Update to emboss 1.4.0.

PR:		ports/20898
Submitted by:	Johann Visagie <johann@egenetics.com>

4 files changed, 83 insertions, 52 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 7264cc695ce4..e246f10d8e31 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.1.0
+PORTVERSION=	1.4.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/
 DISTNAME=	EMBOSS-${PORTVERSION}
@@ -22,6 +22,15 @@ USE_LIBTOOL=	yes
 CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
 		LIBS="-L${LOCALBASE}/lib"
 
+DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
+
+post-patch:
+.for DIR in ${DOC_DIRS}
+	@ ${PERL} -pi.orig -e \
+	  "s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \
+	  ${WRKSRC}/${DIR}/Makefile.in
+.endfor
+
 post-install:
 	@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
 	  ${PREFIX}/etc/emboss.default.sample
@@ -29,13 +38,4 @@ post-install:
 	@ ${CAT} ${PKGMESSAGE}
 .endif
 
-DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
-
-post-patch:
-.for DIR in ${DOC_DIRS}
-	@perl -pi.orig -e \
-		"s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \
-		${WRKSRC}/${DIR}/Makefile.in
-.endfor
-
 .include <bsd.port.mk>
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index e9fc3c64e55c..f42c83e49367 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1 +1 @@
-MD5 (EMBOSS-1.1.0.tar.gz) = 9de4ee8a02d397d154cad177b560eaaa
+MD5 (EMBOSS-1.4.0.tar.gz) = ba096906cc10d0badbc1c479e61926c9
diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa
index 4289821e32b0..f4b1bc46f7a1 100644
--- a/biology/emboss/files/patch-aa
+++ b/biology/emboss/files/patch-aa
@@ -1,24 +1,26 @@
-Add ${PREFIX}/etc as an acceptable location for emboss.default.  (This should
-be incorporated into the next version of EMBOSS.)
+Add ${PREFIX}/etc as an acceptable location for emboss.default.  (I'm still
+waiting for this to be incorporated into an official release of EMBOSS.)
 
 The port installs ${PREFIX}/etc/emboss.default.sample
 
 -- Johann <johann@egenetics.com>
 
 
---- ajax/ajnam.c.orig	Wed Aug  2 10:18:59 2000
-+++ ajax/ajnam.c	Thu Aug 10 10:06:20 2000
-@@ -982,6 +982,13 @@
-     prefixRootFile = fopen (ajStrStr(namRootStr), "r");
-   }
+--- ajax/ajnam.c.orig	Thu Aug 17 20:31:30 2000
++++ ajax/ajnam.c	Mon Aug 28 15:12:09 2000
+@@ -984,6 +984,15 @@
+ 	prefixRootFile = fopen (ajStrStr(namRootStr), "r");
+     }
  
-+  /* look for $(PREFIX)_ROOT/../emboss.default */
++    /* look for $(PREFIX)_ROOT/../emboss.default */
 +
-+  if (!prefixRootFile) {
-+    ajFmtPrintS (&namRootStr, "%s/etc/%s.default", prefixRoot, prefix);
-+    prefixRootFile = fopen (ajStrStr(namRootStr), "r");
-+  }
++    if (!prefixRootFile)
++    {
++      ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
++		   namInstallRoot, prefixCap, prefix);
++      prefixRootFile = fopen (ajStrStr(namRootStr), "r");
++    }
 +
-   if (namFileOrig)
-     (void) ajStrAppC (&namFileOrig, ", ");
-   (void) ajStrApp (&namFileOrig, namRootStr);
+     if (namFileOrig)
+ 	(void) ajStrAppC (&namFileOrig, ", ");
+     (void) ajStrApp (&namFileOrig, namRootStr);
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index dd8d44bd0230..b62a97f96d93 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -19,11 +19,14 @@ bin/dbifasta
 bin/dbiflat
 bin/dbigcg
 bin/descseq
+bin/diffseq
 bin/digest
 bin/dotmatcher
+bin/dotpath
 bin/dottup
 bin/dreg
 bin/einverted
+bin/iep
 bin/embossdata
 bin/emma
 bin/equicktandem
@@ -39,13 +42,13 @@ bin/garnier
 bin/geecee
 bin/getorf
 bin/helixturnhelix
-bin/iep
 bin/infoseq
 bin/isochore
 bin/lindna
 bin/maskfeat
 bin/maskseq
 bin/matcher
+bin/megamerger
 bin/merger
 bin/msbar
 bin/needle
@@ -73,6 +76,7 @@ bin/preg
 bin/prettyplot
 bin/prettyseq
 bin/prima
+bin/primersearch
 bin/printsextract
 bin/profit
 bin/prophecy
@@ -96,6 +100,7 @@ bin/showorf
 bin/showseq
 bin/shuffleseq
 bin/sigcleave
+bin/silent
 bin/splitter
 bin/stretcher
 bin/stssearch
@@ -108,6 +113,7 @@ bin/tfscan
 bin/tmap
 bin/transeq
 bin/trimseq
+bin/vectorstrip
 bin/water
 bin/wobble
 bin/wordcount
@@ -154,8 +160,10 @@ share/doc/EMBOSS/programs/html/dbifasta.html
 share/doc/EMBOSS/programs/html/dbigcg.html
 share/doc/EMBOSS/programs/html/dbiflat.html
 share/doc/EMBOSS/programs/html/descseq.html
+share/doc/EMBOSS/programs/html/diffseq.html
 share/doc/EMBOSS/programs/html/digest.html
 share/doc/EMBOSS/programs/html/dotmatcher.html
+share/doc/EMBOSS/programs/html/dotpath.html
 share/doc/EMBOSS/programs/html/dottup.html
 share/doc/EMBOSS/programs/html/dreg.html
 share/doc/EMBOSS/programs/html/einverted.html
@@ -181,6 +189,7 @@ share/doc/EMBOSS/programs/html/lindna.html
 share/doc/EMBOSS/programs/html/maskfeat.html
 share/doc/EMBOSS/programs/html/maskseq.html
 share/doc/EMBOSS/programs/html/matcher.html
+share/doc/EMBOSS/programs/html/megamerger.html
 share/doc/EMBOSS/programs/html/merger.html
 share/doc/EMBOSS/programs/html/msbar.html
 share/doc/EMBOSS/programs/html/needle.html
@@ -208,6 +217,7 @@ share/doc/EMBOSS/programs/html/preg.html
 share/doc/EMBOSS/programs/html/prettyplot.html
 share/doc/EMBOSS/programs/html/prettyseq.html
 share/doc/EMBOSS/programs/html/prima.html
+share/doc/EMBOSS/programs/html/primersearch.html
 share/doc/EMBOSS/programs/html/printsextract.html
 share/doc/EMBOSS/programs/html/profit.html
 share/doc/EMBOSS/programs/html/prophecy.html
@@ -217,8 +227,8 @@ share/doc/EMBOSS/programs/html/pscan.html
 share/doc/EMBOSS/programs/html/rebaseextract.html
 share/doc/EMBOSS/programs/html/redata.html
 share/doc/EMBOSS/programs/html/remap.html
-share/doc/EMBOSS/programs/html/revseq.html
 share/doc/EMBOSS/programs/html/restrict.html
+share/doc/EMBOSS/programs/html/revseq.html
 share/doc/EMBOSS/programs/html/seealso.html
 share/doc/EMBOSS/programs/html/seqmatchall.html
 share/doc/EMBOSS/programs/html/seqret.html
@@ -230,6 +240,7 @@ share/doc/EMBOSS/programs/html/showorf.html
 share/doc/EMBOSS/programs/html/showseq.html
 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/stretcher.html
 share/doc/EMBOSS/programs/html/stssearch.html
@@ -242,6 +253,7 @@ share/doc/EMBOSS/programs/html/tfscan.html
 share/doc/EMBOSS/programs/html/tmap.html
 share/doc/EMBOSS/programs/html/transeq.html
 share/doc/EMBOSS/programs/html/trimseq.html
+share/doc/EMBOSS/programs/html/vectorstrip.html
 share/doc/EMBOSS/programs/html/water.html
 share/doc/EMBOSS/programs/html/wobble.html
 share/doc/EMBOSS/programs/html/wordcount.html
@@ -271,8 +283,10 @@ share/doc/EMBOSS/programs/text/dbifasta.txt
 share/doc/EMBOSS/programs/text/dbiflat.txt
 share/doc/EMBOSS/programs/text/dbigcg.txt
 share/doc/EMBOSS/programs/text/descseq.txt
+share/doc/EMBOSS/programs/text/diffseq.txt
 share/doc/EMBOSS/programs/text/digest.txt
 share/doc/EMBOSS/programs/text/dotmatcher.txt
+share/doc/EMBOSS/programs/text/dotpath.txt
 share/doc/EMBOSS/programs/text/dottup.txt
 share/doc/EMBOSS/programs/text/dreg.txt
 share/doc/EMBOSS/programs/text/einverted.txt
@@ -293,12 +307,12 @@ share/doc/EMBOSS/programs/text/getorf.txt
 share/doc/EMBOSS/programs/text/helixturnhelix.txt
 share/doc/EMBOSS/programs/text/iep.txt
 share/doc/EMBOSS/programs/text/infoseq.txt
-share/doc/EMBOSS/programs/text/tfm.txt
 share/doc/EMBOSS/programs/text/isochore.txt
 share/doc/EMBOSS/programs/text/lindna.txt
 share/doc/EMBOSS/programs/text/maskfeat.txt
 share/doc/EMBOSS/programs/text/maskseq.txt
 share/doc/EMBOSS/programs/text/matcher.txt
+share/doc/EMBOSS/programs/text/megamerger.txt
 share/doc/EMBOSS/programs/text/merger.txt
 share/doc/EMBOSS/programs/text/msbar.txt
 share/doc/EMBOSS/programs/text/needle.txt
@@ -326,6 +340,7 @@ share/doc/EMBOSS/programs/text/preg.txt
 share/doc/EMBOSS/programs/text/prettyplot.txt
 share/doc/EMBOSS/programs/text/prettyseq.txt
 share/doc/EMBOSS/programs/text/prima.txt
+share/doc/EMBOSS/programs/text/primersearch.txt
 share/doc/EMBOSS/programs/text/printsextract.txt
 share/doc/EMBOSS/programs/text/profit.txt
 share/doc/EMBOSS/programs/text/prophecy.txt
@@ -348,6 +363,7 @@ share/doc/EMBOSS/programs/text/showorf.txt
 share/doc/EMBOSS/programs/text/showseq.txt
 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/stretcher.txt
 share/doc/EMBOSS/programs/text/stssearch.txt
@@ -355,10 +371,12 @@ share/doc/EMBOSS/programs/text/supermatcher.txt
 share/doc/EMBOSS/programs/text/syco.txt
 share/doc/EMBOSS/programs/text/textsearch.txt
 share/doc/EMBOSS/programs/text/tfextract.txt
+share/doc/EMBOSS/programs/text/tfm.txt
 share/doc/EMBOSS/programs/text/tfscan.txt
 share/doc/EMBOSS/programs/text/tmap.txt
 share/doc/EMBOSS/programs/text/transeq.txt
 share/doc/EMBOSS/programs/text/trimseq.txt
+share/doc/EMBOSS/programs/text/vectorstrip.txt
 share/doc/EMBOSS/programs/text/water.txt
 share/doc/EMBOSS/programs/text/wobble.txt
 share/doc/EMBOSS/programs/text/wordcount.txt
@@ -370,28 +388,13 @@ share/doc/EMBOSS/tutorials/Makefile.in
 share/doc/EMBOSS/tutorials/Makefile.in.orig
 share/EMBOSS/plstnd5.fnt
 share/EMBOSS/plxtnd5.fnt
+share/EMBOSS/acd/Makefile
+share/EMBOSS/acd/Makefile.am
+share/EMBOSS/acd/Makefile.in
 share/EMBOSS/acd/ajbad.acd
 share/EMBOSS/acd/ajfeatest.acd
 share/EMBOSS/acd/ajtest.acd
 share/EMBOSS/acd/ajtest2.acd
-share/EMBOSS/acd/cluster.acd
-share/EMBOSS/acd/demofeatures.acd
-share/EMBOSS/acd/demolist.acd
-share/EMBOSS/acd/demosequence.acd
-share/EMBOSS/acd/demostring.acd
-share/EMBOSS/acd/demotable.acd
-share/EMBOSS/acd/entrails.acd
-share/EMBOSS/acd/histogramtest.acd
-share/EMBOSS/acd/patmattest.acd
-share/EMBOSS/acd/plplottest.acd
-share/EMBOSS/acd/proteinmotifsearch.acd
-share/EMBOSS/acd/seqinfo.acd
-share/EMBOSS/acd/seqretallfeat.acd
-share/EMBOSS/acd/seqretfeat.acd
-share/EMBOSS/acd/seqtofeat.acd
-share/EMBOSS/acd/simplesw.acd
-share/EMBOSS/acd/testplot.acd
-share/EMBOSS/acd/treetypedisplay.acd
 share/EMBOSS/acd/antigenic.acd
 share/EMBOSS/acd/backtranseq.acd
 share/EMBOSS/acd/banana.acd
@@ -399,7 +402,9 @@ share/EMBOSS/acd/chaos.acd
 share/EMBOSS/acd/checktrans.acd
 share/EMBOSS/acd/chips.acd
 share/EMBOSS/acd/cirdna.acd
+share/EMBOSS/acd/cluster.acd
 share/EMBOSS/acd/codcmp.acd
+share/EMBOSS/acd/codes.english
 share/EMBOSS/acd/complex.acd
 share/EMBOSS/acd/compseq.acd
 share/EMBOSS/acd/cpgplot.acd
@@ -411,17 +416,26 @@ share/EMBOSS/acd/dbiblast.acd
 share/EMBOSS/acd/dbifasta.acd
 share/EMBOSS/acd/dbiflat.acd
 share/EMBOSS/acd/dbigcg.acd
+share/EMBOSS/acd/demofeatures.acd
+share/EMBOSS/acd/demolist.acd
+share/EMBOSS/acd/demosequence.acd
+share/EMBOSS/acd/demostring.acd
+share/EMBOSS/acd/demotable.acd
 share/EMBOSS/acd/descseq.acd
+share/EMBOSS/acd/diffseq.acd
 share/EMBOSS/acd/digest.acd
-share/EMBOSS/acd/dottup.acd
 share/EMBOSS/acd/dotmatcher.acd
+share/EMBOSS/acd/dotpath.acd
+share/EMBOSS/acd/dottup.acd
 share/EMBOSS/acd/dreg.acd
 share/EMBOSS/acd/einverted.acd
+share/EMBOSS/acd/emboss.default
 share/EMBOSS/acd/embossdata.acd
 share/EMBOSS/acd/emma.acd
+share/EMBOSS/acd/entrails.acd
+share/EMBOSS/acd/etandem.acd
 share/EMBOSS/acd/equicktandem.acd
 share/EMBOSS/acd/est2genome.acd
-share/EMBOSS/acd/etandem.acd
 share/EMBOSS/acd/extractseq.acd
 share/EMBOSS/acd/findkm.acd
 share/EMBOSS/acd/freak.acd
@@ -432,6 +446,7 @@ share/EMBOSS/acd/garnier.acd
 share/EMBOSS/acd/geecee.acd
 share/EMBOSS/acd/getorf.acd
 share/EMBOSS/acd/helixturnhelix.acd
+share/EMBOSS/acd/histogramtest.acd
 share/EMBOSS/acd/iep.acd
 share/EMBOSS/acd/infoseq.acd
 share/EMBOSS/acd/isochore.acd
@@ -439,6 +454,7 @@ share/EMBOSS/acd/lindna.acd
 share/EMBOSS/acd/maskfeat.acd
 share/EMBOSS/acd/maskseq.acd
 share/EMBOSS/acd/matcher.acd
+share/EMBOSS/acd/megamerger.acd
 share/EMBOSS/acd/merger.acd
 share/EMBOSS/acd/msbar.acd
 share/EMBOSS/acd/needle.acd
@@ -453,60 +469,73 @@ share/EMBOSS/acd/palindrome.acd
 share/EMBOSS/acd/pasteseq.acd
 share/EMBOSS/acd/patmatdb.acd
 share/EMBOSS/acd/patmatmotifs.acd
+share/EMBOSS/acd/patmattest.acd
 share/EMBOSS/acd/pepcoil.acd
 share/EMBOSS/acd/pepinfo.acd
 share/EMBOSS/acd/pepnet.acd
 share/EMBOSS/acd/pepstats.acd
 share/EMBOSS/acd/pepwheel.acd
 share/EMBOSS/acd/pepwindow.acd
-share/EMBOSS/acd/plotorf.acd
 share/EMBOSS/acd/pepwindowall.acd
+share/EMBOSS/acd/plotorf.acd
+share/EMBOSS/acd/plplottest.acd
 share/EMBOSS/acd/polydot.acd
 share/EMBOSS/acd/preg.acd
 share/EMBOSS/acd/prettyplot.acd
 share/EMBOSS/acd/prettyseq.acd
 share/EMBOSS/acd/prima.acd
+share/EMBOSS/acd/primersearch.acd
 share/EMBOSS/acd/printsextract.acd
 share/EMBOSS/acd/profit.acd
 share/EMBOSS/acd/prophecy.acd
 share/EMBOSS/acd/prophet.acd
 share/EMBOSS/acd/prosextract.acd
+share/EMBOSS/acd/proteinmotifsearch.acd
 share/EMBOSS/acd/pscan.acd
 share/EMBOSS/acd/rebaseextract.acd
 share/EMBOSS/acd/redata.acd
 share/EMBOSS/acd/remap.acd
 share/EMBOSS/acd/restrict.acd
 share/EMBOSS/acd/revseq.acd
+share/EMBOSS/acd/seealso.acd
+share/EMBOSS/acd/seqinfo.acd
 share/EMBOSS/acd/seqmatchall.acd
 share/EMBOSS/acd/seqret.acd
 share/EMBOSS/acd/seqretall.acd
+share/EMBOSS/acd/seqretallfeat.acd
+share/EMBOSS/acd/seqretfeat.acd
 share/EMBOSS/acd/seqretset.acd
 share/EMBOSS/acd/seqretsplit.acd
 share/EMBOSS/acd/seqrettype.acd
+share/EMBOSS/acd/seqtofeat.acd
 share/EMBOSS/acd/showdb.acd
 share/EMBOSS/acd/showfeat.acd
 share/EMBOSS/acd/showorf.acd
 share/EMBOSS/acd/showseq.acd
 share/EMBOSS/acd/shuffleseq.acd
 share/EMBOSS/acd/sigcleave.acd
+share/EMBOSS/acd/silent.acd
+share/EMBOSS/acd/simplesw.acd
 share/EMBOSS/acd/splitter.acd
 share/EMBOSS/acd/stretcher.acd
 share/EMBOSS/acd/stssearch.acd
 share/EMBOSS/acd/supermatcher.acd
 share/EMBOSS/acd/syco.acd
+share/EMBOSS/acd/testplot.acd
+share/EMBOSS/acd/tfm.acd
 share/EMBOSS/acd/textsearch.acd
 share/EMBOSS/acd/tfextract.acd
-share/EMBOSS/acd/tfm.acd
 share/EMBOSS/acd/tfscan.acd
 share/EMBOSS/acd/tmap.acd
 share/EMBOSS/acd/transeq.acd
+share/EMBOSS/acd/treetypedisplay.acd
 share/EMBOSS/acd/trimseq.acd
+share/EMBOSS/acd/vectorstrip.acd
 share/EMBOSS/acd/water.acd
 share/EMBOSS/acd/wobble.acd
 share/EMBOSS/acd/wordcount.acd
 share/EMBOSS/acd/wordmatch.acd
 share/EMBOSS/acd/wossname.acd
-share/EMBOSS/acd/codes.english
 share/EMBOSS/data/CODONS/Eacc.cut
 share/EMBOSS/data/CODONS/Eadenovirus5.cut
 share/EMBOSS/data/CODONS/Eadenovirus7.cut