Update to version 1.10.0

PR: 25228
Submitted by: MAINTAINER

5 files changed, 51 insertions, 24 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 7d7b477bbce9..fc4491ab6234 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.9.1
-PORTREVISION=	1
+PORTVERSION=	1.10.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
@@ -39,7 +38,7 @@ SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
 
 WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
 EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
-EMNU_VERSION=	1.0.3
+EMNU_VERSION=	1.0.4
 MSE_VERSION=	0.0.4
 TOPO_VERSION=	0.1
 PHYLIP_VERSION=	3.573c
@@ -105,7 +104,10 @@ post-install:
 	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
 	  ${MAKE_ARGS} ${INSTALL_TARGET})
 .endfor
-	@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
+	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
+	  ${WRKSRC}/emboss/acd/emboss.default > \
+	  ${PREFIX}/etc/emboss.default.sample && \
+	  ${CHOWN} ${SHAREOWN}:${SHAREGRP} \
 	  ${PREFIX}/etc/emboss.default.sample
 .if !defined(BATCH)
 	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index c4a6dc2e7ca1..24c47e951d8d 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,5 +1,5 @@
-MD5 (emboss/EMBOSS-1.9.1.tar.gz) = 569ff1f9f2df08928b2dfb8ae1a331b9
-MD5 (emboss/EMNU-1.0.3.tar.gz) = 829dedc516e72144563d3a1a77793678
-MD5 (emboss/MSE-0.0.4.tar.gz) = 83b989776fbd59e346a2f90e7dc7f266
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = bb1d9da41c6bfdb47828a7a9e0e40b2f
-MD5 (emboss/TOPO-0.1.tar.gz) = 039b26ed333a3ba6bed20d1caf707834
+MD5 (emboss/EMBOSS-1.10.0.tar.gz) = cfe21d6af3683ad99546a380ac18699b
+MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8
+MD5 (emboss/MSE-0.0.4.tar.gz) = ec94c169918038aa318e035cd7bd2d83
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = e1ca6cb87756836f0e1b3b6b026e826b
+MD5 (emboss/TOPO-0.1.tar.gz) = d570fe3e41380d99646d99b5d1586da1
diff --git a/biology/emboss/files/patch-emboss-acd-emboss.default b/biology/emboss/files/patch-emboss-acd-emboss.default
index 8311f5b23837..1346c5d78ce6 100644
--- a/biology/emboss/files/patch-emboss-acd-emboss.default
+++ b/biology/emboss/files/patch-emboss-acd-emboss.default
@@ -1,6 +1,6 @@
---- emboss/acd/emboss.default.orig	Mon Jan 22 23:26:54 2001
-+++ emboss/acd/emboss.default	Mon Jan 29 16:23:15 2001
-@@ -1,9 +1,26 @@
+--- emboss/acd/emboss.default.orig	Sun Feb 18 16:57:08 2001
++++ emboss/acd/emboss.default	Tue Feb 20 10:45:57 2001
+@@ -1,9 +1,31 @@
 -SET emboss_tempdata /nfs/WWW/data/EMBOSS/test
 +#####################################################
 +### Configuration options for FreeBSD EMBOSS port ###
@@ -8,20 +8,26 @@
  
 -# Logfile - set this to a file that any user can append to
 -# and EMBOSS applications will automatically write log information
-+# This is the compiled-in default.  Change only if
-+# you know what you're doing!
++# The directory where EMBOSS expects to find run-time
++# databases.  This is the compiled-in default - change
++# only if you know what you're doing!
 +#
-+#SET emboss_data /usr/local/share/EMBOSS/data
++#SET emboss_data %%PREFIX%%/share/EMBOSS/data
  
-+# This is where your local databases reside
-+# (this will differ from site to site):
+-#SET emboss_logfile /packages/emboss/emboss/log
++# This is an alias which is internal to this
++# configuration file and is set here merely as a
++# convenience.  It points to the location where you
++# have placed your local databases (this will differ
++# from site to site).
 +#
-+SET emboss_tempdata /var/db/bio
++SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases
 +
-+# Logfile - set this to a file that any user can append to and EMBOSS
-+# applications will automatically write log information
++# Logfile.  If this is uncommented and set to a file
++# that any user can append to, EMBOSS applications
++# will automatically log usage information.
 +#
- #SET emboss_logfile /packages/emboss/emboss/log
++#SET emboss_logfile /var/log/emboss.log
 +
 +
 +###########################################
diff --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message
index 22386f8457b6..1108081f5f0b 100644
--- a/biology/emboss/pkg-message
+++ b/biology/emboss/pkg-message
@@ -2,11 +2,10 @@
 
 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.
+In order to see graphical output from some EMBOSS programs, you will need to
+set the following environment variable in your shell startup file:
 
 - set PLPLOT_LIB to:     "%%PREFIX%%/share/EMBOSS"
-- set EMBOSS_ACDROOT to: "%%PREFIX%%/share/EMBOSS/acd"
 
 NB:  A sample configuration file has been installed to %%PREFIX%%/etc as
 emboss.default.sample.  This must be renamed to emboss.default and edited
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 426f0514ed51..7d5178d51294 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -83,6 +83,7 @@ bin/dbigcg
 bin/descseq
 bin/diffseq
 bin/digest
+bin/domainer
 bin/dotmatcher
 bin/dotpath
 bin/dottup
@@ -109,6 +110,7 @@ bin/iep
 bin/infoseq
 bin/isochore
 bin/lindna
+bin/marscan
 bin/maskfeat
 bin/maskseq
 bin/matcher
@@ -121,6 +123,7 @@ bin/newcpgseek
 bin/newseq
 bin/noreturn
 bin/notseq
+bin/nrscope
 bin/nthseq
 bin/octanol
 bin/oddcomp
@@ -156,6 +159,7 @@ bin/remap
 bin/restover
 bin/restrict
 bin/revseq
+bin/scope
 bin/seealso
 bin/seqmatchall
 bin/seqret
@@ -238,6 +242,7 @@ share/EMBOSS/acd/demotable.acd
 share/EMBOSS/acd/descseq.acd
 share/EMBOSS/acd/diffseq.acd
 share/EMBOSS/acd/digest.acd
+share/EMBOSS/acd/domainer.acd
 share/EMBOSS/acd/dotmatcher.acd
 share/EMBOSS/acd/dotpath.acd
 share/EMBOSS/acd/dottup.acd
@@ -267,6 +272,7 @@ share/EMBOSS/acd/iep.acd
 share/EMBOSS/acd/infoseq.acd
 share/EMBOSS/acd/isochore.acd
 share/EMBOSS/acd/lindna.acd
+share/EMBOSS/acd/marscan.acd
 share/EMBOSS/acd/maskfeat.acd
 share/EMBOSS/acd/maskseq.acd
 share/EMBOSS/acd/matcher.acd
@@ -279,6 +285,7 @@ share/EMBOSS/acd/newcpgseek.acd
 share/EMBOSS/acd/newseq.acd
 share/EMBOSS/acd/noreturn.acd
 share/EMBOSS/acd/notseq.acd
+share/EMBOSS/acd/nrscope.acd
 share/EMBOSS/acd/nthseq.acd
 share/EMBOSS/acd/octanol.acd
 share/EMBOSS/acd/oddcomp.acd
@@ -338,6 +345,7 @@ share/EMBOSS/acd/sigcleave.acd
 share/EMBOSS/acd/silent.acd
 share/EMBOSS/acd/simplesw.acd
 share/EMBOSS/acd/splitter.acd
+share/EMBOSS/acd/stamps.acd
 share/EMBOSS/acd/stretcher.acd
 share/EMBOSS/acd/stssearch.acd
 share/EMBOSS/acd/supermatcher.acd
@@ -789,6 +797,7 @@ share/doc/EMBOSS/programs/html/dnapars.html
 share/doc/EMBOSS/programs/html/dnapenny.html
 share/doc/EMBOSS/programs/html/dollop.html
 share/doc/EMBOSS/programs/html/dolpenny.html
+share/doc/EMBOSS/programs/html/domainer.html
 share/doc/EMBOSS/programs/html/dotmatcher.html
 share/doc/EMBOSS/programs/html/dotmatcher0.gif
 share/doc/EMBOSS/programs/html/dotpath.html
@@ -854,6 +863,7 @@ share/doc/EMBOSS/programs/html/isochore.html
 share/doc/EMBOSS/programs/html/isochore0.gif
 share/doc/EMBOSS/programs/html/kitsch.html
 share/doc/EMBOSS/programs/html/lindna.html
+share/doc/EMBOSS/programs/html/marscan.html
 share/doc/EMBOSS/programs/html/maskfeat.html
 share/doc/EMBOSS/programs/html/maskseq.html
 share/doc/EMBOSS/programs/html/matcher.html
@@ -873,6 +883,7 @@ 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/nrscope.html
 share/doc/EMBOSS/programs/html/nthseq.html
 share/doc/EMBOSS/programs/html/octanol.html
 share/doc/EMBOSS/programs/html/octanol0.gif
@@ -919,6 +930,7 @@ share/doc/EMBOSS/programs/html/protdist.html
 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/protein_structure_group.html
 share/doc/EMBOSS/programs/html/pscan.html
 share/doc/EMBOSS/programs/html/re_group.html
 share/doc/EMBOSS/programs/html/rebaseextract.html
@@ -928,8 +940,11 @@ 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/restover.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/scope.html
 share/doc/EMBOSS/programs/html/secondary_structure_group.html
 share/doc/EMBOSS/programs/html/seealso.html
 share/doc/EMBOSS/programs/html/seqboot.html
@@ -1022,6 +1037,7 @@ share/doc/EMBOSS/programs/text/dnapars.txt
 share/doc/EMBOSS/programs/text/dnapenny.txt
 share/doc/EMBOSS/programs/text/dollop.txt
 share/doc/EMBOSS/programs/text/dolpenny.txt
+share/doc/EMBOSS/programs/text/domainer.txt
 share/doc/EMBOSS/programs/text/dotmatcher.txt
 share/doc/EMBOSS/programs/text/dotpath.txt
 share/doc/EMBOSS/programs/text/dottup.txt
@@ -1077,6 +1093,7 @@ share/doc/EMBOSS/programs/text/infoseq.txt
 share/doc/EMBOSS/programs/text/isochore.txt
 share/doc/EMBOSS/programs/text/kitsch.txt
 share/doc/EMBOSS/programs/text/lindna.txt
+share/doc/EMBOSS/programs/text/marscan.txt
 share/doc/EMBOSS/programs/text/maskfeat.txt
 share/doc/EMBOSS/programs/text/maskseq.txt
 share/doc/EMBOSS/programs/text/matcher.txt
@@ -1092,6 +1109,7 @@ 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/nrscope.txt
 share/doc/EMBOSS/programs/text/nthseq.txt
 share/doc/EMBOSS/programs/text/octanol.txt
 share/doc/EMBOSS/programs/text/oddcomp.txt
@@ -1127,8 +1145,10 @@ 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
+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/scope.txt
 share/doc/EMBOSS/programs/text/seealso.txt
 share/doc/EMBOSS/programs/text/seqboot.txt
 share/doc/EMBOSS/programs/text/seqmatchall.txt