Add emboss, the European Molecular Biology Open Software Suite

PR:		ports/20317
Submitted by:	Johann Visagie <johann@egenetics.com>

6 files changed, 700 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 6508ab53e363..d95edb241605 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -5,6 +5,7 @@
     SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += deft
+    SUBDIR += emboss
     SUBDIR += gperiodic
     SUBDIR += hmmer
     SUBDIR += kinemage
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
new file mode 100644
index 000000000000..cc038a5ff719
--- /dev/null
+++ b/biology/emboss/Makefile
@@ -0,0 +1,26 @@
+# New ports collection makefile for:	emboss
+# Date created:		31 July 2000
+# Whom:	      		Johann Visagie <johann@egenetics.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	emboss
+PORTVERSION=	1.0.0
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/
+DISTNAME=	EMBOSS-${PORTVERSION}
+
+MAINTAINER=	johann@egenetics.com
+
+LIB_DEPENDS=	gd.1:${PORTSDIR}/graphics/gd \
+		png.4:${PORTSDIR}/graphics/png
+
+USE_GMAKE=	yes
+GNU_CONFIGURE=	yes
+USE_LIBTOOL=	yes
+
+CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
+		LIBS="-L${LOCALBASE}/lib"
+
+.include <bsd.port.mk>
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
new file mode 100644
index 000000000000..274c24a97dfa
--- /dev/null
+++ b/biology/emboss/distinfo
@@ -0,0 +1 @@
+MD5 (EMBOSS-1.0.0.tar.gz) = 7b8e7bebdef3adfb6fe45a2d346318fb
diff --git a/biology/emboss/pkg-comment b/biology/emboss/pkg-comment
new file mode 100644
index 000000000000..5b05a785f6fc
--- /dev/null
+++ b/biology/emboss/pkg-comment
@@ -0,0 +1 @@
+A collection of open source tools for genetic sequence analysis
diff --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr
new file mode 100644
index 000000000000..3b212c44b033
--- /dev/null
+++ b/biology/emboss/pkg-descr
@@ -0,0 +1,15 @@
+The European Molecular Biology Open Software Suite (EMBOSS) is a
+comprehensive set (about 100) of open source tools for genetic sequence
+analysis.  EMBOSS is produced by the European Molecular Biology Network
+(EMBnet - http://www.embnet.org/).
+
+All EMBOSS tools are all built around the same set of core libraries - AJAX
+and NUCLEUS - and therefore share a unified user interface and a uniform
+sequence addressing methodology.
+
+The various components of EMBOSS are distributed under the GPL, except the
+core libraries which are under the LGPL.
+
+WWW: http://www.uk.embnet.org/Software/EMBOSS/
+
+-- Johann Visagie <johann@egenetics.com>
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
new file mode 100644
index 000000000000..0f02fc997526
--- /dev/null
+++ b/biology/emboss/pkg-plist
@@ -0,0 +1,656 @@
+bin/acdc
+bin/antigenic
+bin/backtranseq
+bin/banana
+bin/chaos
+bin/checktrans
+bin/chips
+bin/cirdna
+bin/codcmp
+bin/complex
+bin/compseq
+bin/cpgplot
+bin/cpgreport
+bin/cusp
+bin/cutseq
+bin/dan
+bin/dbiblast
+bin/dbiflat
+bin/dbigcg
+bin/descseq
+bin/digest
+bin/dotmatcher
+bin/dottup
+bin/dreg
+bin/einverted
+bin/embossdata
+bin/emma
+bin/equicktandem
+bin/est2genome
+bin/etandem
+bin/extractseq
+bin/findkm
+bin/freak
+bin/fuzznuc
+bin/fuzzpro
+bin/fuzztran
+bin/garnier
+bin/geecee
+bin/getorf
+bin/helixturnhelix
+bin/iep
+bin/infoseq
+bin/isochore
+bin/lindna
+bin/maskfeat
+bin/maskseq
+bin/matcher
+bin/merger
+bin/msbar
+bin/needle
+bin/newcpgreport
+bin/newcpgseek
+bin/newseq
+bin/noreturn
+bin/nthseq
+bin/octanol
+bin/oddcomp
+bin/palindrome
+bin/pasteseq
+bin/patmatdb
+bin/patmatmotifs
+bin/pepcoil
+bin/pepinfo
+bin/pepnet
+bin/pepstats
+bin/pepwheel
+bin/pepwindow
+bin/pepwindowall
+bin/plotorf
+bin/polydot
+bin/preg
+bin/prettyplot
+bin/prettyseq
+bin/prima
+bin/printsextract
+bin/profit
+bin/prophecy
+bin/prophet
+bin/prosextract
+bin/pscan
+bin/rebaseextract
+bin/redata
+bin/remap
+bin/restrict
+bin/revseq
+bin/seealso
+bin/seqmatchall
+bin/seqret
+bin/seqretall
+bin/seqretset
+bin/seqretsplit
+bin/showdb
+bin/showfeat
+bin/showorf
+bin/showseq
+bin/shuffleseq
+bin/sigcleave
+bin/splitter
+bin/stretcher
+bin/stssearch
+bin/supermatcher
+bin/syco
+bin/textsearch
+bin/tfextract
+bin/tfscan
+bin/tmap
+bin/transeq
+bin/trimseq
+bin/water
+bin/wobble
+bin/wordcount
+bin/wordmatch
+bin/wossname
+lib/libplplot.so.4
+lib/libplplot.so
+lib/libplplot.a
+lib/libajax.so.1
+lib/libajax.so
+lib/libajax.a
+lib/libajaxg.so.1
+lib/libajaxg.so
+lib/libajaxg.a
+lib/libnucleus.so.1
+lib/libnucleus.so
+lib/libnucleus.a
+share/EMBOSS/plstnd5.fnt
+share/EMBOSS/plxtnd5.fnt
+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
+share/EMBOSS/acd/chaos.acd
+share/EMBOSS/acd/checktrans.acd
+share/EMBOSS/acd/chips.acd
+share/EMBOSS/acd/cirdna.acd
+share/EMBOSS/acd/codcmp.acd
+share/EMBOSS/acd/complex.acd
+share/EMBOSS/acd/compseq.acd
+share/EMBOSS/acd/cpgplot.acd
+share/EMBOSS/acd/cpgreport.acd
+share/EMBOSS/acd/cusp.acd
+share/EMBOSS/acd/cutseq.acd
+share/EMBOSS/acd/dan.acd
+share/EMBOSS/acd/dbiblast.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/dreg.acd
+share/EMBOSS/acd/einverted.acd
+share/EMBOSS/acd/embossdata.acd
+share/EMBOSS/acd/emma.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
+share/EMBOSS/acd/fuzznuc.acd
+share/EMBOSS/acd/fuzzpro.acd
+share/EMBOSS/acd/fuzztran.acd
+share/EMBOSS/acd/garnier.acd
+share/EMBOSS/acd/geecee.acd
+share/EMBOSS/acd/getorf.acd
+share/EMBOSS/acd/helixturnhelix.acd
+share/EMBOSS/acd/iep.acd
+share/EMBOSS/acd/infoseq.acd
+share/EMBOSS/acd/isochore.acd
+share/EMBOSS/acd/lindna.acd
+share/EMBOSS/acd/maskfeat.acd
+share/EMBOSS/acd/maskseq.acd
+share/EMBOSS/acd/matcher.acd
+share/EMBOSS/acd/merger.acd
+share/EMBOSS/acd/msbar.acd
+share/EMBOSS/acd/needle.acd
+share/EMBOSS/acd/newcpgreport.acd
+share/EMBOSS/acd/newcpgseek.acd
+share/EMBOSS/acd/newseq.acd
+share/EMBOSS/acd/noreturn.acd
+share/EMBOSS/acd/nthseq.acd
+share/EMBOSS/acd/octanol.acd
+share/EMBOSS/acd/oddcomp.acd
+share/EMBOSS/acd/palindrome.acd
+share/EMBOSS/acd/pasteseq.acd
+share/EMBOSS/acd/patmatdb.acd
+share/EMBOSS/acd/patmatmotifs.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/pepwindowall.acd
+share/EMBOSS/acd/plotorf.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/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/pscan.acd
+share/EMBOSS/acd/rebaseextract.acd
+share/EMBOSS/acd/redata.acd
+share/EMBOSS/acd/remap.acd
+share/EMBOSS/acd/restrict.acd
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+share/EMBOSS/acd/seqmatchall.acd
+share/EMBOSS/acd/seqret.acd
+share/EMBOSS/acd/seqretall.acd
+share/EMBOSS/acd/seqretset.acd
+share/EMBOSS/acd/seqretsplit.acd
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+share/EMBOSS/acd/seqrettype.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/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/textsearch.acd
+share/EMBOSS/acd/tfextract.acd
+share/EMBOSS/acd/tfscan.acd
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+share/EMBOSS/data/CODONS/Makefile.in
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