4 files changed, 9 insertions, 71 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index eb18b8723f2a..17f1fd3f4626 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.13.1
+PORTVERSION=	1.13.3
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index 6d195e979827..23a0d3c5749b 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,5 +1,5 @@
-MD5 (emboss/EMBOSS-1.13.1.tar.gz) = 313440f1c5f41cb8615f01dfba445358
+MD5 (emboss/EMBOSS-1.13.3.tar.gz) = ef3ebd34154abf04293f58bd9974267b
 MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8
-MD5 (emboss/MSE-0.0.4.tar.gz) = 8b5e9cb6919be5cae1ea977ea7327e79
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = c001525bfbedc8903da34d859eeedf0c
-MD5 (emboss/TOPO-0.1.tar.gz) = c3ea9c55af1d48644f9096ac793cc5a1
+MD5 (emboss/MSE-0.0.4.tar.gz) = d671afc3a3cc211f038f7752fb09c8f6
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = 3539ae2d0753a6e95e60d59d0177c305
+MD5 (emboss/TOPO-0.1.tar.gz) = 8666694007cf866f5cdfe2aba7c01e3b
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 8ce5313cae3f..a559dc57ee5e 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -75,6 +75,7 @@ bin/cons
 bin/cpgplot
 bin/cpgreport
 bin/cusp
+bin/cutgextract
 bin/cutseq
 bin/dan
 bin/dbiblast
@@ -237,6 +238,7 @@ share/EMBOSS/acd/corbatest.acd
 share/EMBOSS/acd/cpgplot.acd
 share/EMBOSS/acd/cpgreport.acd
 share/EMBOSS/acd/cusp.acd
+share/EMBOSS/acd/cutgextract.acd
 share/EMBOSS/acd/cutseq.acd
 share/EMBOSS/acd/dan.acd
 share/EMBOSS/acd/dbiblast.acd
@@ -842,9 +844,9 @@ share/doc/EMBOSS/programs/html/einverted.html
 share/doc/EMBOSS/programs/html/ekitsch.html
 share/doc/EMBOSS/programs/html/emboss_icon.gif
 share/doc/EMBOSS/programs/html/embossdata.html
-share/doc/EMBOSS/programs/html/embossversion.html
 share/doc/EMBOSS/programs/html/emix.html
 share/doc/EMBOSS/programs/html/emma.html
+share/doc/EMBOSS/programs/html/emnu.html
 share/doc/EMBOSS/programs/html/emowse.html
 share/doc/EMBOSS/programs/html/eneighbor.html
 share/doc/EMBOSS/programs/html/entret.html
@@ -971,7 +973,6 @@ share/doc/EMBOSS/programs/html/restml.html
 share/doc/EMBOSS/programs/html/restover.html
 share/doc/EMBOSS/programs/html/restrict.html
 share/doc/EMBOSS/programs/html/revseq.html
-share/doc/EMBOSS/programs/html/scopalign.html
 share/doc/EMBOSS/programs/html/scope.html
 share/doc/EMBOSS/programs/html/seealso.html
 share/doc/EMBOSS/programs/html/seqboot.html
@@ -981,7 +982,6 @@ share/doc/EMBOSS/programs/html/seqretall.html
 share/doc/EMBOSS/programs/html/seqretfeat.html
 share/doc/EMBOSS/programs/html/seqretset.html
 share/doc/EMBOSS/programs/html/seqretsplit.html
-share/doc/EMBOSS/programs/html/showalign.html
 share/doc/EMBOSS/programs/html/showdb.html
 share/doc/EMBOSS/programs/html/showfeat.html
 share/doc/EMBOSS/programs/html/showorf.html
@@ -990,7 +990,6 @@ share/doc/EMBOSS/programs/html/shuffleseq.html
 share/doc/EMBOSS/programs/html/sigcleave.html
 share/doc/EMBOSS/programs/html/silent.html
 share/doc/EMBOSS/programs/html/splitter.html
-share/doc/EMBOSS/programs/html/stamps.html
 share/doc/EMBOSS/programs/html/stretcher.html
 share/doc/EMBOSS/programs/html/stssearch.html
 share/doc/EMBOSS/programs/html/supermatcher.html
@@ -1086,9 +1085,9 @@ share/doc/EMBOSS/programs/text/egendist.txt
 share/doc/EMBOSS/programs/text/einverted.txt
 share/doc/EMBOSS/programs/text/ekitsch.txt
 share/doc/EMBOSS/programs/text/embossdata.txt
-share/doc/EMBOSS/programs/text/embossversion.txt
 share/doc/EMBOSS/programs/text/emix.txt
 share/doc/EMBOSS/programs/text/emma.txt
+share/doc/EMBOSS/programs/text/emnu.txt
 share/doc/EMBOSS/programs/text/emowse.txt
 share/doc/EMBOSS/programs/text/eneighbor.txt
 share/doc/EMBOSS/programs/text/entret.txt
@@ -1175,7 +1174,6 @@ share/doc/EMBOSS/programs/text/restml.txt
 share/doc/EMBOSS/programs/text/restover.txt
 share/doc/EMBOSS/programs/text/restrict.txt
 share/doc/EMBOSS/programs/text/revseq.txt
-share/doc/EMBOSS/programs/text/scopalign.txt
 share/doc/EMBOSS/programs/text/scope.txt
 share/doc/EMBOSS/programs/text/seealso.txt
 share/doc/EMBOSS/programs/text/seqboot.txt
@@ -1185,7 +1183,6 @@ share/doc/EMBOSS/programs/text/seqretall.txt
 share/doc/EMBOSS/programs/text/seqretfeat.txt
 share/doc/EMBOSS/programs/text/seqretset.txt
 share/doc/EMBOSS/programs/text/seqretsplit.txt
-share/doc/EMBOSS/programs/text/showalign.txt
 share/doc/EMBOSS/programs/text/showdb.txt
 share/doc/EMBOSS/programs/text/showfeat.txt
 share/doc/EMBOSS/programs/text/showorf.txt
@@ -1194,7 +1191,6 @@ share/doc/EMBOSS/programs/text/shuffleseq.txt
 share/doc/EMBOSS/programs/text/sigcleave.txt
 share/doc/EMBOSS/programs/text/silent.txt
 share/doc/EMBOSS/programs/text/splitter.txt
-share/doc/EMBOSS/programs/text/stamps.txt
 share/doc/EMBOSS/programs/text/stretcher.txt
 share/doc/EMBOSS/programs/text/stssearch.txt
 share/doc/EMBOSS/programs/text/supermatcher.txt
diff --git a/biology/emboss/pkg-plist.embassy b/biology/emboss/pkg-plist.embassy
deleted file mode 100644
index 862a8acfecdc..000000000000
--- a/biology/emboss/pkg-plist.embassy
+++ /dev/null
@@ -1,58 +0,0 @@
-%%PLIST_EMNU%%bin/emnu
-%%PLIST_EMNU%%share/EMBOSS/acd/emnu.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_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/eneighbor
-%%PLIST_PHYLIP%%bin/epenny
-%%PLIST_PHYLIP%%bin/eprotdist
-%%PLIST_PHYLIP%%bin/eprotpars
-%%PLIST_PHYLIP%%bin/erestml
-%%PLIST_PHYLIP%%bin/eseqboot
-%%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%%bin/topo
-%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd