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Update to version 1.10.0

Browse Source 
PR: 25228
Submitted by: MAINTAINER
This commit is contained in:
Kevin Lo 2001-02-20 15:51:34 +00:00
parent 685a4695eb
commit 9b3eb6afbe
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=38518
5 changed files with 51 additions and 24 deletions
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10
biology/emboss/Makefile
View File

@ -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}#' \

10
biology/emboss/distinfo
View File

@ -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

30
biology/emboss/files/patch-emboss-acd-emboss.default
View File

@ -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
+
+
+###########################################

5
biology/emboss/pkg-message
View File

@ -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

20
biology/emboss/pkg-plist
View File

@ -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