[new port] biology/embassy

PR:		ports/74330
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>

5 files changed, 271 insertions, 0 deletions

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 <fernan@iib.unsamn.edu.ar>
+#
+# $FreeBSD$
+#
+
+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 <bsd.port.pre.mk>
+
+.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 <bsd.port.post.mk>
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