Update the EMBOSS suite (biology/emboss) to version 1.12.0
PR: 27179 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
This commit is contained in:
James E. Housley
parent
ef5b919982
commit
cd9bb0cadd
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=42360
@ -6,7 +6,7 @@
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#
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PORTNAME= emboss
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PORTVERSION= 1.11.0
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PORTVERSION= 1.12.0
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
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ftp://ftp.no.embnet.org/pub/EMBOSS/ \
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@ -1,5 +1,5 @@
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MD5 (emboss/EMBOSS-1.11.0.tar.gz) = b7376e98ea7d86eb4b5411013bd98dd3
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MD5 (emboss/EMBOSS-1.12.0.tar.gz) = 7d2d770dcc037624e5ee52c143c8923b
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MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8
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MD5 (emboss/MSE-0.0.4.tar.gz) = 96f87f4f321e6c6d65793391971504a1
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MD5 (emboss/PHYLIP-3.573c.tar.gz) = d6062201d6492676c82f2b7b8e9d8c95
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MD5 (emboss/TOPO-0.1.tar.gz) = ab3ff940e689d044476528b47e983184
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MD5 (emboss/MSE-0.0.4.tar.gz) = f490638c4f0b789d0c1117513406d76a
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MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4a4fff45f4a51a430731a46f3f37f37f
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MD5 (emboss/TOPO-0.1.tar.gz) = fa1a85bfde1054136af5aa9587c2433f
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@ -62,6 +62,7 @@ bin/antigenic
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bin/backtranseq
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bin/banana
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bin/btwisted
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bin/cai
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bin/chaos
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bin/charge
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bin/checktrans
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@ -84,6 +85,7 @@ bin/degapseq
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bin/descseq
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bin/diffseq
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bin/digest
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bin/distmat
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bin/domainer
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bin/dotmatcher
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bin/dotpath
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@ -161,6 +163,7 @@ bin/remap
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bin/restover
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bin/restrict
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bin/revseq
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bin/scopalign
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bin/scope
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bin/seealso
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bin/seqmatchall
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@ -215,6 +218,7 @@ share/EMBOSS/acd/antigenic.acd
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share/EMBOSS/acd/backtranseq.acd
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share/EMBOSS/acd/banana.acd
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share/EMBOSS/acd/btwisted.acd
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share/EMBOSS/acd/cai.acd
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share/EMBOSS/acd/chaos.acd
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share/EMBOSS/acd/charge.acd
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share/EMBOSS/acd/checktrans.acd
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@ -738,134 +742,27 @@ share/EMBOSS/test/wormpep/acnum.trg
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share/EMBOSS/test/wormpep/division.lkp
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share/EMBOSS/test/wormpep/entrynam.idx
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share/EMBOSS/test/wormpep/wormpep
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share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt
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share/doc/EMBOSS/manuals/admin.aux
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share/doc/EMBOSS/manuals/admin.dvi
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share/doc/EMBOSS/manuals/admin.log
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share/doc/EMBOSS/manuals/admin.pdf
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share/doc/EMBOSS/manuals/admin.ps
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share/doc/EMBOSS/manuals/admin.sty
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share/doc/EMBOSS/manuals/admin.tex
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share/doc/EMBOSS/manuals/admin.toc
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share/doc/EMBOSS/manuals/adminguide.tar.gz
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share/doc/EMBOSS/manuals/emboss_qg.pdf
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share/doc/EMBOSS/manuals/emboss_qg.ps
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share/doc/EMBOSS/manuals/program.ps.gz
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share/doc/EMBOSS/programs/html/SITE-DIRECTED.html
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share/doc/EMBOSS/programs/html/abi_trace_files_group.html
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share/doc/EMBOSS/programs/html/abiview.html
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share/doc/EMBOSS/programs/html/abiview0.gif
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share/doc/EMBOSS/programs/html/alignment_global_group.html
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share/doc/EMBOSS/programs/html/alignment_group.html
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share/doc/EMBOSS/programs/html/alignment_local_group.html
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share/doc/EMBOSS/programs/html/alignment_multiple_group.html
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share/doc/EMBOSS/programs/html/antigenic.html
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share/doc/EMBOSS/programs/html/assorted_group.html
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share/doc/EMBOSS/programs/html/backtranseq.html
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share/doc/EMBOSS/programs/html/banana.html
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share/doc/EMBOSS/programs/html/banana0.gif
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share/doc/EMBOSS/programs/html/btwisted.html
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share/doc/EMBOSS/programs/html/chaos.html
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share/doc/EMBOSS/programs/html/chaos0.gif
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share/doc/EMBOSS/programs/html/checktrans.html
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share/doc/EMBOSS/programs/html/chips.html
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share/doc/EMBOSS/programs/html/cirdna.html
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share/doc/EMBOSS/programs/html/clique.html
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share/doc/EMBOSS/programs/html/codcmp.html
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share/doc/EMBOSS/programs/html/coderet.html
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share/doc/EMBOSS/programs/html/coding_regions_group.html
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share/doc/EMBOSS/programs/html/comparison_group.html
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share/doc/EMBOSS/programs/html/compseq.html
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share/doc/EMBOSS/programs/html/cons.html
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share/doc/EMBOSS/programs/html/consense.html
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share/doc/EMBOSS/programs/html/contml.html
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share/doc/EMBOSS/programs/html/contrast.html
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share/doc/EMBOSS/programs/html/cpg_islands_group.html
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share/doc/EMBOSS/programs/html/cpgplot.html
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share/doc/EMBOSS/programs/html/cpgplot0.gif
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share/doc/EMBOSS/programs/html/cpgreport.html
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share/doc/EMBOSS/programs/html/cusp.html
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share/doc/EMBOSS/programs/html/cutseq.html
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share/doc/EMBOSS/programs/html/dan.html
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share/doc/EMBOSS/programs/html/database_entry_extraction_group.html
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share/doc/EMBOSS/programs/html/database_indexing_group.html
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share/doc/EMBOSS/programs/html/database_information_group.html
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share/doc/EMBOSS/programs/html/dbiblast.html
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share/doc/EMBOSS/programs/html/dbifasta.html
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share/doc/EMBOSS/programs/html/dbiflat.html
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share/doc/EMBOSS/programs/html/dbigcg.html
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share/doc/EMBOSS/programs/html/degapseq.html
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share/doc/EMBOSS/programs/html/descseq.html
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share/doc/EMBOSS/programs/html/diffseq.html
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share/doc/EMBOSS/programs/html/digest.html
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share/doc/EMBOSS/programs/html/display_alignment_multiple_group.html
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share/doc/EMBOSS/programs/html/dna_sequence_composition_group.html
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share/doc/EMBOSS/programs/html/dna_sequence_features_group.html
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share/doc/EMBOSS/programs/html/dna_sequence_properties_group.html
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share/doc/EMBOSS/programs/html/dnacomp.html
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share/doc/EMBOSS/programs/html/dnadist.html
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share/doc/EMBOSS/programs/html/dnainvar.html
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share/doc/EMBOSS/programs/html/dnaml.html
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share/doc/EMBOSS/programs/html/dnamlk.html
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share/doc/EMBOSS/programs/html/dnapars.html
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share/doc/EMBOSS/programs/html/dnapenny.html
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share/doc/EMBOSS/programs/html/dollop.html
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share/doc/EMBOSS/programs/html/dolpenny.html
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share/doc/EMBOSS/programs/html/domainer.html
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share/doc/EMBOSS/programs/html/dotmatcher.html
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share/doc/EMBOSS/programs/html/dotmatcher0.gif
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share/doc/EMBOSS/programs/html/dotpath.html
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share/doc/EMBOSS/programs/html/dottup.html
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share/doc/EMBOSS/programs/html/dottup0.gif
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share/doc/EMBOSS/programs/html/dreg.html
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share/doc/EMBOSS/programs/html/eclique.html
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share/doc/EMBOSS/programs/html/econsense.html
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share/doc/EMBOSS/programs/html/econtml.html
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share/doc/EMBOSS/programs/html/econtrast.html
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share/doc/EMBOSS/programs/html/ednacomp.html
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share/doc/EMBOSS/programs/html/ednadist.html
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share/doc/EMBOSS/programs/html/ednainvar.html
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share/doc/EMBOSS/programs/html/ednaml.html
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share/doc/EMBOSS/programs/html/ednamlk.html
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share/doc/EMBOSS/programs/html/ednapars.html
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share/doc/EMBOSS/programs/html/ednapenny.html
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share/doc/EMBOSS/programs/html/edollop.html
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share/doc/EMBOSS/programs/html/edolpenny.html
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share/doc/EMBOSS/programs/html/efactor.html
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share/doc/EMBOSS/programs/html/efitch.html
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share/doc/EMBOSS/programs/html/egendist.html
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share/doc/EMBOSS/programs/html/einverted.html
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share/doc/EMBOSS/programs/html/ekitsch.html
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share/doc/EMBOSS/programs/html/emboss_icon.gif
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share/doc/EMBOSS/programs/html/embossdata.html
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share/doc/EMBOSS/programs/html/emix.html
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share/doc/EMBOSS/programs/html/emma.html
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share/doc/EMBOSS/programs/html/emnu.html
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share/doc/EMBOSS/programs/html/emowse.html
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share/doc/EMBOSS/programs/html/eneighbor.html
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share/doc/EMBOSS/programs/html/entret.html
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share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html
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share/doc/EMBOSS/programs/html/epenny.html
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share/doc/EMBOSS/programs/html/eprotdist.html
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share/doc/EMBOSS/programs/html/eprotpars.html
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share/doc/EMBOSS/programs/html/equicktandem.html
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share/doc/EMBOSS/programs/html/erestml.html
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share/doc/EMBOSS/programs/html/eseqboot.html
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share/doc/EMBOSS/programs/html/est2genome.html
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share/doc/EMBOSS/programs/html/etandem.html
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share/doc/EMBOSS/programs/html/extractseq.html
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share/doc/EMBOSS/programs/html/factor.html
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share/doc/EMBOSS/programs/html/findkm.html
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share/doc/EMBOSS/programs/html/findkm0.gif
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share/doc/EMBOSS/programs/html/fitch.html
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share/doc/EMBOSS/programs/html/freak.html
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share/doc/EMBOSS/programs/html/fuzznuc.html
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share/doc/EMBOSS/programs/html/fuzzpro.html
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share/doc/EMBOSS/programs/html/fuzztran.html
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share/doc/EMBOSS/programs/html/garnier.html
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share/doc/EMBOSS/programs/html/geecee.html
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share/doc/EMBOSS/programs/html/gendist.html
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share/doc/EMBOSS/programs/html/gene_finding_group.html
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share/doc/EMBOSS/programs/html/getorf.html
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share/doc/EMBOSS/programs/html/groups.html
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share/doc/EMBOSS/programs/html/helixturnhelix.html
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share/doc/EMBOSS/programs/html/hydropathy_group.html
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share/doc/EMBOSS/programs/html/iep.html
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share/doc/EMBOSS/programs/html/index.html
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share/doc/EMBOSS/programs/html/infoseq.html
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share/doc/EMBOSS/programs/html/isochore.html
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share/doc/EMBOSS/programs/html/isochore0.gif
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share/doc/EMBOSS/programs/html/kitsch.html
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share/doc/EMBOSS/programs/html/lindna.html
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share/doc/EMBOSS/programs/html/marscan.html
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share/doc/EMBOSS/programs/html/maskfeat.html
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@ -890,7 +787,6 @@ share/doc/EMBOSS/programs/html/notseq.html
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share/doc/EMBOSS/programs/html/nrscope.html
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share/doc/EMBOSS/programs/html/nthseq.html
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share/doc/EMBOSS/programs/html/octanol.html
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share/doc/EMBOSS/programs/html/octanol0.gif
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share/doc/EMBOSS/programs/html/oddcomp.html
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share/doc/EMBOSS/programs/html/palindrome.html
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share/doc/EMBOSS/programs/html/pasteseq.html
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@ -900,26 +796,17 @@ share/doc/EMBOSS/programs/html/pattern_matching_group.html
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share/doc/EMBOSS/programs/html/penny.html
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share/doc/EMBOSS/programs/html/pepcoil.html
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share/doc/EMBOSS/programs/html/pepinfo.html
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share/doc/EMBOSS/programs/html/pepinfo1.gif
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share/doc/EMBOSS/programs/html/pepinfo2.gif
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share/doc/EMBOSS/programs/html/pepnet.html
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share/doc/EMBOSS/programs/html/pepnet0.gif
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share/doc/EMBOSS/programs/html/pepstats.html
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share/doc/EMBOSS/programs/html/pepwheel.html
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share/doc/EMBOSS/programs/html/pepwheel0.gif
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share/doc/EMBOSS/programs/html/pepwindow.html
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share/doc/EMBOSS/programs/html/pepwindow0.gif
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share/doc/EMBOSS/programs/html/pepwindowall.html
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share/doc/EMBOSS/programs/html/pepwindowall0.gif
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share/doc/EMBOSS/programs/html/phylogeny_group.html
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share/doc/EMBOSS/programs/html/plotcon.html
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share/doc/EMBOSS/programs/html/plotorf.html
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share/doc/EMBOSS/programs/html/plotorf0.gif
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share/doc/EMBOSS/programs/html/polydot.html
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share/doc/EMBOSS/programs/html/polydot0.gif
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share/doc/EMBOSS/programs/html/preg.html
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share/doc/EMBOSS/programs/html/prettyplot.html
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share/doc/EMBOSS/programs/html/prettyplot3.gif
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share/doc/EMBOSS/programs/html/prettyplot4.gif
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share/doc/EMBOSS/programs/html/prettyseq.html
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share/doc/EMBOSS/programs/html/prima.html
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share/doc/EMBOSS/programs/html/primers_group.html
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@ -976,16 +863,12 @@ share/doc/EMBOSS/programs/html/stretcher.html
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share/doc/EMBOSS/programs/html/stssearch.html
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share/doc/EMBOSS/programs/html/supermatcher.html
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share/doc/EMBOSS/programs/html/syco.html
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share/doc/EMBOSS/programs/html/syco0.gif
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share/doc/EMBOSS/programs/html/syco1.gif
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share/doc/EMBOSS/programs/html/text_search_group.html
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share/doc/EMBOSS/programs/html/textsearch.html
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share/doc/EMBOSS/programs/html/tfextract.html
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share/doc/EMBOSS/programs/html/tfm.html
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share/doc/EMBOSS/programs/html/tfscan.html
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share/doc/EMBOSS/programs/html/tmap.html
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share/doc/EMBOSS/programs/html/tmap0.gif
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share/doc/EMBOSS/programs/html/topo.gif
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share/doc/EMBOSS/programs/html/topo.html
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share/doc/EMBOSS/programs/html/transcription_group.html
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share/doc/EMBOSS/programs/html/transeq.html
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@ -997,7 +880,6 @@ share/doc/EMBOSS/programs/html/utilities_keyword_search_group.html
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share/doc/EMBOSS/programs/html/vectorstrip.html
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share/doc/EMBOSS/programs/html/water.html
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share/doc/EMBOSS/programs/html/wobble.html
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share/doc/EMBOSS/programs/html/wobble0.gif
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share/doc/EMBOSS/programs/html/wordcount.html
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share/doc/EMBOSS/programs/html/wordmatch.html
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share/doc/EMBOSS/programs/html/wossname.html
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@ -1007,7 +889,9 @@ share/doc/EMBOSS/programs/text/antigenic.txt
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share/doc/EMBOSS/programs/text/backtranseq.txt
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share/doc/EMBOSS/programs/text/banana.txt
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share/doc/EMBOSS/programs/text/btwisted.txt
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share/doc/EMBOSS/programs/text/cai.txt
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share/doc/EMBOSS/programs/text/chaos.txt
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share/doc/EMBOSS/programs/text/charge.txt
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share/doc/EMBOSS/programs/text/checktrans.txt
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share/doc/EMBOSS/programs/text/chips.txt
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share/doc/EMBOSS/programs/text/cirdna.txt
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share/doc/EMBOSS/programs/text/descseq.txt
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share/doc/EMBOSS/programs/text/diffseq.txt
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share/doc/EMBOSS/programs/text/digest.txt
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share/doc/EMBOSS/programs/text/distmat.txt
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share/doc/EMBOSS/programs/text/dnacomp.txt
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share/doc/EMBOSS/programs/text/dnadist.txt
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share/doc/EMBOSS/programs/text/dnainvar.txt
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share/doc/EMBOSS/programs/text/gendist.txt
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share/doc/EMBOSS/programs/text/getorf.txt
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share/doc/EMBOSS/programs/text/helixturnhelix.txt
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share/doc/EMBOSS/programs/text/hmoment.txt
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share/doc/EMBOSS/programs/text/iep.txt
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share/doc/EMBOSS/programs/text/infoseq.txt
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share/doc/EMBOSS/programs/text/isochore.txt
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share/doc/EMBOSS/programs/text/wossname.txt
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share/doc/EMBOSS/tutorials/biblio.bib
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share/doc/EMBOSS/tutorials/dottup.ps.gz
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share/doc/EMBOSS/tutorials/emboss-talk.ppt
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share/doc/EMBOSS/tutorials/emboss_tutorial.tex
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share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
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share/doc/EMBOSS/tutorials/pepinfo2.ps.gz
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