIST_DOMAINATRIX%%bin/interface +%%PLIST_DOMAINATRIX%%bin/libscan +%%PLIST_DOMAINATRIX%%bin/pdbparse +%%PLIST_DOMAINATRIX%%bin/pdbplus +%%PLIST_DOMAINATRIX%%bin/pdbtosp +%%PLIST_DOMAINATRIX%%bin/profgen +%%PLIST_DOMAINATRIX%%bin/rocplot +%%PLIST_DOMAINATRIX%%bin/scopalign +%%PLIST_DOMAINATRIX%%bin/scopnr +%%PLIST_DOMAINATRIX%%bin/scopparse +%%PLIST_DOMAINATRIX%%bin/scoprep +%%PLIST_DOMAINATRIX%%bin/scopreso +%%PLIST_DOMAINATRIX%%bin/scopseqs +%%PLIST_DOMAINATRIX%%bin/seqalign +%%PLIST_DOMAINATRIX%%bin/seqnr +%%PLIST_DOMAINATRIX%%bin/seqsearch +%%PLIST_DOMAINATRIX%%bin/seqsort +%%PLIST_DOMAINATRIX%%bin/seqwords +%%PLIST_DOMAINATRIX%%bin/siggen +%%PLIST_DOMAINATRIX%%bin/sigplot +%%PLIST_DOMAINATRIX%%bin/sigscan +%%PLIST_EMNU%%bin/emnu +%%PLIST_ESIM4%%bin/esim4 +%%PLIST_MEME%%bin/meme +%%PLIST_HMMER%%bin/ehmmcalibrate +%%PLIST_HMMER%%bin/ehmmconvert +%%PLIST_HMMER%%bin/ehmmemit +%%PLIST_HMMER%%bin/ehmmfetch +%%PLIST_HMMER%%bin/ehmmindex +%%PLIST_HMMER%%bin/ehmmbuild +%%PLIST_HMMER%%bin/ehmmalign +%%PLIST_HMMER%%bin/ehmmpfam +%%PLIST_HMMER%%bin/ehmmsearch +%%PLIST_HMMER%%bin/ealistat +%%PLIST_MSE%%bin/mse +%%PLIST_PHYLIP%%bin/eclique +%%PLIST_PHYLIP%%bin/econsense +%%PLIST_PHYLIP%%bin/econtml +%%PLIST_PHYLIP%%bin/econtrast +%%PLIST_PHYLIP%%bin/ednacomp +%%PLIST_PHYLIP%%bin/ednadist +%%PLIST_PHYLIP%%bin/ednainvar +%%PLIST_PHYLIP%%bin/ednaml +%%PLIST_PHYLIP%%bin/ednamlk +%%PLIST_PHYLIP%%bin/ednapars +%%PLIST_PHYLIP%%bin/ednapenny +%%PLIST_PHYLIP%%bin/edollop +%%PLIST_PHYLIP%%bin/edolpenny +%%PLIST_PHYLIP%%bin/efactor +%%PLIST_PHYLIP%%bin/efitch +%%PLIST_PHYLIP%%bin/egendist +%%PLIST_PHYLIP%%bin/ekitsch +%%PLIST_PHYLIP%%bin/emix +%%PLIST_PHYLIP%%bin/epenny +%%PLIST_PHYLIP%%bin/eprotdist +%%PLIST_PHYLIP%%bin/eprotpars +%%PLIST_PHYLIP%%bin/erestml +%%PLIST_PHYLIP%%bin/eseqboot +%%PLIST_PHYLIP%%bin/eneighbor +%%PLIST_TOPO%%bin/topo +%%PLIST_MEME%%lib/libmeme.so.2 +%%PLIST_MEME%%lib/libmeme.so +%%PLIST_MEME%%lib/libmeme.la +%%PLIST_MEME%%lib/libmeme.a +%%PLIST_HMMER%%lib/libhmmer.so.2 +%%PLIST_HMMER%%lib/libhmmer.so +%%PLIST_HMMER%%lib/libhmmer.la +%%PLIST_HMMER%%lib/libhmmer.a +%%PLIST_MSE%%lib/libckit.so.1 +%%PLIST_MSE%%lib/libckit.so +%%PLIST_MSE%%lib/libckit.la +%%PLIST_MSE%%lib/libckit.a +%%PLIST_MSE%%share/EMBOSS/acd/mse.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/contacts.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainer.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/fraggle.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hetparse.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hmmgen.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/interface.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/libscan.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbparse.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbplus.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbtosp.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/profgen.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocplot.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopalign.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopnr.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scoprep.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopreso.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopseqs.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqalign.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqnr.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsearch.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsort.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqwords.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/siggen.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigplot.acd +%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigscan.acd +%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd +%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd +%%PLIST_MEME%%share/EMBOSS/acd/meme.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd +%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd +%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd +@dirrm share/EMBOSS/acd +@dirrm share/EMBOSS