Date: Wed, 30 May 2001 13:08:21 +0200 (SAST) From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/27768: Port update: biology/emboss (MAINTAINER) Message-ID: <200105301108.f4UB8LC96799@shuffle.egenetics.com>
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>Number: 27768 >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: Wed May 30 04:10:01 PDT 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - Update the EMBOSS suite (biology/emboss) to version 1.13.1 - Added file: files/patch-emboss-emboss.default.template - Deleted file: files/patch-emboss-acd-emboss.default >How-To-Repeat: >Fix: Binary files emboss.bak/.Makefile.swp and emboss/.Makefile.swp differ diff -ruN emboss.bak/Makefile emboss/Makefile --- emboss.bak/Makefile Wed May 30 13:05:42 2001 +++ emboss/Makefile Wed May 30 10:05:16 2001 @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 1.12.0 +PORTVERSION= 1.13.1 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ \ @@ -42,6 +42,7 @@ TOPO_VERSION= 0.1 PHYLIP_VERSION= 3.573c DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html +CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template .for app in EMNU MSE PHYLIP TOPO SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}" @@ -104,8 +105,7 @@ ${MAKE_ARGS} ${INSTALL_TARGET}) .endfor @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \ - ${WRKSRC}/emboss/acd/emboss.default > \ - ${PREFIX}/etc/emboss.default.sample && \ + ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \ ${CHOWN} ${SHAREOWN}:${SHAREGRP} \ ${PREFIX}/etc/emboss.default.sample .if !defined(BATCH) diff -ruN emboss.bak/distinfo emboss/distinfo --- emboss.bak/distinfo Wed May 30 13:05:42 2001 +++ emboss/distinfo Tue May 29 18:06:09 2001 @@ -1,5 +1,5 @@ -MD5 (emboss/EMBOSS-1.12.0.tar.gz) = 7d2d770dcc037624e5ee52c143c8923b +MD5 (emboss/EMBOSS-1.13.1.tar.gz) = 313440f1c5f41cb8615f01dfba445358 MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8 -MD5 (emboss/MSE-0.0.4.tar.gz) = f490638c4f0b789d0c1117513406d76a -MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4a4fff45f4a51a430731a46f3f37f37f -MD5 (emboss/TOPO-0.1.tar.gz) = fa1a85bfde1054136af5aa9587c2433f +MD5 (emboss/MSE-0.0.4.tar.gz) = 8b5e9cb6919be5cae1ea977ea7327e79 +MD5 (emboss/PHYLIP-3.573c.tar.gz) = c001525bfbedc8903da34d859eeedf0c +MD5 (emboss/TOPO-0.1.tar.gz) = c3ea9c55af1d48644f9096ac793cc5a1 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 Wed May 30 13:05:42 2001 +++ emboss/files/patch-emboss-acd-emboss.default Thu Jan 1 02:00:00 1970 @@ -1,38 +0,0 @@ ---- 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 ### -+##################################################### - --# Logfile - set this to a file that any user can append to --# and EMBOSS applications will automatically write log information -+# 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 %%PREFIX%%/share/EMBOSS/data - --#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 %%PREFIX%%/share/EMBOSS/databases -+ -+# 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 /var/log/emboss.log -+ -+ -+########################################### -+### Configuration options for databases ### -+########################################### - - # swissprot (Puffer fish entries) - # ========= diff -ruN emboss.bak/files/patch-emboss-emboss.default.template emboss/files/patch-emboss-emboss.default.template --- emboss.bak/files/patch-emboss-emboss.default.template Thu Jan 1 02:00:00 1970 +++ emboss/files/patch-emboss-emboss.default.template Wed May 30 10:25:55 2001 @@ -0,0 +1,38 @@ +--- emboss/emboss.default.template.orig Thu May 24 19:36:39 2001 ++++ emboss/emboss.default.template Wed May 30 10:23:48 2001 +@@ -1,9 +1,31 @@ +-#SET emboss_tempdata name_of_emboss_test_database_directory ++##################################################### ++### Configuration options for FreeBSD EMBOSS port ### ++##################################################### + +-# Logfile - set this to a file that any user can append to +-# and EMBOSS applications will automatically write log information ++# 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 %%PREFIX%%/share/EMBOSS/data + +-#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 %%PREFIX%%/share/EMBOSS/databases ++ ++# 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 /var/log/emboss.log ++ ++ ++########################################### ++### Configuration options for databases ### ++########################################### + + # swissprot (Puffer fish entries) + # ========= diff -ruN emboss.bak/pkg-plist emboss/pkg-plist --- emboss.bak/pkg-plist Wed May 30 13:05:42 2001 +++ emboss/pkg-plist Wed May 30 12:45:02 2001 @@ -93,6 +93,7 @@ bin/dreg bin/einverted bin/embossdata +bin/embossversion bin/emma bin/emowse bin/entret @@ -157,7 +158,7 @@ bin/prosextract bin/pscan bin/rebaseextract -bin/recode +bin/recoder bin/redata bin/remap bin/restover @@ -171,6 +172,7 @@ bin/seqretall bin/seqretset bin/seqretsplit +bin/showalign bin/showdb bin/showfeat bin/showorf @@ -255,8 +257,8 @@ share/EMBOSS/acd/dottup.acd share/EMBOSS/acd/dreg.acd share/EMBOSS/acd/einverted.acd -share/EMBOSS/acd/emboss.default share/EMBOSS/acd/embossdata.acd +share/EMBOSS/acd/embossversion.acd share/EMBOSS/acd/emma.acd share/EMBOSS/acd/emowse.acd share/EMBOSS/acd/entrails.acd @@ -326,7 +328,7 @@ share/EMBOSS/acd/proteinmotifsearch.acd share/EMBOSS/acd/pscan.acd share/EMBOSS/acd/rebaseextract.acd -share/EMBOSS/acd/recode.acd +share/EMBOSS/acd/recoder.acd share/EMBOSS/acd/redata.acd share/EMBOSS/acd/remap.acd share/EMBOSS/acd/restover.acd @@ -344,6 +346,7 @@ share/EMBOSS/acd/seqretsplit.acd share/EMBOSS/acd/seqrettype.acd share/EMBOSS/acd/seqtofeat.acd +share/EMBOSS/acd/showalign.acd share/EMBOSS/acd/showdb.acd share/EMBOSS/acd/showfeat.acd share/EMBOSS/acd/showorf.acd @@ -646,6 +649,7 @@ share/EMBOSS/data/PROSITE/dummyfile share/EMBOSS/data/REBASE/dummyfile share/EMBOSS/data/embossre.equ +share/EMBOSS/emboss.default.template share/EMBOSS/plstnd5.fnt share/EMBOSS/plxtnd5.fnt share/EMBOSS/test/data/dna.acedb @@ -674,6 +678,7 @@ share/EMBOSS/test/data/dna.staden share/EMBOSS/test/data/dna.strider share/EMBOSS/test/data/dna.text +share/EMBOSS/test/data/paamir.pep share/EMBOSS/test/data/prot.acedb share/EMBOSS/test/data/prot.codata share/EMBOSS/test/data/prot.fasta @@ -695,6 +700,7 @@ share/EMBOSS/test/embl/division.lkp share/EMBOSS/test/embl/entrynam.idx share/EMBOSS/test/embl/est.dat +share/EMBOSS/test/embl/fun.dat share/EMBOSS/test/embl/hum1.dat share/EMBOSS/test/embl/inv.dat share/EMBOSS/test/embl/pro.dat @@ -755,14 +761,127 @@ share/doc/EMBOSS/manuals/emboss_qg.pdf share/doc/EMBOSS/manuals/emboss_qg.ps share/doc/EMBOSS/manuals/program.ps.gz +share/doc/EMBOSS/programs/html/abiview.html share/doc/EMBOSS/programs/html/abiview0.gif +share/doc/EMBOSS/programs/html/alignment_consensus_group.html +share/doc/EMBOSS/programs/html/alignment_differences_group.html +share/doc/EMBOSS/programs/html/alignment_dot_plots_group.html +share/doc/EMBOSS/programs/html/alignment_global_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/backtranseq.html +share/doc/EMBOSS/programs/html/banana.html share/doc/EMBOSS/programs/html/banana0.gif +share/doc/EMBOSS/programs/html/btwisted.html +share/doc/EMBOSS/programs/html/cai.html +share/doc/EMBOSS/programs/html/chaos.html share/doc/EMBOSS/programs/html/chaos0.gif +share/doc/EMBOSS/programs/html/charge.html +share/doc/EMBOSS/programs/html/checktrans.html +share/doc/EMBOSS/programs/html/chips.html +share/doc/EMBOSS/programs/html/cirdna.html +share/doc/EMBOSS/programs/html/clique.html +share/doc/EMBOSS/programs/html/codcmp.html +share/doc/EMBOSS/programs/html/coderet.html +share/doc/EMBOSS/programs/html/compseq.html +share/doc/EMBOSS/programs/html/cons.html +share/doc/EMBOSS/programs/html/consense.html +share/doc/EMBOSS/programs/html/contml.html +share/doc/EMBOSS/programs/html/contrast.html +share/doc/EMBOSS/programs/html/cpgplot.html 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+share/doc/EMBOSS/programs/html/eseqboot.html +share/doc/EMBOSS/programs/html/est2genome.html +share/doc/EMBOSS/programs/html/etandem.html +share/doc/EMBOSS/programs/html/extractseq.html +share/doc/EMBOSS/programs/html/factor.html +share/doc/EMBOSS/programs/html/feature_tables_group.html +share/doc/EMBOSS/programs/html/findkm.html share/doc/EMBOSS/programs/html/findkm0.gif +share/doc/EMBOSS/programs/html/fitch.html +share/doc/EMBOSS/programs/html/freak.html +share/doc/EMBOSS/programs/html/fuzznuc.html +share/doc/EMBOSS/programs/html/fuzzpro.html +share/doc/EMBOSS/programs/html/fuzztran.html +share/doc/EMBOSS/programs/html/garnier.html +share/doc/EMBOSS/programs/html/geecee.html +share/doc/EMBOSS/programs/html/gendist.html +share/doc/EMBOSS/programs/html/getorf.html +share/doc/EMBOSS/programs/html/groups.html +share/doc/EMBOSS/programs/html/helixturnhelix.html +share/doc/EMBOSS/programs/html/hmoment.html +share/doc/EMBOSS/programs/html/iep.html +share/doc/EMBOSS/programs/html/index.html +share/doc/EMBOSS/programs/html/information_group.html +share/doc/EMBOSS/programs/html/infoseq.html +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.gif share/doc/EMBOSS/programs/html/lindna.html share/doc/EMBOSS/programs/html/marscan.html share/doc/EMBOSS/programs/html/maskfeat.html @@ -772,13 +891,10 @@ 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 share/doc/EMBOSS/programs/html/msbar.html share/doc/EMBOSS/programs/html/mse.html -share/doc/EMBOSS/programs/html/mutation_group.html share/doc/EMBOSS/programs/html/needle.html share/doc/EMBOSS/programs/html/neighbor.html -share/doc/EMBOSS/programs/html/new_group_group.html share/doc/EMBOSS/programs/html/newcpgreport.html share/doc/EMBOSS/programs/html/newcpgseek.html share/doc/EMBOSS/programs/html/newseq.html @@ -786,70 +902,86 @@ 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/nucleic_2d_structure_group.html +share/doc/EMBOSS/programs/html/nucleic_codon_usage_group.html +share/doc/EMBOSS/programs/html/nucleic_composition_group.html +share/doc/EMBOSS/programs/html/nucleic_cpg_islands_group.html +share/doc/EMBOSS/programs/html/nucleic_gene_finding_group.html +share/doc/EMBOSS/programs/html/nucleic_motifs_group.html +share/doc/EMBOSS/programs/html/nucleic_mutation_group.html +share/doc/EMBOSS/programs/html/nucleic_primers_group.html +share/doc/EMBOSS/programs/html/nucleic_profiles_group.html +share/doc/EMBOSS/programs/html/nucleic_repeats_group.html +share/doc/EMBOSS/programs/html/nucleic_restriction_group.html +share/doc/EMBOSS/programs/html/nucleic_transcription_group.html +share/doc/EMBOSS/programs/html/nucleic_translation_group.html share/doc/EMBOSS/programs/html/octanol.html +share/doc/EMBOSS/programs/html/octanol0.gif share/doc/EMBOSS/programs/html/oddcomp.html share/doc/EMBOSS/programs/html/palindrome.html share/doc/EMBOSS/programs/html/pasteseq.html share/doc/EMBOSS/programs/html/patmatdb.html share/doc/EMBOSS/programs/html/patmatmotifs.html -share/doc/EMBOSS/programs/html/pattern_matching_group.html share/doc/EMBOSS/programs/html/penny.html share/doc/EMBOSS/programs/html/pepcoil.html share/doc/EMBOSS/programs/html/pepinfo.html +share/doc/EMBOSS/programs/html/pepinfo1.gif +share/doc/EMBOSS/programs/html/pepinfo2.gif share/doc/EMBOSS/programs/html/pepnet.html +share/doc/EMBOSS/programs/html/pepnet0.gif share/doc/EMBOSS/programs/html/pepstats.html share/doc/EMBOSS/programs/html/pepwheel.html +share/doc/EMBOSS/programs/html/pepwheel0.gif share/doc/EMBOSS/programs/html/pepwindow.html +share/doc/EMBOSS/programs/html/pepwindow0.gif share/doc/EMBOSS/programs/html/pepwindowall.html 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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/protein_2d_structure_group.html +share/doc/EMBOSS/programs/html/protein_3d_structure_group.html +share/doc/EMBOSS/programs/html/protein_composition_group.html +share/doc/EMBOSS/programs/html/protein_motifs_group.html +share/doc/EMBOSS/programs/html/protein_mutation_group.html +share/doc/EMBOSS/programs/html/protein_profiles_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/recoder.html share/doc/EMBOSS/programs/html/redata.html 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