5 files changed, 78 insertions, 42 deletions

diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile
index 34fa252f4426..4f0187c96867 100644
--- a/biology/embassy/Makefile
+++ b/biology/embassy/Makefile
@@ -1,3 +1,4 @@
+# ex:ts=8
 # New ports collection makefile for:	embassy
 # Date created:		1.November.2004
 # Whom:	      		Fernan Aguero <fernan@iib.unsamn.edu.ar>
@@ -6,7 +7,7 @@
 #
 
 PORTNAME=	embassy
-PORTVERSION=	2.9.0
+PORTVERSION=	2.10.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
@@ -16,8 +17,7 @@ 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:${PORTSDIR}/biology/emboss:install
+LIB_DEPENDS=	nucleus.1:${PORTSDIR}/biology/emboss
 
 USE_SUBMAKE=	yes
 USE_GMAKE=	yes
@@ -30,7 +30,7 @@ OPTIONS=	DOMAINATRIX	"Protein structure and domain apps" on \
 		ESIM4		"Align cDNA/EST to genome" on \
 		HMMER		"HMM alignment and searches" on \
 		MEME		"Motif detection" on \
-		MSE		"Sequence editor" on \
+		MSE		"A multiple sequence screen editor" on \
 		PHYLIP		"Phylogeny inference" on \
 		TOPO		"Transmembrane display" on
 
@@ -74,6 +74,16 @@ do-extract:
 	  fi
 .endfor
 
+.if !defined(WITHOUT_DOMAINATRIX)
+pre-configure::
+	@${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/domainatrix-patch-Makefile.in
+.endif
+
+.if !defined(WITHOUT_EMNU)
+pre-configure::
+	@${PATCH} ${PATCH_ARGS} < ${PATCHDIR}/emnu-patch-Makefile.in
+.endif
+
 do-configure:
 .for app in ${APPLIST}
 	@ cd ${${app}_WRKSRC} && \
diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo
index b84869ad3c93..c82f7d7f686f 100644
--- a/biology/embassy/distinfo
+++ b/biology/embassy/distinfo
@@ -1,16 +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
+MD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 9deff6f5bf526408f0f02c002488ad59
+SIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 471604
+MD5 (embassy/EMNU-1.05.tar.gz) = df29ae1e8201081f4413862d7f10edb5
+SIZE (embassy/EMNU-1.05.tar.gz) = 339355
+MD5 (embassy/ESIM4-1.0.0.tar.gz) = 3b8137b3b8ff0e84bc6e1243c7343578
+SIZE (embassy/ESIM4-1.0.0.tar.gz) = 378342
+MD5 (embassy/HMMER-2.1.1.tar.gz) = 56816b26a43c8542f7d12f9069e77843
+SIZE (embassy/HMMER-2.1.1.tar.gz) = 562855
+MD5 (embassy/MEME-2.3.1.tar.gz) = a9fb38886665f3f654da1244c2e1476f
+SIZE (embassy/MEME-2.3.1.tar.gz) = 421914
+MD5 (embassy/MSE-1.0.0.tar.gz) = b666681aceb9f07f968585f2edc4a039
+SIZE (embassy/MSE-1.0.0.tar.gz) = 411772
+MD5 (embassy/PHYLIP-3.57c.tar.gz) = 83201895898feb15dbbae6affabd3609
+SIZE (embassy/PHYLIP-3.57c.tar.gz) = 858348
+MD5 (embassy/TOPO-1.0.0.tar.gz) = 0a8fcc84fdba071b20f3046de9fdb487
+SIZE (embassy/TOPO-1.0.0.tar.gz) = 345938
diff --git a/biology/embassy/files/domainatrix-patch-Makefile.in b/biology/embassy/files/domainatrix-patch-Makefile.in
new file mode 100644
index 000000000000..d544a23f136b
--- /dev/null
+++ b/biology/embassy/files/domainatrix-patch-Makefile.in
@@ -0,0 +1,11 @@
+--- EMBASSY/DOMAINATRIX-1.0.0/src/Makefile.in.orig	Sat May 28 12:21:57 2005
++++ EMBASSY/DOMAINATRIX-1.0.0/src/Makefile.in	Sat May 28 12:22:14 2005
+@@ -315,7 +315,7 @@
+ @LOCALLINK_TRUE@	../../../plplot/libplplot.la \
+ @LOCALLINK_TRUE@	$(am__DEPENDENCIES_1)
+ DEFAULT_INCLUDES = -I. -I$(srcdir)
+-depcomp = $(SHELL) $(top_srcdir)/../../depcomp
++depcomp = $(SHELL) $(top_srcdir)/depcomp
+ am__depfiles_maybe = depfiles
+ COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+ 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
diff --git a/biology/embassy/files/emnu-patch-Makefile.in b/biology/embassy/files/emnu-patch-Makefile.in
new file mode 100644
index 000000000000..31688dfd589b
--- /dev/null
+++ b/biology/embassy/files/emnu-patch-Makefile.in
@@ -0,0 +1,11 @@
+--- EMBASSY/EMNU-1.05/source/Makefile.in.orig	Sat May 28 12:57:17 2005
++++ EMBASSY/EMNU-1.05/source/Makefile.in	Sat May 28 13:03:33 2005
+@@ -63,7 +63,7 @@
+ @LOCALLINK_TRUE@	../../../plplot/libplplot.la \
+ @LOCALLINK_TRUE@	$(am__DEPENDENCIES_1)
+ DEFAULT_INCLUDES = -I. -I$(srcdir)
+-depcomp = $(SHELL) $(top_srcdir)/../../depcomp
++depcomp = $(SHELL) $(top_srcdir)/depcomp
+ am__depfiles_maybe = depfiles
+ COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+ 	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist
index 9f368de07280..22c88962c326 100644
--- a/biology/embassy/pkg-plist
+++ b/biology/embassy/pkg-plist
@@ -1,29 +1,32 @@
+%%PLIST_DOMAINATRIX%%bin/allversusall
+%%PLIST_DOMAINATRIX%%bin/cathparse
 %%PLIST_DOMAINATRIX%%bin/contacts
+%%PLIST_DOMAINATRIX%%bin/domainalign
 %%PLIST_DOMAINATRIX%%bin/domainer
-%%PLIST_DOMAINATRIX%%bin/fraggle
+%%PLIST_DOMAINATRIX%%bin/domainnr
+%%PLIST_DOMAINATRIX%%bin/domainrep
+%%PLIST_DOMAINATRIX%%bin/domainreso
+%%PLIST_DOMAINATRIX%%bin/domainseqs
+%%PLIST_DOMAINATRIX%%bin/domainsse
 %%PLIST_DOMAINATRIX%%bin/hetparse
-%%PLIST_DOMAINATRIX%%bin/hmmgen
 %%PLIST_DOMAINATRIX%%bin/interface
-%%PLIST_DOMAINATRIX%%bin/libscan
+%%PLIST_DOMAINATRIX%%bin/libgen
 %%PLIST_DOMAINATRIX%%bin/pdbparse
 %%PLIST_DOMAINATRIX%%bin/pdbplus
 %%PLIST_DOMAINATRIX%%bin/pdbtosp
-%%PLIST_DOMAINATRIX%%bin/profgen
+%%PLIST_DOMAINATRIX%%bin/rocon
 %%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/seqfraggle
 %%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_DOMAINATRIX%%bin/sites
+%%PLIST_DOMAINATRIX%%bin/ssematch
 %%PLIST_EMNU%%bin/emnu
 %%PLIST_ESIM4%%bin/esim4
 %%PLIST_MEME%%bin/meme
@@ -76,32 +79,35 @@
 %%PLIST_MSE%%lib/libckit.la
 %%PLIST_MSE%%lib/libckit.a
 %%PLIST_MSE%%share/EMBOSS/acd/mse.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/allversusall.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd
 %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/contacts.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainalign.acd
 %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainer.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/fraggle.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainrep.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.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/libgen.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/rocon.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/seqfraggle.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_DOMAINATRIX%%share/EMBOSS/acd/sites.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
 %%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
 %%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
 %%PLIST_MEME%%share/EMBOSS/acd/meme.acd
@@ -140,5 +146,3 @@
 %%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