Date: Tue, 20 Feb 2001 13:44:51 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/25228: Port update: biology/emboss (MAINTAINER) Message-ID: <E14VBDv-0000jR-00@fling.sanbi.ac.za>
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>Number: 25228 >Category: ports >Synopsis: Port update: biology/emboss (MAINTAINER) >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Feb 20 03:50:01 PST 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - Update EMBOSS suite (biology/emboss) from 1.9.1 to 1.10.0 - One or two other minor fixes, notably to default configuration file >How-To-Repeat: >Fix: diff -ruN emboss.bak/Makefile emboss/Makefile --- emboss.bak/Makefile Tue Feb 20 13:41:58 2001 +++ emboss/Makefile Tue Feb 20 11:39:21 2001 @@ -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 @@ 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 @@ ${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 -ruN emboss.bak/distinfo emboss/distinfo --- emboss.bak/distinfo Tue Feb 20 13:41:58 2001 +++ emboss/distinfo Tue Feb 20 11:22:26 2001 @@ -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 -ruN emboss.bak/files/patch-emboss-acd-emboss.default emboss/files/patch-emboss-acd-emboss.default --- emboss.bak/files/patch-emboss-acd-emboss.default Tue Feb 20 13:41:57 2001 +++ emboss/files/patch-emboss-acd-emboss.default Tue Feb 20 11:54:05 2001 @@ -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 -ruN emboss.bak/pkg-message emboss/pkg-message --- emboss.bak/pkg-message Tue Feb 20 13:41:58 2001 +++ emboss/pkg-message Tue Feb 20 10:36:14 2001 @@ -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 -ruN emboss.bak/pkg-plist emboss/pkg-plist --- emboss.bak/pkg-plist Tue Feb 20 13:41:58 2001 +++ emboss/pkg-plist Tue Feb 20 11:56:19 2001 @@ -83,6 +83,7 @@ bin/descseq bin/diffseq bin/digest +bin/domainer bin/dotmatcher bin/dotpath bin/dottup @@ -109,6 +110,7 @@ bin/infoseq bin/isochore bin/lindna +bin/marscan bin/maskfeat bin/maskseq bin/matcher @@ -121,6 +123,7 @@ bin/newseq bin/noreturn bin/notseq +bin/nrscope bin/nthseq bin/octanol bin/oddcomp @@ -156,6 +159,7 @@ bin/restover bin/restrict bin/revseq +bin/scope bin/seealso bin/seqmatchall bin/seqret @@ -238,6 +242,7 @@ 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/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/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/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/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/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/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/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/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/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/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/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/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 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