Update to emboss 1.1.0, fixing some style bugs too.

PR:		ports/20519
Submitted by:	Johann Visagie <johann@egenetics.com> (maintainer)

5 files changed, 321 insertions, 6 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index cc038a5ff719..2279b54b1d9b 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.0.0
+PORTVERSION=	1.1.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/
 DISTNAME=	EMBOSS-${PORTVERSION}
@@ -23,4 +23,20 @@ USE_LIBTOOL=	yes
 CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
 		LIBS="-L${LOCALBASE}/lib"
 
+post-install:
+	@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
+	  ${PREFIX}/etc/emboss.default.sample
+.if !defined(BATCH)
+	@ ${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 274c24a97dfa..e9fc3c64e55c 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1 +1 @@
-MD5 (EMBOSS-1.0.0.tar.gz) = 7b8e7bebdef3adfb6fe45a2d346318fb
+MD5 (EMBOSS-1.1.0.tar.gz) = 9de4ee8a02d397d154cad177b560eaaa
diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa
new file mode 100644
index 000000000000..4289821e32b0
--- /dev/null
+++ b/biology/emboss/files/patch-aa
@@ -0,0 +1,24 @@
+Add ${PREFIX}/etc as an acceptable location for emboss.default.  (This should
+be incorporated into the next version 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");
+   }
+ 
++  /* look for $(PREFIX)_ROOT/../emboss.default */
++
++  if (!prefixRootFile) {
++    ajFmtPrintS (&namRootStr, "%s/etc/%s.default", prefixRoot, prefix);
++    prefixRootFile = fopen (ajStrStr(namRootStr), "r");
++  }
++
+   if (namFileOrig)
+     (void) ajStrAppC (&namFileOrig, ", ");
+   (void) ajStrApp (&namFileOrig, namRootStr);
diff --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message
new file mode 100644
index 000000000000..f14bff524b5a
--- /dev/null
+++ b/biology/emboss/pkg-message
@@ -0,0 +1,22 @@
+--------------------------------------------------------------------------
+
+The EMBOSS suite has been successfully installed.
+
+In order to use the EMBOSS programs, you will need to set some environment
+variables in your shell startup file.  If EMBOSS was installed to the
+default prefix, then:
+
+- set PLPLOT_LIB to:     "/usr/local/share/EMBOSS"
+- set EMBOSS_ACDROOT to: "/usr/local/share/EMBOSS/acd"
+
+NB:  A sample configuration file has been installed to /usr/local/etc as
+emboss.default.sample.  This must be renamed to emboss.default and edited
+to suit your site and its requirements.
+
+A .embossrc in a user's home directory overrides settings in the
+system-wide emboss.default.
+
+Further EMBOSS documentation is available at:
+	http://www.uk.embnet.org/Software/EMBOSS/Doc/
+
+--------------------------------------------------------------------------
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 0f02fc997526..dd8d44bd0230 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -15,6 +15,7 @@ bin/cusp
 bin/cutseq
 bin/dan
 bin/dbiblast
+bin/dbifasta
 bin/dbiflat
 bin/dbigcg
 bin/descseq
@@ -102,6 +103,7 @@ bin/supermatcher
 bin/syco
 bin/textsearch
 bin/tfextract
+bin/tfm
 bin/tfscan
 bin/tmap
 bin/transeq
@@ -111,6 +113,7 @@ bin/wobble
 bin/wordcount
 bin/wordmatch
 bin/wossname
+etc/emboss.default.sample
 lib/libplplot.so.4
 lib/libplplot.so
 lib/libplplot.a
@@ -123,6 +126,248 @@ lib/libajaxg.a
 lib/libnucleus.so.1
 lib/libnucleus.so
 lib/libnucleus.a
+share/doc/EMBOSS/manuals/Makefile
+share/doc/EMBOSS/manuals/Makefile.am
+share/doc/EMBOSS/manuals/Makefile.in
+share/doc/EMBOSS/manuals/Makefile.in.orig
+share/doc/EMBOSS/programs/html/Makefile
+share/doc/EMBOSS/programs/html/Makefile.am
+share/doc/EMBOSS/programs/html/Makefile.in
+share/doc/EMBOSS/programs/html/Makefile.in.orig
+share/doc/EMBOSS/programs/html/antigenic.html
+share/doc/EMBOSS/programs/html/backtranseq.html
+share/doc/EMBOSS/programs/html/banana.html
+share/doc/EMBOSS/programs/html/chaos.html
+share/doc/EMBOSS/programs/html/checktrans.html
+share/doc/EMBOSS/programs/html/chips.html
+share/doc/EMBOSS/programs/html/cirdna.html
+share/doc/EMBOSS/programs/html/codcmp.html
+share/doc/EMBOSS/programs/html/complex.html
+share/doc/EMBOSS/programs/html/compseq.html
+share/doc/EMBOSS/programs/html/cpgplot.html
+share/doc/EMBOSS/programs/html/cpgreport.html
+share/doc/EMBOSS/programs/html/cusp.html
+share/doc/EMBOSS/programs/html/cutseq.html
+share/doc/EMBOSS/programs/html/dan.html
+share/doc/EMBOSS/programs/html/dbiblast.html
+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/digest.html
+share/doc/EMBOSS/programs/html/dotmatcher.html
+share/doc/EMBOSS/programs/html/dottup.html
+share/doc/EMBOSS/programs/html/dreg.html
+share/doc/EMBOSS/programs/html/einverted.html
+share/doc/EMBOSS/programs/html/embossdata.html
+share/doc/EMBOSS/programs/html/emma.html
+share/doc/EMBOSS/programs/html/equicktandem.html
+share/doc/EMBOSS/programs/html/est2genome.html
+share/doc/EMBOSS/programs/html/etandem.html
+share/doc/EMBOSS/programs/html/extractseq.html
+share/doc/EMBOSS/programs/html/findkm.html
+share/doc/EMBOSS/programs/html/freak.html
+share/doc/EMBOSS/programs/html/fuzznuc.html
+share/doc/EMBOSS/programs/html/fuzzpro.html
+share/doc/EMBOSS/programs/html/fuzztran.html
+share/doc/EMBOSS/programs/html/garnier.html
+share/doc/EMBOSS/programs/html/geecee.html
+share/doc/EMBOSS/programs/html/getorf.html
+share/doc/EMBOSS/programs/html/helixturnhelix.html
+share/doc/EMBOSS/programs/html/iep.html
+share/doc/EMBOSS/programs/html/infoseq.html
+share/doc/EMBOSS/programs/html/isochore.html
+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/merger.html
+share/doc/EMBOSS/programs/html/msbar.html
+share/doc/EMBOSS/programs/html/needle.html
+share/doc/EMBOSS/programs/html/newcpgreport.html
+share/doc/EMBOSS/programs/html/newcpgseek.html
+share/doc/EMBOSS/programs/html/newseq.html
+share/doc/EMBOSS/programs/html/noreturn.html
+share/doc/EMBOSS/programs/html/nthseq.html
+share/doc/EMBOSS/programs/html/octanol.html
+share/doc/EMBOSS/programs/html/oddcomp.html
+share/doc/EMBOSS/programs/html/palindrome.html
+share/doc/EMBOSS/programs/html/pasteseq.html
+share/doc/EMBOSS/programs/html/patmatdb.html
+share/doc/EMBOSS/programs/html/patmatmotifs.html
+share/doc/EMBOSS/programs/html/pepcoil.html
+share/doc/EMBOSS/programs/html/pepinfo.html
+share/doc/EMBOSS/programs/html/pepnet.html
+share/doc/EMBOSS/programs/html/pepstats.html
+share/doc/EMBOSS/programs/html/pepwheel.html
+share/doc/EMBOSS/programs/html/pepwindow.html
+share/doc/EMBOSS/programs/html/pepwindowall.html
+share/doc/EMBOSS/programs/html/plotorf.html
+share/doc/EMBOSS/programs/html/polydot.html
+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/printsextract.html
+share/doc/EMBOSS/programs/html/profit.html
+share/doc/EMBOSS/programs/html/prophecy.html
+share/doc/EMBOSS/programs/html/prophet.html
+share/doc/EMBOSS/programs/html/prosextract.html
+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/seealso.html
+share/doc/EMBOSS/programs/html/seqmatchall.html
+share/doc/EMBOSS/programs/html/seqret.html
+share/doc/EMBOSS/programs/html/seqretall.html
+share/doc/EMBOSS/programs/html/seqretset.html
+share/doc/EMBOSS/programs/html/showdb.html
+share/doc/EMBOSS/programs/html/showfeat.html
+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/splitter.html
+share/doc/EMBOSS/programs/html/stretcher.html
+share/doc/EMBOSS/programs/html/stssearch.html
+share/doc/EMBOSS/programs/html/supermatcher.html
+share/doc/EMBOSS/programs/html/syco.html
+share/doc/EMBOSS/programs/html/textsearch.html
+share/doc/EMBOSS/programs/html/tfextract.html
+share/doc/EMBOSS/programs/html/tfm.html
+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/water.html
+share/doc/EMBOSS/programs/html/wobble.html
+share/doc/EMBOSS/programs/html/wordcount.html
+share/doc/EMBOSS/programs/html/wordmatch.html
+share/doc/EMBOSS/programs/html/wossname.html
+share/doc/EMBOSS/programs/text/Makefile
+share/doc/EMBOSS/programs/text/Makefile.am
+share/doc/EMBOSS/programs/text/Makefile.in
+share/doc/EMBOSS/programs/text/Makefile.in.orig
+share/doc/EMBOSS/programs/text/antigenic.txt
+share/doc/EMBOSS/programs/text/backtranseq.txt
+share/doc/EMBOSS/programs/text/banana.txt
+share/doc/EMBOSS/programs/text/chaos.txt
+share/doc/EMBOSS/programs/text/checktrans.txt
+share/doc/EMBOSS/programs/text/chips.txt
+share/doc/EMBOSS/programs/text/cirdna.txt
+share/doc/EMBOSS/programs/text/codcmp.txt
+share/doc/EMBOSS/programs/text/complex.txt
+share/doc/EMBOSS/programs/text/compseq.txt
+share/doc/EMBOSS/programs/text/cpgplot.txt
+share/doc/EMBOSS/programs/text/cpgreport.txt
+share/doc/EMBOSS/programs/text/cusp.txt
+share/doc/EMBOSS/programs/text/cutseq.txt
+share/doc/EMBOSS/programs/text/dan.txt
+share/doc/EMBOSS/programs/text/dbiblast.txt
+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/digest.txt
+share/doc/EMBOSS/programs/text/dotmatcher.txt
+share/doc/EMBOSS/programs/text/dottup.txt
+share/doc/EMBOSS/programs/text/dreg.txt
+share/doc/EMBOSS/programs/text/einverted.txt
+share/doc/EMBOSS/programs/text/embossdata.txt
+share/doc/EMBOSS/programs/text/emma.txt
+share/doc/EMBOSS/programs/text/equicktandem.txt
+share/doc/EMBOSS/programs/text/est2genome.txt
+share/doc/EMBOSS/programs/text/etandem.txt
+share/doc/EMBOSS/programs/text/extractseq.txt
+share/doc/EMBOSS/programs/text/findkm.txt
+share/doc/EMBOSS/programs/text/freak.txt
+share/doc/EMBOSS/programs/text/fuzznuc.txt
+share/doc/EMBOSS/programs/text/fuzzpro.txt
+share/doc/EMBOSS/programs/text/fuzztran.txt
+share/doc/EMBOSS/programs/text/garnier.txt
+share/doc/EMBOSS/programs/text/geecee.txt
+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/merger.txt
+share/doc/EMBOSS/programs/text/msbar.txt
+share/doc/EMBOSS/programs/text/needle.txt
+share/doc/EMBOSS/programs/text/newcpgreport.txt
+share/doc/EMBOSS/programs/text/newcpgseek.txt
+share/doc/EMBOSS/programs/text/newseq.txt
+share/doc/EMBOSS/programs/text/noreturn.txt
+share/doc/EMBOSS/programs/text/nthseq.txt
+share/doc/EMBOSS/programs/text/octanol.txt
+share/doc/EMBOSS/programs/text/oddcomp.txt
+share/doc/EMBOSS/programs/text/palindrome.txt
+share/doc/EMBOSS/programs/text/pasteseq.txt
+share/doc/EMBOSS/programs/text/patmatdb.txt
+share/doc/EMBOSS/programs/text/patmatmotifs.txt
+share/doc/EMBOSS/programs/text/pepcoil.txt
+share/doc/EMBOSS/programs/text/pepinfo.txt
+share/doc/EMBOSS/programs/text/pepnet.txt
+share/doc/EMBOSS/programs/text/pepstats.txt
+share/doc/EMBOSS/programs/text/pepwheel.txt
+share/doc/EMBOSS/programs/text/pepwindow.txt
+share/doc/EMBOSS/programs/text/pepwindowall.txt
+share/doc/EMBOSS/programs/text/plotorf.txt
+share/doc/EMBOSS/programs/text/polydot.txt
+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/printsextract.txt
+share/doc/EMBOSS/programs/text/profit.txt
+share/doc/EMBOSS/programs/text/prophecy.txt
+share/doc/EMBOSS/programs/text/prophet.txt
+share/doc/EMBOSS/programs/text/prosextract.txt
+share/doc/EMBOSS/programs/text/pscan.txt
+share/doc/EMBOSS/programs/text/rebaseextract.txt
+share/doc/EMBOSS/programs/text/redata.txt
+share/doc/EMBOSS/programs/text/remap.txt
+share/doc/EMBOSS/programs/text/restrict.txt
+share/doc/EMBOSS/programs/text/revseq.txt
+share/doc/EMBOSS/programs/text/seealso.txt
+share/doc/EMBOSS/programs/text/seqmatchall.txt
+share/doc/EMBOSS/programs/text/seqret.txt
+share/doc/EMBOSS/programs/text/seqretall.txt
+share/doc/EMBOSS/programs/text/seqretset.txt
+share/doc/EMBOSS/programs/text/showdb.txt
+share/doc/EMBOSS/programs/text/showfeat.txt
+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/splitter.txt
+share/doc/EMBOSS/programs/text/stretcher.txt
+share/doc/EMBOSS/programs/text/stssearch.txt
+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/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/water.txt
+share/doc/EMBOSS/programs/text/wobble.txt
+share/doc/EMBOSS/programs/text/wordcount.txt
+share/doc/EMBOSS/programs/text/wordmatch.txt
+share/doc/EMBOSS/programs/text/wossname.txt
+share/doc/EMBOSS/tutorials/Makefile
+share/doc/EMBOSS/tutorials/Makefile.am
+share/doc/EMBOSS/tutorials/Makefile.in
+share/doc/EMBOSS/tutorials/Makefile.in.orig
 share/EMBOSS/plstnd5.fnt
 share/EMBOSS/plxtnd5.fnt
 share/EMBOSS/acd/ajbad.acd
@@ -163,12 +408,13 @@ share/EMBOSS/acd/cusp.acd
 share/EMBOSS/acd/cutseq.acd
 share/EMBOSS/acd/dan.acd
 share/EMBOSS/acd/dbiblast.acd
+share/EMBOSS/acd/dbifasta.acd
 share/EMBOSS/acd/dbiflat.acd
 share/EMBOSS/acd/dbigcg.acd
 share/EMBOSS/acd/descseq.acd
 share/EMBOSS/acd/digest.acd
-share/EMBOSS/acd/dotmatcher.acd
 share/EMBOSS/acd/dottup.acd
+share/EMBOSS/acd/dotmatcher.acd
 share/EMBOSS/acd/dreg.acd
 share/EMBOSS/acd/einverted.acd
 share/EMBOSS/acd/embossdata.acd
@@ -213,8 +459,8 @@ share/EMBOSS/acd/pepnet.acd
 share/EMBOSS/acd/pepstats.acd
 share/EMBOSS/acd/pepwheel.acd
 share/EMBOSS/acd/pepwindow.acd
-share/EMBOSS/acd/pepwindowall.acd
 share/EMBOSS/acd/plotorf.acd
+share/EMBOSS/acd/pepwindowall.acd
 share/EMBOSS/acd/polydot.acd
 share/EMBOSS/acd/preg.acd
 share/EMBOSS/acd/prettyplot.acd
@@ -236,8 +482,8 @@ share/EMBOSS/acd/seqret.acd
 share/EMBOSS/acd/seqretall.acd
 share/EMBOSS/acd/seqretset.acd
 share/EMBOSS/acd/seqretsplit.acd
-share/EMBOSS/acd/showdb.acd
 share/EMBOSS/acd/seqrettype.acd
+share/EMBOSS/acd/showdb.acd
 share/EMBOSS/acd/showfeat.acd
 share/EMBOSS/acd/showorf.acd
 share/EMBOSS/acd/showseq.acd
@@ -250,6 +496,7 @@ share/EMBOSS/acd/supermatcher.acd
 share/EMBOSS/acd/syco.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
@@ -640,12 +887,18 @@ share/EMBOSS/test/wormpep/acnum.trg
 share/EMBOSS/test/wormpep/division.lkp
 share/EMBOSS/test/wormpep/entrynam.idx
 share/EMBOSS/test/wormpep/wormpep
+@dirrm share/doc/EMBOSS/manuals
+@dirrm share/doc/EMBOSS/programs/html
+@dirrm share/doc/EMBOSS/programs/text
+@dirrm share/doc/EMBOSS/programs
+@dirrm share/doc/EMBOSS/tutorials
+@dirrm share/doc/EMBOSS
+@dirrm share/EMBOSS/acd
 @dirrm share/EMBOSS/data/CODONS
 @dirrm share/EMBOSS/data/REBASE
 @dirrm share/EMBOSS/data/PRINTS
 @dirrm share/EMBOSS/data/PROSITE
 @dirrm share/EMBOSS/data
-@dirrm share/EMBOSS/acd
 @dirrm share/EMBOSS/test/data
 @dirrm share/EMBOSS/test/embl
 @dirrm share/EMBOSS/test/pir