- Update port to version 2.0.1

- Add two new EMBASSY applications, MEME and HMMER.

1 files changed, 83 insertions, 10 deletions

diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index a559dc57ee5..dc31f5f5c51 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -1,5 +1,35 @@
 %%PLIST_EMNU%%bin/emnu
 %%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
+%%PLIST_HMMER%%bin/ealistat
+%%PLIST_HMMER%%bin/ehmmalign
+%%PLIST_HMMER%%bin/ehmmbuild
+%%PLIST_HMMER%%bin/ehmmcalibrate
+%%PLIST_HMMER%%bin/ehmmconvert
+%%PLIST_HMMER%%bin/ehmmemit
+%%PLIST_HMMER%%bin/ehmmfetch
+%%PLIST_HMMER%%bin/ehmmindex
+%%PLIST_HMMER%%bin/ehmmpfam
+%%PLIST_HMMER%%bin/ehmmsearch
+%%PLIST_HMMER%%lib/libhmmer.a
+%%PLIST_HMMER%%lib/libhmmer.la
+%%PLIST_HMMER%%lib/libhmmer.so
+%%PLIST_HMMER%%lib/libhmmer.so.2
+%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
+%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
+%%PLIST_MEME%%bin/meme
+%%PLIST_MEME%%lib/libmeme.a
+%%PLIST_MEME%%lib/libmeme.la
+%%PLIST_MEME%%lib/libmeme.so
+%%PLIST_MEME%%lib/libmeme.so.2
+%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
 %%PLIST_MSE%%bin/mse
 %%PLIST_MSE%%lib/libckit.a
 %%PLIST_MSE%%lib/libckit.la
@@ -72,6 +102,7 @@ bin/codcmp
 bin/coderet
 bin/compseq
 bin/cons
+bin/contacts
 bin/cpgplot
 bin/cpgreport
 bin/cusp
@@ -113,6 +144,7 @@ bin/getorf
 bin/helixturnhelix
 bin/hmoment
 bin/iep
+bin/infoalign
 bin/infoseq
 bin/isochore
 bin/lindna
@@ -171,6 +203,7 @@ bin/seealso
 bin/seqmatchall
 bin/seqret
 bin/seqretall
+bin/seqretallfeat
 bin/seqretset
 bin/seqretsplit
 bin/showalign
@@ -180,11 +213,13 @@ bin/showorf
 bin/showseq
 bin/shuffleseq
 bin/sigcleave
+bin/siggen
 bin/silent
 bin/splitter
 bin/stretcher
 bin/stssearch
 bin/supermatcher
+bin/swissparse
 bin/syco
 bin/textsearch
 bin/tfextract
@@ -216,7 +251,6 @@ share/EMBOSS/acd/abiview.acd
 share/EMBOSS/acd/ajbad.acd
 share/EMBOSS/acd/ajfeatest.acd
 share/EMBOSS/acd/ajtest.acd
-share/EMBOSS/acd/ajtest2.acd
 share/EMBOSS/acd/antigenic.acd
 share/EMBOSS/acd/backtranseq.acd
 share/EMBOSS/acd/banana.acd
@@ -227,7 +261,6 @@ share/EMBOSS/acd/charge.acd
 share/EMBOSS/acd/checktrans.acd
 share/EMBOSS/acd/chips.acd
 share/EMBOSS/acd/cirdna.acd
-share/EMBOSS/acd/cluster.acd
 share/EMBOSS/acd/codcmp.acd
 share/EMBOSS/acd/coderet.acd
 share/EMBOSS/acd/codes.english
@@ -245,6 +278,7 @@ share/EMBOSS/acd/dbiblast.acd
 share/EMBOSS/acd/dbifasta.acd
 share/EMBOSS/acd/dbiflat.acd
 share/EMBOSS/acd/dbigcg.acd
+share/EMBOSS/acd/degapseq.acd
 share/EMBOSS/acd/demofeatures.acd
 share/EMBOSS/acd/demolist.acd
 share/EMBOSS/acd/demosequence.acd
@@ -253,6 +287,7 @@ share/EMBOSS/acd/demotable.acd
 share/EMBOSS/acd/descseq.acd
 share/EMBOSS/acd/diffseq.acd
 share/EMBOSS/acd/digest.acd
+share/EMBOSS/acd/distmat.acd
 share/EMBOSS/acd/domainer.acd
 share/EMBOSS/acd/dotmatcher.acd
 share/EMBOSS/acd/dotpath.acd
@@ -281,6 +316,7 @@ share/EMBOSS/acd/helixturnhelix.acd
 share/EMBOSS/acd/histogramtest.acd
 share/EMBOSS/acd/hmoment.acd
 share/EMBOSS/acd/iep.acd
+share/EMBOSS/acd/infoalign.acd
 share/EMBOSS/acd/infoseq.acd
 share/EMBOSS/acd/isochore.acd
 share/EMBOSS/acd/lindna.acd
@@ -315,7 +351,6 @@ share/EMBOSS/acd/pepwindow.acd
 share/EMBOSS/acd/pepwindowall.acd
 share/EMBOSS/acd/plotcon.acd
 share/EMBOSS/acd/plotorf.acd
-share/EMBOSS/acd/plplottest.acd
 share/EMBOSS/acd/polydot.acd
 share/EMBOSS/acd/preg.acd
 share/EMBOSS/acd/prettyplot.acd
@@ -327,8 +362,8 @@ share/EMBOSS/acd/profit.acd
 share/EMBOSS/acd/prophecy.acd
 share/EMBOSS/acd/prophet.acd
 share/EMBOSS/acd/prosextract.acd
-share/EMBOSS/acd/proteinmotifsearch.acd
 share/EMBOSS/acd/pscan.acd
+share/EMBOSS/acd/psiblasts.acd
 share/EMBOSS/acd/rebaseextract.acd
 share/EMBOSS/acd/recoder.acd
 share/EMBOSS/acd/redata.acd
@@ -336,6 +371,7 @@ share/EMBOSS/acd/remap.acd
 share/EMBOSS/acd/restover.acd
 share/EMBOSS/acd/restrict.acd
 share/EMBOSS/acd/revseq.acd
+share/EMBOSS/acd/scopalign.acd
 share/EMBOSS/acd/scope.acd
 share/EMBOSS/acd/seealso.acd
 share/EMBOSS/acd/seqinfo.acd
@@ -343,11 +379,9 @@ share/EMBOSS/acd/seqmatchall.acd
 share/EMBOSS/acd/seqret.acd
 share/EMBOSS/acd/seqretall.acd
 share/EMBOSS/acd/seqretallfeat.acd
-share/EMBOSS/acd/seqretfeat.acd
 share/EMBOSS/acd/seqretset.acd
 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
@@ -355,10 +389,10 @@ share/EMBOSS/acd/showorf.acd
 share/EMBOSS/acd/showseq.acd
 share/EMBOSS/acd/shuffleseq.acd
 share/EMBOSS/acd/sigcleave.acd
+share/EMBOSS/acd/siggen.acd
+share/EMBOSS/acd/sigscan.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
@@ -630,7 +664,11 @@ share/EMBOSS/data/Edna.melt
 share/EMBOSS/data/Eembl.ior
 share/EMBOSS/data/Eenergy.dat
 share/EMBOSS/data/Efeatures.embl
+share/EMBOSS/data/Efeatures.emboss
 share/EMBOSS/data/Efeatures.gff
+share/EMBOSS/data/Efeatures.pir
+share/EMBOSS/data/Efeatures.protein
+share/EMBOSS/data/Efeatures.swiss
 share/EMBOSS/data/Efreqs.dat
 share/EMBOSS/data/Ehth.dat
 share/EMBOSS/data/Ehth87.dat
@@ -645,7 +683,11 @@ share/EMBOSS/data/Erna.melt
 share/EMBOSS/data/Esig.euk
 share/EMBOSS/data/Esig.pro
 share/EMBOSS/data/Etags.embl
+share/EMBOSS/data/Etags.emboss
 share/EMBOSS/data/Etags.gff
+share/EMBOSS/data/Etags.pir
+share/EMBOSS/data/Etags.protein
+share/EMBOSS/data/Etags.swiss
 share/EMBOSS/data/Ewhite-wimley.dat
 share/EMBOSS/data/PRINTS/dummyfile
 share/EMBOSS/data/PROSITE/dummyfile
@@ -680,6 +722,9 @@ share/EMBOSS/test/data/dna.phylip3
 share/EMBOSS/test/data/dna.staden
 share/EMBOSS/test/data/dna.strider
 share/EMBOSS/test/data/dna.text
+share/EMBOSS/test/data/feat.emft
+share/EMBOSS/test/data/feat.fasta
+share/EMBOSS/test/data/feat.pir
 share/EMBOSS/test/data/paamir.pep
 share/EMBOSS/test/data/prot.acedb
 share/EMBOSS/test/data/prot.codata
@@ -705,10 +750,16 @@ 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/pln.dat
 share/EMBOSS/test/embl/pro.dat
 share/EMBOSS/test/embl/rod.dat
+share/EMBOSS/test/embl/sts.dat
 share/EMBOSS/test/embl/vrl.dat
 share/EMBOSS/test/embl/vrt.dat
+share/EMBOSS/test/pir/acnum.hit
+share/EMBOSS/test/pir/acnum.trg
+share/EMBOSS/test/pir/division.lkp
+share/EMBOSS/test/pir/entrynam.idx
 share/EMBOSS/test/pir/pir1.header
 share/EMBOSS/test/pir/pir1.names
 share/EMBOSS/test/pir/pir1.numbers
@@ -789,6 +840,7 @@ 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/contacts.html
 share/doc/EMBOSS/programs/html/contml.html
 share/doc/EMBOSS/programs/html/contrast.html
 share/doc/EMBOSS/programs/html/cpgplot.html
@@ -844,9 +896,9 @@ share/doc/EMBOSS/programs/html/einverted.html
 share/doc/EMBOSS/programs/html/ekitsch.html
 share/doc/EMBOSS/programs/html/emboss_icon.gif
 share/doc/EMBOSS/programs/html/embossdata.html
+share/doc/EMBOSS/programs/html/embossversion.html
 share/doc/EMBOSS/programs/html/emix.html
 share/doc/EMBOSS/programs/html/emma.html
-share/doc/EMBOSS/programs/html/emnu.html
 share/doc/EMBOSS/programs/html/emowse.html
 share/doc/EMBOSS/programs/html/eneighbor.html
 share/doc/EMBOSS/programs/html/entret.html
@@ -878,6 +930,7 @@ 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/infoalign.html
 share/doc/EMBOSS/programs/html/information_group.html
 share/doc/EMBOSS/programs/html/infoseq.html
 share/doc/EMBOSS/programs/html/isochore.html
@@ -963,6 +1016,7 @@ 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/protein_structure_group.html
 share/doc/EMBOSS/programs/html/pscan.html
 share/doc/EMBOSS/programs/html/rebaseextract.html
 share/doc/EMBOSS/programs/html/recode.html
@@ -973,26 +1027,33 @@ 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/revseq.html
+share/doc/EMBOSS/programs/html/scopalign.html
 share/doc/EMBOSS/programs/html/scope.html
 share/doc/EMBOSS/programs/html/seealso.html
 share/doc/EMBOSS/programs/html/seqboot.html
 share/doc/EMBOSS/programs/html/seqmatchall.html
 share/doc/EMBOSS/programs/html/seqret.html
 share/doc/EMBOSS/programs/html/seqretall.html
+share/doc/EMBOSS/programs/html/seqretallfeat.html
 share/doc/EMBOSS/programs/html/seqretfeat.html
 share/doc/EMBOSS/programs/html/seqretset.html
 share/doc/EMBOSS/programs/html/seqretsplit.html
+share/doc/EMBOSS/programs/html/showalign.html
 share/doc/EMBOSS/programs/html/showdb.html
 share/doc/EMBOSS/programs/html/showfeat.html
 share/doc/EMBOSS/programs/html/showorf.html
 share/doc/EMBOSS/programs/html/showseq.html
 share/doc/EMBOSS/programs/html/shuffleseq.html
 share/doc/EMBOSS/programs/html/sigcleave.html
+share/doc/EMBOSS/programs/html/siggen.html
+share/doc/EMBOSS/programs/html/sigscan.html
 share/doc/EMBOSS/programs/html/silent.html
 share/doc/EMBOSS/programs/html/splitter.html
+share/doc/EMBOSS/programs/html/stamps.html
 share/doc/EMBOSS/programs/html/stretcher.html
 share/doc/EMBOSS/programs/html/stssearch.html
 share/doc/EMBOSS/programs/html/supermatcher.html
+share/doc/EMBOSS/programs/html/swissparse.html
 share/doc/EMBOSS/programs/html/syco.html
 share/doc/EMBOSS/programs/html/syco0.gif
 share/doc/EMBOSS/programs/html/syco1.gif
@@ -1036,6 +1097,7 @@ share/doc/EMBOSS/programs/text/complex.txt
 share/doc/EMBOSS/programs/text/compseq.txt
 share/doc/EMBOSS/programs/text/cons.txt
 share/doc/EMBOSS/programs/text/consense.txt
+share/doc/EMBOSS/programs/text/contacts.txt
 share/doc/EMBOSS/programs/text/contml.txt
 share/doc/EMBOSS/programs/text/contrast.txt
 share/doc/EMBOSS/programs/text/cpgplot.txt
@@ -1085,9 +1147,9 @@ share/doc/EMBOSS/programs/text/egendist.txt
 share/doc/EMBOSS/programs/text/einverted.txt
 share/doc/EMBOSS/programs/text/ekitsch.txt
 share/doc/EMBOSS/programs/text/embossdata.txt
+share/doc/EMBOSS/programs/text/embossversion.txt
 share/doc/EMBOSS/programs/text/emix.txt
 share/doc/EMBOSS/programs/text/emma.txt
-share/doc/EMBOSS/programs/text/emnu.txt
 share/doc/EMBOSS/programs/text/emowse.txt
 share/doc/EMBOSS/programs/text/eneighbor.txt
 share/doc/EMBOSS/programs/text/entret.txt
@@ -1114,6 +1176,7 @@ share/doc/EMBOSS/programs/text/getorf.txt
 share/doc/EMBOSS/programs/text/helixturnhelix.txt
 share/doc/EMBOSS/programs/text/hmoment.txt
 share/doc/EMBOSS/programs/text/iep.txt
+share/doc/EMBOSS/programs/text/infoalign.txt
 share/doc/EMBOSS/programs/text/infoseq.txt
 share/doc/EMBOSS/programs/text/isochore.txt
 share/doc/EMBOSS/programs/text/kitsch.txt
@@ -1174,26 +1237,33 @@ 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/scopalign.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
 share/doc/EMBOSS/programs/text/seqret.txt
 share/doc/EMBOSS/programs/text/seqretall.txt
+share/doc/EMBOSS/programs/text/seqretallfeat.txt
 share/doc/EMBOSS/programs/text/seqretfeat.txt
 share/doc/EMBOSS/programs/text/seqretset.txt
 share/doc/EMBOSS/programs/text/seqretsplit.txt
+share/doc/EMBOSS/programs/text/showalign.txt
 share/doc/EMBOSS/programs/text/showdb.txt
 share/doc/EMBOSS/programs/text/showfeat.txt
 share/doc/EMBOSS/programs/text/showorf.txt
 share/doc/EMBOSS/programs/text/showseq.txt
 share/doc/EMBOSS/programs/text/shuffleseq.txt
 share/doc/EMBOSS/programs/text/sigcleave.txt
+share/doc/EMBOSS/programs/text/siggen.txt
+share/doc/EMBOSS/programs/text/sigscan.txt
 share/doc/EMBOSS/programs/text/silent.txt
 share/doc/EMBOSS/programs/text/splitter.txt
+share/doc/EMBOSS/programs/text/stamps.txt
 share/doc/EMBOSS/programs/text/stretcher.txt
 share/doc/EMBOSS/programs/text/stssearch.txt
 share/doc/EMBOSS/programs/text/supermatcher.txt
+share/doc/EMBOSS/programs/text/swissparse.txt
 share/doc/EMBOSS/programs/text/syco.txt
 share/doc/EMBOSS/programs/text/textsearch.txt
 share/doc/EMBOSS/programs/text/tfextract.txt
@@ -1211,7 +1281,10 @@ share/doc/EMBOSS/programs/text/wordmatch.txt
 share/doc/EMBOSS/programs/text/wossname.txt
 share/doc/EMBOSS/tutorials/biblio.bib
 share/doc/EMBOSS/tutorials/dottup.ps.gz
+share/doc/EMBOSS/tutorials/emboss-gcg.ppt
+share/doc/EMBOSS/tutorials/emboss-interfaces.ppt
 share/doc/EMBOSS/tutorials/emboss-talk.ppt
+share/doc/EMBOSS/tutorials/emboss_tutorial.ps.gz
 share/doc/EMBOSS/tutorials/emboss_tutorial.tex
 share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
 share/doc/EMBOSS/tutorials/pepinfo2.ps.gz