3 files changed, 134 insertions, 16 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index b7e0b08af0e7..2df4733f8a2e 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,11 +6,10 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	6.0.1
-PORTREVISION=	3
+PORTVERSION=	6.2.0
 RELEASE=	${PORTNAME:U}-${PORTVERSION}
 CATEGORIES=	biology
-MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/old/${PORTVERSION}/
+MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/
 DISTNAME=	${RELEASE}
 DIST_SUBDIR=	${PORTNAME}
 
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index 760dab2e11e9..2f53731960d5 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,3 +1,3 @@
-MD5 (emboss/EMBOSS-6.0.1.tar.gz) = 2182b148dace6bea403deed8facae40d
-SHA256 (emboss/EMBOSS-6.0.1.tar.gz) = 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
-SIZE (emboss/EMBOSS-6.0.1.tar.gz) = 20204153
+MD5 (emboss/EMBOSS-6.2.0.tar.gz) = 2e2937dd0493814ca0f64981f4c79319
+SHA256 (emboss/EMBOSS-6.2.0.tar.gz) = 4726371c0bcf3e232a5ee6b334e74b8c284dcbdcb176a475e77699515f8d122b
+SIZE (emboss/EMBOSS-6.2.0.tar.gz) = 23430911
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index bc0bb59e818d..aba7ba2a1667 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -100,6 +100,7 @@ bin/msbar
 bin/mwcontam
 bin/mwfilter
 bin/needle
+bin/needleall
 bin/newcpgreport
 bin/newcpgseek
 bin/newseq
@@ -109,6 +110,7 @@ bin/nospace
 bin/notab
 bin/notseq
 bin/nthseq
+bin/nthseqset
 bin/octanol
 bin/oddcomp
 bin/palindrome
@@ -147,11 +149,13 @@ bin/runJemboss.csh
 bin/seealso
 bin/seqmatchall
 bin/seqret
+bin/seqretsetall
 bin/seqretsplit
 bin/showalign
 bin/showdb
 bin/showfeat
 bin/showorf
+bin/showpep
 bin/showseq
 bin/shuffleseq
 bin/sigcleave
@@ -161,6 +165,7 @@ bin/sixpack
 bin/sizeseq
 bin/skipredundant
 bin/skipseq
+bin/splitsource
 bin/splitter
 bin/stretcher
 bin/stssearch
@@ -211,7 +216,6 @@ include/ajfileio.h
 include/ajfmt.h
 include/ajgraph.h
 include/ajgraphstruct.h
-include/ajgraphxml.h
 include/ajhist.h
 include/ajindex.h
 include/ajjava.h
@@ -237,6 +241,7 @@ include/ajseqread.h
 include/ajseqtype.h
 include/ajseqwrite.h
 include/ajsort.h
+include/ajsql.h
 include/ajstr.h
 include/ajsys.h
 include/ajtable.h
@@ -245,6 +250,8 @@ include/ajtranslate.h
 include/ajtree.h
 include/ajutil.h
 include/ajvector.h
+include/crc32.h
+include/deflate.h
 include/embaln.h
 include/embcom.h
 include/embcons.h
@@ -271,6 +278,54 @@ include/embread.h
 include/embshow.h
 include/embsig.h
 include/embword.h
+include/ensanalysis.h
+include/ensassemblyexception.h
+include/ensassembly.h
+include/ensassemblymapper.h
+include/ensattribute.h
+include/ensbaseadaptor.h
+include/enscache.h
+include/enscoordsystem.h
+include/ensdatabaseadaptor.h
+include/ensdatabaseconnection.h
+include/ensdatabaseentry.h
+include/ensdata.h
+include/ensdensity.h
+include/ensditag.h
+include/ensembl.h
+include/ensexon.h
+include/ensexternaldatabase.h
+include/ensfeature.h
+include/ensgene.h
+include/ensgvdata.h
+include/ensgvindividual.h
+include/ensgvpopulation.h
+include/ensgvsample.h
+include/ensintron.h
+include/enskaryotype.h
+include/ensmapper.h
+include/ensmarker.h
+include/ensmetacoordinate.h
+include/ensmetainformation.h
+include/ensmiscellaneous.h
+include/ensprediction.h
+include/ensprojectionsegment.h
+include/ensqcalignment.h
+include/ensqcdatabase.h
+include/ensqc.h
+include/ensqcsequence.h
+include/ensregistry.h
+include/ensrepeat.h
+include/ensseqregion.h
+include/enssequence.h
+include/enssequenceedit.h
+include/ensslice.h
+include/ensstorable.h
+include/enstable.h
+include/enstranslation.h
+include/enstranscript.h
+include/ensutility.h
+include/ensvariation.h
 include/eplplot/disptab.h
 include/eplplot/drivers.h
 include/eplplot/metadefs.h
@@ -289,25 +344,61 @@ include/eplplot/plstrm.h
 include/eplplot/plunicode-type1.h
 include/eplplot/plxwd.h
 include/eplplot/ps.h
+include/expat.h
+include/expat_external.h
+include/expatemboss.h
+include/inffast.h
+include/inffixed.h
+include/inflate.h
+include/inftrees.h
 include/pcre.h
-include/pcre_chartables.c
 include/pcre_config.h
-include/pcre_get.c
+include/pcreemboss.h
 include/pcre_internal.h
-include/pcre_printint.c
+include/pcre_printint.src
 include/pcreposix.h
+include/trees.h
+include/ucp.h
+include/zconf.h
+include/zlibemboss.h
+include/zlib.h
+include/zutil.h
+lib/libacd.so.6
+lib/libacd.so
+lib/libacd.la
+lib/libacd.a
 lib/libajax.a
 lib/libajax.la
 lib/libajax.so
 lib/libajax.so.6
+lib/libajaxdb.a
+lib/libajaxdb.la
+lib/libajaxdb.so
+lib/libajaxdb.so.6
 lib/libajaxg.a
 lib/libajaxg.la
 lib/libajaxg.so
 lib/libajaxg.so.6
+lib/libeexpat.a
+lib/libeexpat.la
+lib/libeexpat.so
+lib/libeexpat.so.2
+lib/libensembl.a
+lib/libensembl.la
+lib/libensembl.so
+lib/libensembl.so.6
+lib/libepcre.a
+lib/libepcre.la
+lib/libepcre.so
+lib/libepcre.so.7
 lib/libeplplot.a
 lib/libeplplot.la
 lib/libeplplot.so
 lib/libeplplot.so.5
+lib/libezlib.a
+lib/libezlib.la
+lib/libezlib.so
+lib/libezlib.so.2
 lib/libnucleus.a
 lib/libnucleus.la
 lib/libnucleus.so
@@ -317,6 +408,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/acdc.acd
 %%DATADIR%%/acd/acdlog.acd
 %%DATADIR%%/acd/acdpretty.acd
+%%DATADIR%%/acd/acdrelations.acd
 %%DATADIR%%/acd/acdtable.acd
 %%DATADIR%%/acd/acdtrace.acd
 %%DATADIR%%/acd/acdvalid.acd
@@ -359,6 +451,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/dbxfasta.acd
 %%DATADIR%%/acd/dbxflat.acd
 %%DATADIR%%/acd/dbxgcg.acd
+%%DATADIR%%/acd/dbxreport.acd
 %%DATADIR%%/acd/dbxstat.acd
 %%DATADIR%%/acd/degapseq.acd
 %%DATADIR%%/acd/density.acd
@@ -370,12 +463,14 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/dotpath.acd
 %%DATADIR%%/acd/dottup.acd
 %%DATADIR%%/acd/dreg.acd
+%%DATADIR%%/acd/edamclean.acd
 %%DATADIR%%/acd/edialign.acd
 %%DATADIR%%/acd/einverted.acd
 %%DATADIR%%/acd/embossdata.acd
 %%DATADIR%%/acd/embossversion.acd
 %%DATADIR%%/acd/emma.acd
 %%DATADIR%%/acd/emowse.acd
+%%DATADIR%%/acd/ensembltest.acd
 %%DATADIR%%/acd/entrails.acd
 %%DATADIR%%/acd/entret.acd
 %%DATADIR%%/acd/epestfind.acd
@@ -396,13 +491,14 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/garnier.acd
 %%DATADIR%%/acd/geecee.acd
 %%DATADIR%%/acd/getorf.acd
-%%DATADIR%%/acd/giep.acd
 %%DATADIR%%/acd/groups.standard
 %%DATADIR%%/acd/helixturnhelix.acd
 %%DATADIR%%/acd/histogramtest.acd
 %%DATADIR%%/acd/hmoment.acd
 %%DATADIR%%/acd/iep.acd
 %%DATADIR%%/acd/infoalign.acd
+%%DATADIR%%/acd/infobase.acd
+%%DATADIR%%/acd/inforesidue.acd
 %%DATADIR%%/acd/infoseq.acd
 %%DATADIR%%/acd/intconv.acd
 %%DATADIR%%/acd/isochore.acd
@@ -426,6 +522,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/mwcontam.acd
 %%DATADIR%%/acd/mwfilter.acd
 %%DATADIR%%/acd/needle.acd
+%%DATADIR%%/acd/needleall.acd
 %%DATADIR%%/acd/newcoils.acd
 %%DATADIR%%/acd/newcpgreport.acd
 %%DATADIR%%/acd/newcpgseek.acd
@@ -436,6 +533,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/notab.acd
 %%DATADIR%%/acd/notseq.acd
 %%DATADIR%%/acd/nthseq.acd
+%%DATADIR%%/acd/nthseqset.acd
 %%DATADIR%%/acd/octanol.acd
 %%DATADIR%%/acd/oddcomp.acd
 %%DATADIR%%/acd/origsplitter.acd
@@ -483,6 +581,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/seqretall.acd
 %%DATADIR%%/acd/seqretallfeat.acd
 %%DATADIR%%/acd/seqretset.acd
+%%DATADIR%%/acd/seqretsetall.acd
 %%DATADIR%%/acd/seqretsingle.acd
 %%DATADIR%%/acd/seqretsplit.acd
 %%DATADIR%%/acd/seqrettype.acd
@@ -490,6 +589,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/showdb.acd
 %%DATADIR%%/acd/showfeat.acd
 %%DATADIR%%/acd/showorf.acd
+%%DATADIR%%/acd/showpep.acd
 %%DATADIR%%/acd/showseq.acd
 %%DATADIR%%/acd/shuffleseq.acd
 %%DATADIR%%/acd/sigcleave.acd
@@ -499,7 +599,9 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/sizeseq.acd
 %%DATADIR%%/acd/skipredundant.acd
 %%DATADIR%%/acd/skipseq.acd
+%%DATADIR%%/acd/splitsource.acd
 %%DATADIR%%/acd/splitter.acd
+%%DATADIR%%/acd/sqltest.acd
 %%DATADIR%%/acd/stretcher.acd
 %%DATADIR%%/acd/stssearch.acd
 %%DATADIR%%/acd/supermatcher.acd
@@ -516,6 +618,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/acd/treetypedisplay.acd
 %%DATADIR%%/acd/trimest.acd
 %%DATADIR%%/acd/trimseq.acd
+%%DATADIR%%/acd/trimspace.acd
 %%DATADIR%%/acd/twofeat.acd
 %%DATADIR%%/acd/union.acd
 %%DATADIR%%/acd/variables.standard
@@ -888,6 +991,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/data/Efeatures.gff3protein
 %%DATADIR%%/data/Efeatures.gffprotein
 %%DATADIR%%/data/Efeatures.pir
+%%DATADIR%%/data/Efeatures.refseqp
 %%DATADIR%%/data/Efeatures.protein
 %%DATADIR%%/data/Efeatures.swiss
 %%DATADIR%%/data/Efreqs.dat
@@ -897,9 +1001,13 @@ lib/libnucleus.so.6
 %%DATADIR%%/data/Emass.dat
 %%DATADIR%%/data/Emassmod.dat
 %%DATADIR%%/data/Ememe.dat
+%%DATADIR%%/data/Emethylsites.dat
 %%DATADIR%%/data/Emolwt.dat
 %%DATADIR%%/data/Emwfilter.dat
 %%DATADIR%%/data/Enakai.dat
+%%DATADIR%%/data/EnsemblAliases.dat
+%%DATADIR%%/data/EnsemblIdentifiers.dat
+%%DATADIR%%/data/Etags.gff3protein
 %%DATADIR%%/data/Epepcoil.dat
 %%DATADIR%%/data/Epk.dat
 %%DATADIR%%/data/Epprofile
@@ -916,6 +1024,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/data/Etags.gffprotein
 %%DATADIR%%/data/Etags.pir
 %%DATADIR%%/data/Etags.protein
+%%DATADIR%%/data/Etags.refseqp
 %%DATADIR%%/data/Etags.swiss
 %%DATADIR%%/data/Etcode.dat
 %%DATADIR%%/data/Evdw.dat
@@ -932,6 +1041,7 @@ lib/libnucleus.so.6
 %%DATADIR%%/data/PRINTS/dummyfile
 %%DATADIR%%/data/PROSITE/dummyfile
 %%DATADIR%%/data/REBASE/dummyfile
+%%DATADIR%%/data/SSSUB
 %%DATADIR%%/data/edialignmat
 %%DATADIR%%/data/embossre.equ
 %%DATADIR%%/data/tp400_dna
@@ -1090,6 +1200,7 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/html/mwcontam.html
 %%DOCSDIR%%/programs/html/mwfilter.html
 %%DOCSDIR%%/programs/html/needle.html
+%%DOCSDIR%%/programs/html/needleall.html
 %%DOCSDIR%%/programs/html/newcpgreport.html
 %%DOCSDIR%%/programs/html/newcpgseek.html
 %%DOCSDIR%%/programs/html/newseq.html
@@ -1099,6 +1210,7 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/html/notab.html
 %%DOCSDIR%%/programs/html/notseq.html
 %%DOCSDIR%%/programs/html/nthseq.html
+%%DOCSDIR%%/programs/html/nthseqset.html
 %%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
 %%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
 %%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
@@ -1178,11 +1290,13 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/html/seealso.html
 %%DOCSDIR%%/programs/html/seqmatchall.html
 %%DOCSDIR%%/programs/html/seqret.html
+%%DOCSDIR%%/programs/html/seqretsetall.html
 %%DOCSDIR%%/programs/html/seqretsplit.html
 %%DOCSDIR%%/programs/html/showalign.html
 %%DOCSDIR%%/programs/html/showdb.html
 %%DOCSDIR%%/programs/html/showfeat.html
 %%DOCSDIR%%/programs/html/showorf.html
+%%DOCSDIR%%/programs/html/showpep.html
 %%DOCSDIR%%/programs/html/showseq.html
 %%DOCSDIR%%/programs/html/shuffleseq.html
 %%DOCSDIR%%/programs/html/sigcleave.html
@@ -1192,6 +1306,7 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/html/sizeseq.html
 %%DOCSDIR%%/programs/html/skipredundant.html
 %%DOCSDIR%%/programs/html/skipseq.html
+%%DOCSDIR%%/programs/html/splitsource.html
 %%DOCSDIR%%/programs/html/splitter.html
 %%DOCSDIR%%/programs/html/stretcher.html
 %%DOCSDIR%%/programs/html/stssearch.html
@@ -1300,7 +1415,6 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/text/featreport.txt
 %%DOCSDIR%%/programs/text/findkm.txt
 %%DOCSDIR%%/programs/text/freak.txt
-%%DOCSDIR%%/programs/text/frestdist.txt
 %%DOCSDIR%%/programs/text/fuzznuc.txt
 %%DOCSDIR%%/programs/text/fuzzpro.txt
 %%DOCSDIR%%/programs/text/fuzztran.txt
@@ -1334,6 +1448,7 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/text/mwcontam.txt
 %%DOCSDIR%%/programs/text/mwfilter.txt
 %%DOCSDIR%%/programs/text/needle.txt
+%%DOCSDIR%%/programs/text/needleall.txt
 %%DOCSDIR%%/programs/text/newcpgreport.txt
 %%DOCSDIR%%/programs/text/newcpgseek.txt
 %%DOCSDIR%%/programs/text/newseq.txt
@@ -1343,6 +1458,7 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/text/notab.txt
 %%DOCSDIR%%/programs/text/notseq.txt
 %%DOCSDIR%%/programs/text/nthseq.txt
+%%DOCSDIR%%/programs/text/nthseqset.txt
 %%DOCSDIR%%/programs/text/octanol.txt
 %%DOCSDIR%%/programs/text/oddcomp.txt
 %%DOCSDIR%%/programs/text/palindrome.txt
@@ -1380,10 +1496,12 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/text/seealso.txt
 %%DOCSDIR%%/programs/text/seqmatchall.txt
 %%DOCSDIR%%/programs/text/seqret.txt
+%%DOCSDIR%%/programs/text/seqretsetall.txt
 %%DOCSDIR%%/programs/text/seqretsplit.txt
 %%DOCSDIR%%/programs/text/showalign.txt
 %%DOCSDIR%%/programs/text/showdb.txt
 %%DOCSDIR%%/programs/text/showfeat.txt
+%%DOCSDIR%%/programs/text/showpep.txt
 %%DOCSDIR%%/programs/text/showorf.txt
 %%DOCSDIR%%/programs/text/showseq.txt
 %%DOCSDIR%%/programs/text/shuffleseq.txt
@@ -1394,6 +1512,7 @@ lib/libnucleus.so.6
 %%DOCSDIR%%/programs/text/sizeseq.txt
 %%DOCSDIR%%/programs/text/skipredundant.txt
 %%DOCSDIR%%/programs/text/skipseq.txt
+%%DOCSDIR%%/programs/text/splitsource.txt
 %%DOCSDIR%%/programs/text/splitter.txt
 %%DOCSDIR%%/programs/text/stretcher.txt
 %%DOCSDIR%%/programs/text/stssearch.txt
@@ -1506,7 +1625,6 @@ lib/libnucleus.so.6
 %%DATADIR%%/jemboss/images/Job_manager_button.gif
 %%DATADIR%%/jemboss/images/Refresh_button.gif
 %%DATADIR%%/jemboss/images/Refresh_button2.gif
-%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar
 %%DATADIR%%/jemboss/lib/README
 %%DATADIR%%/jemboss/lib/activation.jar
 %%DATADIR%%/jemboss/lib/axis/axis-ant.jar
@@ -1518,11 +1636,10 @@ lib/libnucleus.so.6
 %%DATADIR%%/jemboss/lib/axis/saaj.jar
 %%DATADIR%%/jemboss/lib/axis/servlet.jar
 %%DATADIR%%/jemboss/lib/axis/wsdl4j.jar
-%%DATADIR%%/jemboss/lib/grout.jar
 %%DATADIR%%/jemboss/lib/jakarta-regexp-1.2.jar
-%%DATADIR%%/jemboss/lib/jalview.jar
+%%DATADIR%%/jemboss/lib/jalviewApplet.jar
+%%DATADIR%%/jemboss/lib/jemboss.jar
 %%DATADIR%%/jemboss/lib/mail.jar
-%%DATADIR%%/jemboss/lib/xerces.jar
 %%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java
@@ -1667,12 +1784,14 @@ lib/libnucleus.so.6
 %%DATADIR%%/jemboss/resources/readme.html
 %%DATADIR%%/jemboss/resources/readmeAlign.html
 %%DATADIR%%/jemboss/resources/readmeDNADraw.html
+%%DATADIR%%/jemboss/resources/resources.jar
 %%DATADIR%%/jemboss/resources/results.html
 %%DATADIR%%/jemboss/resources/seqList.html
 %%DATADIR%%/jemboss/resources/version
 %%DATADIR%%/jemboss/runJemboss.sh
 %%DATADIR%%/jemboss/utils/README
 %%DATADIR%%/jemboss/utils/install-jemboss-server.sh
+%%DATADIR%%/jemboss/utils/jws-launch-button.png
 %%DATADIR%%/jemboss/utils/keys.sh
 %%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
 %%DATADIR%%/jemboss/utils/makeJNLP.sh