For EMBOSS:

	This patch brings EMBOSS up to date with the current version.

	i.   The patches included in files/ are bugfixes for files in
	     EMBOSS-3.0.0 that appeared after the release. They are
   	     documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

	     This is just 'for the record' so that we remember to remove these
	     patches in the next update.

	ii.  EMBOSS is now installed by default in LOCALBASE/emboss
	     This is to avoid CONFLICTS with other ports that install files
	     with the same names. Installing EMBOSS to another PREFIX is also
	     possible.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)

5 files changed, 238 insertions, 188 deletions

diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile
index 6c572598b54e..5d3ed872749a 100644
--- a/biology/embassy/Makefile
+++ b/biology/embassy/Makefile
@@ -7,18 +7,21 @@
 #
 
 PORTNAME=	embassy
-PORTVERSION=	2.10.0
+PORTVERSION=	3.0.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
+MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
+		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}
+DIST_SUBDIR=	emboss
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of contributed EMBOSS applications
 
-LIB_DEPENDS=	nucleus.1:${PORTSDIR}/biology/emboss
+LIB_DEPENDS=	nucleus.3:${PORTSDIR}/biology/emboss
 
+PREFIX?=	${LOCALBASE}/emboss
+NO_MTREE=	yes
 USE_SUBMAKE=	yes
 USE_ICONV=	yes
 USE_GMAKE=	yes
@@ -26,12 +29,17 @@ GNU_CONFIGURE=	yes
 USE_XLIB=	yes
 USE_MOTIF=	yes
 
-OPTIONS=	DOMAINATRIX	"Protein structure and domain apps" on \
+OPTIONS=	DOMAINATRIX	"Protein domain apps" on \
+		DOMALIGN	"Protein domain apps" on \
+		DOMSEARCH	"Protein domain apps" on \
+		SIGNATURE	"Protein domain apps" on \
+		STRUCTURE	"Protein 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		"A multiple sequence screen editor" on \
+		MYEMBOSS	"Examples for developers of EMBOSS apps" on \
 		PHYLIP		"Phylogeny inference" on \
 		TOPO		"Transmembrane display" on
 
@@ -39,15 +47,21 @@ 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
+DOMAINATRIX_VERSION=	0.1.0
 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
+PHYLIP_VERSION=		3.6b
+DOMALIGN_VERSION=	0.1.0
+DOMSEARCH_VERSION=	0.1.0
+SIGNATURE_VERSION=	0.1.0
+STRUCTURE_VERSION=	0.1.0
+MYEMBOSS_VERSION=	3.0.0
+EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO \
+			DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS
 
 .include <bsd.port.pre.mk>
 
@@ -75,16 +89,6 @@ 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 62e43dd5e562..486dd95d3995 100644
--- a/biology/embassy/distinfo
+++ b/biology/embassy/distinfo
@@ -1,24 +1,39 @@
-MD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 9deff6f5bf526408f0f02c002488ad59
-SHA256 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 50abb58f3196f2f3d04af2649ace36457315c378fa73345cb635b51e913db8fc
-SIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 471604
-MD5 (embassy/EMNU-1.05.tar.gz) = df29ae1e8201081f4413862d7f10edb5
-SHA256 (embassy/EMNU-1.05.tar.gz) = 4bcdc64c9ec2d818b3ba00eef34eee39e11ef99d87cf292a214b7be51bf6bf48
-SIZE (embassy/EMNU-1.05.tar.gz) = 339355
-MD5 (embassy/ESIM4-1.0.0.tar.gz) = 3b8137b3b8ff0e84bc6e1243c7343578
-SHA256 (embassy/ESIM4-1.0.0.tar.gz) = 6e24466905c457d3f464f3a7fb24680a01326cb22acf7d090b84a51da0382d2a
-SIZE (embassy/ESIM4-1.0.0.tar.gz) = 378342
-MD5 (embassy/HMMER-2.1.1.tar.gz) = 56816b26a43c8542f7d12f9069e77843
-SHA256 (embassy/HMMER-2.1.1.tar.gz) = 63f3d4e6a509b8d1a815a9dc7e74fe7c458a9478e4885608349eeb2aa8c2df87
-SIZE (embassy/HMMER-2.1.1.tar.gz) = 562855
-MD5 (embassy/MEME-2.3.1.tar.gz) = a9fb38886665f3f654da1244c2e1476f
-SHA256 (embassy/MEME-2.3.1.tar.gz) = 778589a63705e17db1aded3704b70a3cc3de4b1e41f90ccfcd8d86b7f6dab622
-SIZE (embassy/MEME-2.3.1.tar.gz) = 421914
-MD5 (embassy/MSE-1.0.0.tar.gz) = b666681aceb9f07f968585f2edc4a039
-SHA256 (embassy/MSE-1.0.0.tar.gz) = 13fca33f78cd83e2a53c0b08a0db97da2b9dd572e01a694e8acd6a87316b3fa7
-SIZE (embassy/MSE-1.0.0.tar.gz) = 411772
-MD5 (embassy/PHYLIP-3.57c.tar.gz) = 83201895898feb15dbbae6affabd3609
-SHA256 (embassy/PHYLIP-3.57c.tar.gz) = ff5385d0b5b6c5f42a8b7c53a682ede654e0309f4ab31859f5b907563a4a7b4f
-SIZE (embassy/PHYLIP-3.57c.tar.gz) = 858348
-MD5 (embassy/TOPO-1.0.0.tar.gz) = 0a8fcc84fdba071b20f3046de9fdb487
-SHA256 (embassy/TOPO-1.0.0.tar.gz) = d1e9e6c9c37b36f4bfca485fbda68d1c045c8fa1171eea94089773ed40bc11d3
-SIZE (embassy/TOPO-1.0.0.tar.gz) = 345938
+MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 655f6ec58e0b9dfdac111fd9481359cb
+SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 6bc374c5275dead68ef09d8273bf4d73a03bc56990e795d6eddcee4de25c12a0
+SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 349882
+MD5 (emboss/EMNU-1.05.tar.gz) = b3a7fc11e46f7166ddeec11f2fe03d9b
+SHA256 (emboss/EMNU-1.05.tar.gz) = d7261d615d6547a9824d3d9e3f82ff756c0db5786e8356bc54cc5fa0c516b26f
+SIZE (emboss/EMNU-1.05.tar.gz) = 348924
+MD5 (emboss/ESIM4-1.0.0.tar.gz) = 835393b3246eb4543a694362c6f335ff
+SHA256 (emboss/ESIM4-1.0.0.tar.gz) = f8241c9e37ccc17dbd29df2d9c90063ba7caf4e64cc5c368b6878c3aa3895620
+SIZE (emboss/ESIM4-1.0.0.tar.gz) = 384396
+MD5 (emboss/HMMER-2.1.1.tar.gz) = 382594654e45a7e8d5872b4b1016a494
+SHA256 (emboss/HMMER-2.1.1.tar.gz) = 78647dfb7841e8b52b4c3de34400c68d17a877b698956ac9a5ee5e030569cca6
+SIZE (emboss/HMMER-2.1.1.tar.gz) = 561289
+MD5 (emboss/MEME-2.3.1.tar.gz) = 6f4e516e413582268a34e91fb12e21c3
+SHA256 (emboss/MEME-2.3.1.tar.gz) = bec2c8002b8b551ef9c639bcb58633499060cd8a1bfe4754db5ed201a6a0dffa
+SIZE (emboss/MEME-2.3.1.tar.gz) = 423966
+MD5 (emboss/MSE-1.0.0.tar.gz) = 3b9810e870937ec32220b5c9fe7a83cd
+SHA256 (emboss/MSE-1.0.0.tar.gz) = ddf9092721666d64c56733d9b6d04e749957848cafa8ba4ec6eee083a0ffcab3
+SIZE (emboss/MSE-1.0.0.tar.gz) = 415051
+MD5 (emboss/PHYLIP-3.6b.tar.gz) = 6f2c10438d788acf4a1dff23441b2a2c
+SHA256 (emboss/PHYLIP-3.6b.tar.gz) = 32aba94d0be011ee304e974657db11544297c008e53341cd000a1f412eb874e2
+SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1136746
+MD5 (emboss/TOPO-1.0.0.tar.gz) = 7b3355570ba36f7daf57dcbc717215ce
+SHA256 (emboss/TOPO-1.0.0.tar.gz) = ff10378b4ecad69ddb374cd47a7d3c7fa5975d6695057f05ea264940258ebaa3
+SIZE (emboss/TOPO-1.0.0.tar.gz) = 351796
+MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 4332d7de49b27f257b58a90510223eb7
+SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = de66ddfdb72ccf7291be614c9a83fd8fc47363191cb2c045b372de5cc334a594
+SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 347672
+MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = c62f9b69a9ed9580d4489a8de9ea4863
+SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = f4933b62e19ee6b23a78b70c3cf2d5a9a18eff1d7532f92e2d33b1d683877916
+SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 352793
+MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 1e30e12048609a468b7b4d4affb177cf
+SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = c6bb252beaccac5256d99301933b15da6ef90af3f20d7f92fed1f78b271785ee
+SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 400125
+MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6efc35eb2855738252e0537198f5225d
+SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 7142e207987da46cd85c81088ea475abb866da90ff57e4c3ca1c63bd8f209b64
+SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 362563
+MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 15d5bc7b0ce9dfb113777c06c4e18906
+SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = 0a19ebbe52da849fb87799edaea2281a1bf235e6045725789b9b29e58f0a0dc5
+SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 323628
diff --git a/biology/embassy/files/domainatrix-patch-Makefile.in b/biology/embassy/files/domainatrix-patch-Makefile.in
deleted file mode 100644
index d544a23f136b..000000000000
--- a/biology/embassy/files/domainatrix-patch-Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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
deleted file mode 100644
index 31688dfd589b..000000000000
--- a/biology/embassy/files/emnu-patch-Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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 22c88962c326..a1f0267522e1 100644
--- a/biology/embassy/pkg-plist
+++ b/biology/embassy/pkg-plist
@@ -1,148 +1,201 @@
-%%PLIST_DOMAINATRIX%%bin/allversusall
 %%PLIST_DOMAINATRIX%%bin/cathparse
-%%PLIST_DOMAINATRIX%%bin/contacts
-%%PLIST_DOMAINATRIX%%bin/domainalign
-%%PLIST_DOMAINATRIX%%bin/domainer
 %%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/interface
-%%PLIST_DOMAINATRIX%%bin/libgen
-%%PLIST_DOMAINATRIX%%bin/pdbparse
-%%PLIST_DOMAINATRIX%%bin/pdbplus
-%%PLIST_DOMAINATRIX%%bin/pdbtosp
-%%PLIST_DOMAINATRIX%%bin/rocon
-%%PLIST_DOMAINATRIX%%bin/rocplot
 %%PLIST_DOMAINATRIX%%bin/scopparse
-%%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/sigscan
-%%PLIST_DOMAINATRIX%%bin/sites
 %%PLIST_DOMAINATRIX%%bin/ssematch
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.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/scopparse.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
+%%PLIST_DOMALIGN%%bin/allversusall
+%%PLIST_DOMALIGN%%bin/domainalign
+%%PLIST_DOMALIGN%%bin/domainrep
+%%PLIST_DOMALIGN%%bin/seqalign
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/allversusall.acd
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainalign.acd
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainrep.acd
+%%PLIST_DOMALIGN%%share/EMBOSS/acd/seqalign.acd
+%%PLIST_DOMSEARCH%%bin/seqfraggle
+%%PLIST_DOMSEARCH%%bin/seqnr
+%%PLIST_DOMSEARCH%%bin/seqsearch
+%%PLIST_DOMSEARCH%%bin/seqsort
+%%PLIST_DOMSEARCH%%bin/seqwords
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd
 %%PLIST_EMNU%%bin/emnu
-%%PLIST_ESIM4%%bin/esim4
-%%PLIST_MEME%%bin/meme
+%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
+%%PLIST_HMMER%%bin/ealistat
+%%PLIST_HMMER%%bin/ehmmalign
+%%PLIST_HMMER%%bin/ehmmbuild
 %%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/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/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/interface.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/rocon.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocplot.acd
-%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.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/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
+%%PLIST_HMMER%%lib/libhmmer.la
+%%PLIST_HMMER%%lib/libhmmer.so
+%%PLIST_HMMER%%lib/libhmmer.so.2
+%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.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_MEME%%bin/meme
+%%PLIST_MEME%%lib/libmeme.a
+%%PLIST_MEME%%lib/libmeme.la
+%%PLIST_MEME%%lib/libmeme.so
+%%PLIST_MEME%%lib/libmeme.so.2
+%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
+%%PLIST_MSE%%bin/mse
+%%PLIST_MSE%%lib/libckit.a
+%%PLIST_MSE%%lib/libckit.la
+%%PLIST_MSE%%lib/libckit.so
+%%PLIST_MSE%%lib/libckit.so.1
+%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
+%%PLIST_MYEMBOSS%%bin/myseq
+%%PLIST_MYEMBOSS%%bin/mytest
+%%PLIST_MYEMBOSS%%share/EMBOSS/acd/myseq.acd
+%%PLIST_MYEMBOSS%%share/EMBOSS/acd/mytest.acd
+%%PLIST_PHYLIP%%bin/fclique
+%%PLIST_PHYLIP%%bin/fconsense
+%%PLIST_PHYLIP%%bin/fcontml
+%%PLIST_PHYLIP%%bin/fcontrast
+%%PLIST_PHYLIP%%bin/fdiscboot
+%%PLIST_PHYLIP%%bin/fdnacomp
+%%PLIST_PHYLIP%%bin/fdnadist
+%%PLIST_PHYLIP%%bin/fdnainvar
+%%PLIST_PHYLIP%%bin/fdnaml
+%%PLIST_PHYLIP%%bin/fdnamlk
+%%PLIST_PHYLIP%%bin/fdnamove
+%%PLIST_PHYLIP%%bin/fdnapars
+%%PLIST_PHYLIP%%bin/fdnapenny
+%%PLIST_PHYLIP%%bin/fdollop
+%%PLIST_PHYLIP%%bin/fdolmove
+%%PLIST_PHYLIP%%bin/fdolpenny
+%%PLIST_PHYLIP%%bin/fdrawgram
+%%PLIST_PHYLIP%%bin/fdrawtree
+%%PLIST_PHYLIP%%bin/ffactor
+%%PLIST_PHYLIP%%bin/ffitch
+%%PLIST_PHYLIP%%bin/ffreqboot
+%%PLIST_PHYLIP%%bin/fgendist
+%%PLIST_PHYLIP%%bin/fkitsch
+%%PLIST_PHYLIP%%bin/fmix
+%%PLIST_PHYLIP%%bin/fmove
+%%PLIST_PHYLIP%%bin/fneighbor
+%%PLIST_PHYLIP%%bin/fpars
+%%PLIST_PHYLIP%%bin/fpenny
+%%PLIST_PHYLIP%%bin/fproml
+%%PLIST_PHYLIP%%bin/fpromlk
+%%PLIST_PHYLIP%%bin/fprotdist
+%%PLIST_PHYLIP%%bin/fprotpars
+%%PLIST_PHYLIP%%bin/frestboot
+%%PLIST_PHYLIP%%bin/frestdist
+%%PLIST_PHYLIP%%bin/frestml
+%%PLIST_PHYLIP%%bin/fretree
+%%PLIST_PHYLIP%%bin/fseqboot
+%%PLIST_PHYLIP%%bin/fseqbootall
+%%PLIST_PHYLIP%%bin/ftreedist
+%%PLIST_PHYLIP%%bin/ftreedistpair
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fclique.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fconsense.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontrast.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdiscboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnacomp.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnadist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnainvar.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnaml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamlk.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamove.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdollop.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolmove.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolpenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawgram.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawtree.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ffactor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ffitch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ffreqboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fgendist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fkitsch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fmix.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fmove.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fneighbor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fpars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fpenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fproml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fpromlk.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fprotdist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fprotpars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/frestboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/frestdist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/frestml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fretree.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fseqboot.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/fseqbootall.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedistpair.acd
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font1
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font2
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font3
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font4
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font5
+%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font6
+%%PLIST_PHYLIP%%@dirrm share/PHYLIP/data/phylipnew
+%%PLIST_PHYLIP%%@dirrm share/PHYLIP/data
+%%PLIST_PHYLIP%%@dirrm share/PHYLIP
+%%PLIST_SIGNATURE%%bin/libgen
+%%PLIST_SIGNATURE%%bin/matgen3d
+%%PLIST_SIGNATURE%%bin/rocon
+%%PLIST_SIGNATURE%%bin/rocplot
+%%PLIST_SIGNATURE%%bin/siggen
+%%PLIST_SIGNATURE%%bin/siggenlig
+%%PLIST_SIGNATURE%%bin/sigscan
+%%PLIST_SIGNATURE%%bin/sigscanlig
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/libgen.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/matgen3d.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocon.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocplot.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggen.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggenlig.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscan.acd
+%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscanlig.acd
+%%PLIST_ESIM4%%bin/esim4
+%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
+%%PLIST_STRUCTURE%%bin/contacts
+%%PLIST_STRUCTURE%%bin/domainer
+%%PLIST_STRUCTURE%%bin/hetparse
+%%PLIST_STRUCTURE%%bin/interface
+%%PLIST_STRUCTURE%%bin/pdbparse
+%%PLIST_STRUCTURE%%bin/pdbplus
+%%PLIST_STRUCTURE%%bin/pdbtosp
+%%PLIST_STRUCTURE%%bin/sites
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/contacts.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/domainer.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/hetparse.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/interface.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbparse.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbplus.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbtosp.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/acd/sites.acd
+%%PLIST_TOPO%%bin/topo
 %%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
+@dirrmtry share/EMBOSS/acd
+@dirrmtry share/EMBOSS