- Update to 5.0.0

PR:		ports/122437
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)

3 files changed, 344 insertions, 81 deletions

diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile
index cacec45675aa..2eb8ff563189 100644
--- a/biology/embassy/Makefile
+++ b/biology/embassy/Makefile
@@ -7,19 +7,16 @@
 #
 
 PORTNAME=	embassy
-PORTVERSION=	3.0.0
-PORTREVISION=	2
+PORTVERSION=	5.0.0
 CATEGORIES=	biology
 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=	emboss
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of contributed EMBOSS applications
 
-LIB_DEPENDS=	nucleus.3:${PORTSDIR}/biology/emboss
+LIB_DEPENDS=	nucleus.5:${PORTSDIR}/biology/emboss
 
 PREFIX?=	${LOCALBASE}/emboss
 NO_MTREE=	yes
@@ -27,7 +24,9 @@ USE_SUBMAKE=	yes
 USE_ICONV=	yes
 USE_GMAKE=	yes
 GNU_CONFIGURE=	yes
+USE_XORG=	x11
 USE_MOTIF=	yes
+USE_LDCONFIG=	yes
 
 OPTIONS=	DOMAINATRIX	"Protein domain apps" on \
 		DOMALIGN	"Protein domain apps" on \
@@ -41,7 +40,8 @@ OPTIONS=	DOMAINATRIX	"Protein domain apps" on \
 		MSE		"A multiple sequence screen editor" on \
 		MYEMBOSS	"Examples for developers of EMBOSS apps" on \
 		PHYLIP		"Phylogeny inference" on \
-		TOPO		"Transmembrane display" on
+		TOPO		"Transmembrane display" on \
+		VIENNA		"RNA folding" on
 
 CONFIGURE_ENV+=	CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \
 		LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib"
@@ -50,8 +50,8 @@ EMBASSY_WRKDIR=		${WRKSRC}/EMBASSY
 DOMAINATRIX_VERSION=	0.1.0
 EMNU_VERSION=		1.05
 ESIM4_VERSION=		1.0.0
-HMMER_VERSION=		2.1.1
-MEME_VERSION=		2.3.1
+HMMER_VERSION=		2.3.2
+MEME_VERSION=		0.1.0
 MSE_VERSION=		1.0.0
 TOPO_VERSION=		1.0.0
 PHYLIP_VERSION=		3.6b
@@ -60,8 +60,10 @@ 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
+VIENNA_VERSION=		1.6
+EMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP \
+			TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \
+			VIENNA
 
 .include <bsd.port.pre.mk>
 
diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo
index 486dd95d3995..8ea850198702 100644
--- a/biology/embassy/distinfo
+++ b/biology/embassy/distinfo
@@ -1,39 +1,42 @@
-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
+MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 0be3c59550e1e22924ea2540b11af275
+SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = b81fde3ab329ab75482b341568ef2965d99803765438f3825688a0d2abc05ca6
+SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 420051
+MD5 (emboss/EMNU-1.05.tar.gz) = 64d8b9c2cd1a566aebb3355eb684bd35
+SHA256 (emboss/EMNU-1.05.tar.gz) = 56a55f336b0083ecfd2fd2dae0613f46e802eacb3214c16fc1966e6516795b95
+SIZE (emboss/EMNU-1.05.tar.gz) = 389665
+MD5 (emboss/ESIM4-1.0.0.tar.gz) = ee65d0da0f2d75959f370b13f2218c1c
+SHA256 (emboss/ESIM4-1.0.0.tar.gz) = eee1cc8fef40e19fab74b16f1c1cb0883a49561eb9fdc2075f428085c6722bda
+SIZE (emboss/ESIM4-1.0.0.tar.gz) = 431329
+MD5 (emboss/HMMER-2.3.2.tar.gz) = 3aa5707db81854f2674bf27aaeb1362e
+SHA256 (emboss/HMMER-2.3.2.tar.gz) = 31bbcca1f71b82170a65c4438f9cb9f1dfe3d4e066037a852060b010e3e39b5b
+SIZE (emboss/HMMER-2.3.2.tar.gz) = 565223
+MD5 (emboss/MEME-0.1.0.tar.gz) = d304f3b8a8e15af4dfa7b295655d80ec
+SHA256 (emboss/MEME-0.1.0.tar.gz) = ed4c02010af036515203661c28776b5e773e77eccad59990b7ac1410399d45ef
+SIZE (emboss/MEME-0.1.0.tar.gz) = 448413
+MD5 (emboss/MSE-1.0.0.tar.gz) = 3978a06e3651104f622a5834523c45de
+SHA256 (emboss/MSE-1.0.0.tar.gz) = e35560310ece8bb2dec7eeb88e99f39f313bf7366afc445e3b074b687e7f36b2
+SIZE (emboss/MSE-1.0.0.tar.gz) = 445013
+MD5 (emboss/PHYLIP-3.6b.tar.gz) = 760a90bea49872aba95fd7dd2b67570c
+SHA256 (emboss/PHYLIP-3.6b.tar.gz) = c2397937f4b827844192a33b31f13271a3560c81045543d912a9c28eb6ad894f
+SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1594433
+MD5 (emboss/TOPO-1.0.0.tar.gz) = d45602a1b1f22da50a775c41df5fe672
+SHA256 (emboss/TOPO-1.0.0.tar.gz) = ed1921e92d1bbd9fcc16ab36f2fcbafca9e60cc0d4b4fd1da77660ffd3e7b2f2
+SIZE (emboss/TOPO-1.0.0.tar.gz) = 379381
+MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = e5d004c1223116abaebb6657ae4a80fa
+SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = aa61cfc6da3cc478dd7f476537cdc6d966b00b90e2adedc709eb75e39e840c5c
+SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 460530
+MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = 778ab15bce09a6440fc6859b3a27157d
+SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = 23e069161ec56df5eab5fc491ca3493c056cfee42f2e05f1b5ef258498792a87
+SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 469776
+MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 26deae308cc5aac3dee5dd03df2ae9e8
+SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = 9b0529befdbe5d56b3370cfffe0a4b4cc523f350b50ddd4a61dd24776a1770e8
+SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 573992
+MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6736b4741b15d4cba488a5422fcfaee1
+SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 3ed8ea5373232cd80302ff3b8727838b4de2f6b39aa263ab9530bbbe71d730c1
+SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 530874
+MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 9c3d6ea80166f62cd6ee63dfcb7e57a4
+SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = dc21b1772c2d76ed1c717eba6f8443b86cdf2e3cbcf71e056cdb9723138e4440
+SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 354179
+MD5 (emboss/VIENNA-1.6.tar.gz) = 282ed7ac9c1741160fcb1e8d48539311
+SHA256 (emboss/VIENNA-1.6.tar.gz) = 04c4a57486e23c2cc8ef396d9012c396519b2ab1b13b2500199e6457a34cfa58
+SIZE (emboss/VIENNA-1.6.tar.gz) = 635638
diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist
index a1f0267522e1..e90801ea7428 100644
--- a/biology/embassy/pkg-plist
+++ b/biology/embassy/pkg-plist
@@ -12,6 +12,21 @@
 %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd
 %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
 %%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/index.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/cathparse.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainnr.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainreso.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainseqs.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainsse.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/scopparse.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/ssematch.html
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/cathparse.txt
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainnr.txt
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainreso.txt
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainseqs.txt
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainsse.txt
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/scopparse.txt
+%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/ssematch.txt
 %%PLIST_DOMALIGN%%bin/allversusall
 %%PLIST_DOMALIGN%%bin/domainalign
 %%PLIST_DOMALIGN%%bin/domainrep
@@ -20,63 +35,112 @@
 %%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_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/index.html
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/allversusall.html
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/domainalign.html
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/domainrep.html
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/seqalign.html
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/allversusall.txt
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/domainalign.txt
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/domainrep.txt
+%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/seqalign.txt
 %%PLIST_DOMSEARCH%%bin/seqnr
 %%PLIST_DOMSEARCH%%bin/seqsearch
+%%PLIST_DOMSEARCH%%bin/seqfraggle
 %%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/seqfraggle.acd
 %%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd
 %%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/index.html
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqfraggle.html
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqnr.html
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsearch.html
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsort.html
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqwords.html
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqfraggle.txt
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqnr.txt
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsearch.txt
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsort.txt
+%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqwords.txt
 %%PLIST_EMNU%%bin/emnu
 %%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
-%%PLIST_HMMER%%bin/ealistat
-%%PLIST_HMMER%%bin/ehmmalign
-%%PLIST_HMMER%%bin/ehmmbuild
+%%PLIST_EMNU%%share/EMBOSS/doc/html/embassy/emnu/index.html
+%%PLIST_EMNU%%share/EMBOSS/doc/html/embassy/emnu/emnu.html
+%%PLIST_EMNU%%share/EMBOSS/doc/programs/text/emnu.txt
+%%PLIST_ESIM4%%bin/esim4
+%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
+%%PLIST_ESIM4%%share/EMBOSS/doc/html/embassy/esim4/index.html
+%%PLIST_ESIM4%%share/EMBOSS/doc/html/embassy/esim4/esim4.html
+%%PLIST_ESIM4%%share/EMBOSS/doc/programs/text/esim4.txt
 %%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%%lib/libhmmer.a
-%%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_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_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/index.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmalign.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmbuild.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmcalibrate.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmconvert.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmemit.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmfetch.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmindex.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmpfam.html
+%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmsearch.html
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmalign.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmbuild.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmcalibrate.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmconvert.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmemit.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmfetch.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmindex.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmpfam.txt
+%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmsearch.txt
+%%PLIST_MEME%%bin/emast
+%%PLIST_MEME%%bin/ememe
+%%PLIST_MEME%%share/EMBOSS/acd/emast.acd
+%%PLIST_MEME%%share/EMBOSS/acd/ememe.acd
+%%PLIST_MEME%%share/EMBOSS/doc/html/embassy/memenew/index.html
+%%PLIST_MEME%%share/EMBOSS/doc/html/embassy/memenew/emast.html
+%%PLIST_MEME%%share/EMBOSS/doc/html/embassy/memenew/ememe.html
+%%PLIST_MEME%%share/EMBOSS/doc/programs/text/emast.txt
+%%PLIST_MEME%%share/EMBOSS/doc/programs/text/ememe.txt
 %%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_MSE%%share/EMBOSS/doc/html/embassy/mse/index.html
+%%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/mse.html
+%%PLIST_MSE%%share/EMBOSS/doc/programs/text/mse.txt
+%%PLIST_MSE%%lib/libckit.so.1
+%%PLIST_MSE%%lib/libckit.so
+%%PLIST_MSE%%lib/libckit.la
+%%PLIST_MSE%%lib/libckit.a
 %%PLIST_MYEMBOSS%%bin/myseq
 %%PLIST_MYEMBOSS%%bin/mytest
 %%PLIST_MYEMBOSS%%share/EMBOSS/acd/myseq.acd
 %%PLIST_MYEMBOSS%%share/EMBOSS/acd/mytest.acd
+%%PLIST_MYEMBOSS%%share/EMBOSS/doc/html/embassy/myseq/index.html
+%%PLIST_MYEMBOSS%%share/EMBOSS/doc/html/embassy/myseq/myseq.html
+%%PLIST_MYEMBOSS%%share/EMBOSS/doc/programs/text/myseq.txt
 %%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
@@ -85,14 +149,13 @@
 %%PLIST_PHYLIP%%bin/fdnamove
 %%PLIST_PHYLIP%%bin/fdnapars
 %%PLIST_PHYLIP%%bin/fdnapenny
-%%PLIST_PHYLIP%%bin/fdollop
 %%PLIST_PHYLIP%%bin/fdolmove
+%%PLIST_PHYLIP%%bin/fdollop
 %%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
@@ -104,10 +167,12 @@
 %%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/fdiscboot
+%%PLIST_PHYLIP%%bin/ffreqboot
+%%PLIST_PHYLIP%%bin/frestboot
 %%PLIST_PHYLIP%%bin/fseqboot
 %%PLIST_PHYLIP%%bin/fseqbootall
 %%PLIST_PHYLIP%%bin/ftreedist
@@ -152,6 +217,81 @@
 %%PLIST_PHYLIP%%share/EMBOSS/acd/fseqbootall.acd
 %%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedist.acd
 %%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedistpair.acd
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/index.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fclique.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fconsense.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fcontml.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fcontrast.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdiscboot.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnacomp.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnadist.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnainvar.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnaml.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnamlk.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnapars.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdnapenny.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdollop.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdolpenny.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdrawgram.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fdrawtree.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ffactor.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ffitch.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ffreqboot.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fmix.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fgendist.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fkitsch.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fmove.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fneighbor.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fpars.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fpenny.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fproml.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fpromlk.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fprotdist.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fprotpars.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/frestboot.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/frestml.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fretree.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fseqboot.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/fseqbootall.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ftreedist.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/html/embassy/phylipnew/ftreedistpair.html
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fclique.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fconsense.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fcontml.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fcontrast.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdiscboot.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnacomp.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnadist.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnainvar.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnaml.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnamlk.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnapars.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdnapenny.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdollop.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdolpenny.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdrawgram.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fdrawtree.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ffactor.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ffitch.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ffreqboot.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fgendist.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fkitsch.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fmix.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fmove.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fneighbor.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fpars.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fpenny.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fproml.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fpromlk.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fprotdist.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fprotpars.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/frestboot.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/frestml.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fretree.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fseqboot.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/fseqbootall.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ftreedist.txt
+%%PLIST_PHYLIP%%share/EMBOSS/doc/programs/text/ftreedistpair.txt
 %%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font1
 %%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font2
 %%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font3
@@ -163,22 +303,37 @@
 %%PLIST_PHYLIP%%@dirrm share/PHYLIP
 %%PLIST_SIGNATURE%%bin/libgen
 %%PLIST_SIGNATURE%%bin/matgen3d
-%%PLIST_SIGNATURE%%bin/rocon
 %%PLIST_SIGNATURE%%bin/rocplot
+%%PLIST_SIGNATURE%%bin/rocon
 %%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/rocon.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_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/index.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/libgen.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/matgen3d.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/rocon.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/rocplot.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/siggen.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/siggenlig.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscan.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscanlig.html
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/libgen.txt
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/matgen3d.txt
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/rocon.txt
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/rocplot.txt
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/siggen.txt
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/siggenlig.txt
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/sigscan.txt
+%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/sigscanlig.txt
 %%PLIST_STRUCTURE%%bin/contacts
 %%PLIST_STRUCTURE%%bin/domainer
 %%PLIST_STRUCTURE%%bin/hetparse
@@ -195,7 +350,110 @@
 %%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbplus.acd
 %%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbtosp.acd
 %%PLIST_STRUCTURE%%share/EMBOSS/acd/sites.acd
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/index.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/contacts.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/domainer.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/hetparse.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/interface.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbparse.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbplus.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbtosp.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/sites.html
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/contacts.txt
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/domainer.txt
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/hetparse.txt
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/interface.txt
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbparse.txt
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbplus.txt
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbtosp.txt
+%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/sites.txt
 %%PLIST_TOPO%%bin/topo
 %%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
-@dirrmtry share/EMBOSS/acd
-@dirrmtry share/EMBOSS
+%%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/index.html
+%%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.html
+%%PLIST_TOPO%%share/EMBOSS/doc/programs/text/topo.txt
+%%PLIST_VIENNA%%bin/vrnaalifold
+%%PLIST_VIENNA%%bin/vrnacofoldpf
+%%PLIST_VIENNA%%bin/vrnaevalpair
+%%PLIST_VIENNA%%bin/vrnainverse
+%%PLIST_VIENNA%%bin/vrnaalifoldpf
+%%PLIST_VIENNA%%bin/vrnadistance
+%%PLIST_VIENNA%%bin/vrnafold
+%%PLIST_VIENNA%%bin/vrnalfold
+%%PLIST_VIENNA%%bin/vrnacofold
+%%PLIST_VIENNA%%bin/vrnaduplex
+%%PLIST_VIENNA%%bin/vrnafoldpf
+%%PLIST_VIENNA%%bin/vrnaplot
+%%PLIST_VIENNA%%bin/vrnacofoldconc
+%%PLIST_VIENNA%%bin/vrnaeval
+%%PLIST_VIENNA%%bin/vrnaheat
+%%PLIST_VIENNA%%bin/vrnasubopt
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaalifold.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnadistance.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnafoldpf.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaplot.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaalifoldpf.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaduplex.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaheat.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnasubopt.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnacofold.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaeval.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnainverse.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnacofoldconc.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnaevalpair.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnalfold.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnacofoldpf.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnafold.acd
+%%PLIST_VIENNA%%share/EMBOSS/acd/vrnapaln.acd
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/index.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaalifold.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaalifoldpf.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnacofold.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnacofoldconc.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnacofoldpf.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnadistance.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaduplex.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaeval.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaevalpair.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnafold.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnafoldpf.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaheat.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnainverse.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnalfold.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnaplot.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/html/embassy/vienna/vrnasubopt.html
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaalifold.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaalifoldpf.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnacofold.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnacofoldconc.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnacofoldpf.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnadistance.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaduplex.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaeval.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaevalpair.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnafold.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnafoldpf.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaheat.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnainverse.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnalfold.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnaplot.txt
+%%PLIST_VIENNA%%share/EMBOSS/doc/programs/text/vrnasubopt.txt
+%%PLIST_VIENNA%%lib/libviennarna.so.1
+%%PLIST_VIENNA%%lib/libviennarna.so
+%%PLIST_VIENNA%%lib/libviennarna.la
+%%PLIST_VIENNA%%lib/libviennarna.a
+@dirrmtry share/EMBOSS/doc/html/embassy/vienna
+@dirrmtry share/EMBOSS/doc/html/embassy/topo
+@dirrmtry share/EMBOSS/doc/html/embassy/structure
+@dirrmtry share/EMBOSS/doc/html/embassy/signature
+@dirrmtry share/EMBOSS/doc/html/embassy/phylipnew
+@dirrmtry share/EMBOSS/doc/html/embassy/myseq
+@dirrmtry share/EMBOSS/doc/html/embassy/mse
+@dirrmtry share/EMBOSS/doc/html/embassy/memenew
+@dirrmtry share/EMBOSS/doc/html/embassy/hmmernew
+@dirrmtry share/EMBOSS/doc/html/embassy/esim4
+@dirrmtry share/EMBOSS/doc/html/embassy/emnu
+@dirrmtry share/EMBOSS/doc/html/embassy/domsearch
+@dirrmtry share/EMBOSS/doc/html/embassy/domalign
+@dirrmtry share/EMBOSS/doc/html/embassy/domainatrix
+@dirrmtry share/EMBOSS/doc/html/embassy