Upgrade to version 1.9.0

PR: 24597
Submitted by: MAINTAINER

6 files changed, 47 insertions, 13 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index cf034e5..23e0b1f 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.8.0
+PORTVERSION=	1.9.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
@@ -23,6 +23,7 @@ LIB_DEPENDS=	gd.1:${PORTSDIR}/graphics/gd \
 USE_GMAKE=	yes
 USE_LIBTOOL=	yes
 USE_XLIB=	yes
+USE_MOTIF=	yes
 PLIST=		${WRKDIR}/pkg-plist
 PKGMESSAGE=	${WRKDIR}/pkg-message
 
@@ -31,7 +32,7 @@ PKGMESSAGE=	${WRKDIR}/pkg-message
 .endif
 
 CONFIGURE_ENV+=	CPPFLAGS="-I${LOCALBASE}/include/gd" \
-		LIBS="-L${LOCALBASE}/lib"
+		LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
 
 SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
 		MKDIR="${MKDIR}" \
@@ -39,10 +40,11 @@ SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
 
 WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
 EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
-PHYLIP_VERSION=	3.573c
+EMNU_VERSION=	1.0.2
 MSE_VERSION=	0.0.4
 TOPO_VERSION=	0.1
-.for app in MSE PHYLIP TOPO
+PHYLIP_VERSION=	3.573c
+.for app in EMNU MSE PHYLIP TOPO
 SCRIPTS_ENV+=	${app}_VERSION="${${app}_VERSION}"
 .if defined(WITH_${app})
 APPLIST+=	${app}
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index 1eed31a..fce228f 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,4 +1,5 @@
-MD5 (emboss/EMBOSS-1.8.0.tar.gz) = 4f4b54f5e2c3e053baaffb19f258ad2a
-MD5 (emboss/MSE-0.0.4.tar.gz) = 0585be481f33eb71ceadee89b339f86e
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 7186d27d0909ffb5481720ec41d99222
-MD5 (emboss/TOPO-0.1.tar.gz) = a8709a31b1fc2f5914365d87b7120e72
+MD5 (emboss/EMBOSS-1.9.0.tar.gz) = f2b0ea093986df4f67428b2614583a7c
+MD5 (emboss/EMNU-1.0.2.tar.gz) = 86a8ad78d25de4b56e251a266a64f46b
+MD5 (emboss/MSE-0.0.4.tar.gz) = 28652ee772f31ced0e62415d8770311f
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = a868fbf7bbee8d97b566be6794f51eb3
+MD5 (emboss/TOPO-0.1.tar.gz) = 83c76fddd2cb64d90eed4e7bb4ac0d29
diff --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr
index 37865f3..1f61ba6 100644
--- a/biology/emboss/pkg-descr
+++ b/biology/emboss/pkg-descr
@@ -12,8 +12,8 @@ core libraries which are under the LGPL.
 
 EMBASSY packages are third party applications which have been integrated with
 the EMBOSS suite, but which are not included in the base EMBOSS distribution
-for licensing or other reasons.  This port includes the three currently
-available EMBASSY applications - MSE, PHYLIP and TOPO.  During an interactive
+for licensing or other reasons.  This port includes the currently available
+EMBASSY applications - EMNU, MSE, PHYLIP and TOPO.  During an interactive
 install the user will be asked to choose which of these will be installed
 (default: all).  Note that the EMBASSY version of PHYLIP should not clash
 with the standalone Phylip application due to the fact that its binaries have
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 0c277d0..1cba313 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -1,3 +1,4 @@
+bin/abiview
 bin/acdc
 bin/antigenic
 bin/backtranseq
@@ -61,6 +62,7 @@ bin/newcpgreport
 bin/newcpgseek
 bin/newseq
 bin/noreturn
+bin/notseq
 bin/nthseq
 bin/octanol
 bin/oddcomp
@@ -90,8 +92,10 @@ bin/prophet
 bin/prosextract
 bin/pscan
 bin/rebaseextract
+bin/recode
 bin/redata
 bin/remap
+bin/restover
 bin/restrict
 bin/revseq
 bin/seealso
@@ -138,6 +142,7 @@ lib/libnucleus.so.1
 lib/libplplot.a
 lib/libplplot.so
 lib/libplplot.so.4
+share/EMBOSS/acd/abiview.acd
 share/EMBOSS/acd/ajbad.acd
 share/EMBOSS/acd/ajfeatest.acd
 share/EMBOSS/acd/ajtest.acd
@@ -215,6 +220,7 @@ share/EMBOSS/acd/newcpgreport.acd
 share/EMBOSS/acd/newcpgseek.acd
 share/EMBOSS/acd/newseq.acd
 share/EMBOSS/acd/noreturn.acd
+share/EMBOSS/acd/notseq.acd
 share/EMBOSS/acd/nthseq.acd
 share/EMBOSS/acd/octanol.acd
 share/EMBOSS/acd/oddcomp.acd
@@ -247,8 +253,10 @@ share/EMBOSS/acd/prosextract.acd
 share/EMBOSS/acd/proteinmotifsearch.acd
 share/EMBOSS/acd/pscan.acd
 share/EMBOSS/acd/rebaseextract.acd
+share/EMBOSS/acd/recode.acd
 share/EMBOSS/acd/redata.acd
 share/EMBOSS/acd/remap.acd
+share/EMBOSS/acd/restover.acd
 share/EMBOSS/acd/restrict.acd
 share/EMBOSS/acd/revseq.acd
 share/EMBOSS/acd/scope.acd
@@ -468,7 +476,11 @@ share/EMBOSS/data/EGC.12
 share/EMBOSS/data/EGC.13
 share/EMBOSS/data/EGC.14
 share/EMBOSS/data/EGC.15
+share/EMBOSS/data/EGC.16
 share/EMBOSS/data/EGC.2
+share/EMBOSS/data/EGC.21
+share/EMBOSS/data/EGC.22
+share/EMBOSS/data/EGC.23
 share/EMBOSS/data/EGC.3
 share/EMBOSS/data/EGC.4
 share/EMBOSS/data/EGC.5
@@ -660,11 +672,15 @@ share/doc/EMBOSS/manuals/admin.sty
 share/doc/EMBOSS/manuals/admin.tex
 share/doc/EMBOSS/manuals/program.ps.gz
 share/doc/EMBOSS/programs/html/SITE-DIRECTED.html
+share/doc/EMBOSS/programs/html/abi_trace_files_group.html
+share/doc/EMBOSS/programs/html/abiview.html
+share/doc/EMBOSS/programs/html/abiview0.gif
 share/doc/EMBOSS/programs/html/alignment_global_group.html
 share/doc/EMBOSS/programs/html/alignment_group.html
 share/doc/EMBOSS/programs/html/alignment_local_group.html
 share/doc/EMBOSS/programs/html/alignment_multiple_group.html
 share/doc/EMBOSS/programs/html/antigenic.html
+share/doc/EMBOSS/programs/html/assorted_group.html
 share/doc/EMBOSS/programs/html/backtranseq.html
 share/doc/EMBOSS/programs/html/banana.html
 share/doc/EMBOSS/programs/html/banana0.gif
@@ -743,6 +759,7 @@ share/doc/EMBOSS/programs/html/emboss_icon.gif
 share/doc/EMBOSS/programs/html/embossdata.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
@@ -783,6 +800,7 @@ 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/menus_group.html
 share/doc/EMBOSS/programs/html/merger.html
 share/doc/EMBOSS/programs/html/mix.html
 share/doc/EMBOSS/programs/html/motifs_group.html
@@ -796,6 +814,7 @@ 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/notseq.html
 share/doc/EMBOSS/programs/html/nthseq.html
 share/doc/EMBOSS/programs/html/octanol.html
 share/doc/EMBOSS/programs/html/octanol0.gif
@@ -843,14 +862,15 @@ share/doc/EMBOSS/programs/html/protein_sequence_composition_group.html
 share/doc/EMBOSS/programs/html/protein_sequence_features_group.html
 share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html
 share/doc/EMBOSS/programs/html/pscan.html
+share/doc/EMBOSS/programs/html/re_group.html
 share/doc/EMBOSS/programs/html/rebaseextract.html
+share/doc/EMBOSS/programs/html/recode.html
 share/doc/EMBOSS/programs/html/redata.html
 share/doc/EMBOSS/programs/html/reformatting_group.html
 share/doc/EMBOSS/programs/html/remap.html
 share/doc/EMBOSS/programs/html/repeats_group.html
 share/doc/EMBOSS/programs/html/restml.html
 share/doc/EMBOSS/programs/html/restrict.html
-share/doc/EMBOSS/programs/html/restriction_enzymes_group.html
 share/doc/EMBOSS/programs/html/revseq.html
 share/doc/EMBOSS/programs/html/secondary_structure_group.html
 share/doc/EMBOSS/programs/html/seealso.html
@@ -864,6 +884,7 @@ share/doc/EMBOSS/programs/html/sequence_comparison_group.html
 share/doc/EMBOSS/programs/html/sequence_composition_group.html
 share/doc/EMBOSS/programs/html/sequence_display_group.html
 share/doc/EMBOSS/programs/html/sequence_editing_group.html
+share/doc/EMBOSS/programs/html/sequence_features_group.html
 share/doc/EMBOSS/programs/html/sequence_information_group.html
 share/doc/EMBOSS/programs/html/showdb.html
 share/doc/EMBOSS/programs/html/showfeat.html
@@ -904,6 +925,7 @@ 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/SITE-DIRECTED.txt
+share/doc/EMBOSS/programs/text/abiview.txt
 share/doc/EMBOSS/programs/text/antigenic.txt
 share/doc/EMBOSS/programs/text/backtranseq.txt
 share/doc/EMBOSS/programs/text/banana.txt
@@ -967,6 +989,7 @@ share/doc/EMBOSS/programs/text/ekitsch.txt
 share/doc/EMBOSS/programs/text/embossdata.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
@@ -1010,6 +1033,7 @@ 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/notseq.txt
 share/doc/EMBOSS/programs/text/nthseq.txt
 share/doc/EMBOSS/programs/text/octanol.txt
 share/doc/EMBOSS/programs/text/oddcomp.txt
@@ -1041,6 +1065,7 @@ share/doc/EMBOSS/programs/text/prosextract.txt
 share/doc/EMBOSS/programs/text/protdist.txt
 share/doc/EMBOSS/programs/text/pscan.txt
 share/doc/EMBOSS/programs/text/rebaseextract.txt
+share/doc/EMBOSS/programs/text/recode.txt
 share/doc/EMBOSS/programs/text/redata.txt
 share/doc/EMBOSS/programs/text/remap.txt
 share/doc/EMBOSS/programs/text/restml.txt
diff --git a/biology/emboss/pkg-plist.EMNU b/biology/emboss/pkg-plist.EMNU
new file mode 100644
index 0000000..fcb7fe6
--- /dev/null
+++ b/biology/emboss/pkg-plist.EMNU
@@ -0,0 +1,2 @@
+bin/emnu
+share/EMBOSS/acd/emnu.acd
diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss
index a17b495..b5ad734 100644
--- a/biology/emboss/scripts/configure.emboss
+++ b/biology/emboss/scripts/configure.emboss
@@ -5,13 +5,14 @@ if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then
 fi
 
 if [ "${BATCH}" ]; then
-  set \"MSE\" \"PHYLIP\" \"TOPO\"
+  set \"EMNU\" \"MSE\" \"PHYLIP\" \"TOPO\"
 else
   /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \
   --checklist "\n\
 These third party applications have been adapted to
 function as part of EMBOSS.\n
-Please select EMBASSY applications to install:" -1 -1 3 \
+Please select EMBASSY applications to install:" -1 -1 4 \
+EMNU	"v${EMNU_VERSION} - Text-based menu" ON \
 MSE	"v${MSE_VERSION} - Phylogeny inference" ON \
 PHYLIP	"v${PHYLIP_VERSION} - Sequence editor" ON \
 TOPO	"v${TOPO_VERSION} - Transmembrane display" ON \
@@ -42,6 +43,9 @@ exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
 
 while [ "$1" ]; do
   case $1 in
+    \"EMNU\")
+      echo "WITH_EMNU=	yes"
+    ;;
     \"MSE\")
       echo "WITH_MSE=	yes"
     ;;