- Update to 6.2.0

Submitted by:	Wen Heping(myself)
Approved by:	maintainer(via Email)

6 files changed, 232 insertions, 75 deletions

diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile
index fc3d4588c53d..9a4f00bea333 100644
--- a/biology/embassy/Makefile
+++ b/biology/embassy/Makefile
@@ -7,10 +7,9 @@
 #
 
 PORTNAME=	embassy
-PORTVERSION=	6.0.0
-PORTREVISION=	3
+PORTVERSION=	6.2.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/old/${PORTVERSION}/
+MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/
 DIST_SUBDIR=	emboss
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
@@ -54,15 +53,15 @@ DOMAINATRIX_VERSION=	0.1.0
 EMNU_VERSION=		1.05
 ESIM4_VERSION=		1.0.0
 HMMER_VERSION=		2.3.2
-MEMENEW_VERSION=	0.1.0
-MSE_VERSION=		1.0.0
-TOPO_VERSION=		1.0.0
-PHYLIPNEW_VERSION=	3.67
+MEMENEW_VERSION=	4.0.0
+MSE_VERSION=		3.0.0
+TOPO_VERSION=		2.0.0
+PHYLIPNEW_VERSION=	3.69
 DOMALIGN_VERSION=	0.1.0
 DOMSEARCH_VERSION=	0.1.0
 SIGNATURE_VERSION=	0.1.0
 STRUCTURE_VERSION=	0.1.0
-MYEMBOSS_VERSION=	6.0.0
+MYEMBOSS_VERSION=	6.2.0
 VIENNA_VERSION=		1.7.2
 MIRA_VERSION=		2.8.2
 IPRSCAN_VERSION=	4.3.1
@@ -97,6 +96,9 @@ do-extract:
 	  fi
 .endfor
 
+post-extract:
+	@${REINPLACE_CMD} -e 's#emboss_doc##g' ${EMBASSY_WRKDIR}/MIRA-2.8.2/Makefile.in
+
 post-patch:
 	@${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|'
 
diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo
index d4ab628f009b..564f2279bcc6 100644
--- a/biology/embassy/distinfo
+++ b/biology/embassy/distinfo
@@ -1,51 +1,51 @@
-MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 0f5211a2ee754b4f32332beaf660964c
-SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1
-SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 420983
-MD5 (emboss/EMNU-1.05.tar.gz) = df6c267bb12e3ecd19bffe5f678bfdb3
-SHA256 (emboss/EMNU-1.05.tar.gz) = 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333
-SIZE (emboss/EMNU-1.05.tar.gz) = 390229
-MD5 (emboss/ESIM4-1.0.0.tar.gz) = 36d9e1dc37004ff4189f583d8d3b037b
-SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577
-SIZE (emboss/ESIM4-1.0.0.tar.gz) = 431898
-MD5 (emboss/HMMER-2.3.2.tar.gz) = edc18f5515f1fd712b7d2accf58a9a2e
-SHA256 (emboss/HMMER-2.3.2.tar.gz) = 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258
-SIZE (emboss/HMMER-2.3.2.tar.gz) = 565686
-MD5 (emboss/MEMENEW-0.1.0.tar.gz) = 72f4a3b8544aa1603301b7b83692a133
-SHA256 (emboss/MEMENEW-0.1.0.tar.gz) = 5411d1445feb1b5e460e598a9d7e670a4357fe7aa350d96531b1aa9c79fab636
-SIZE (emboss/MEMENEW-0.1.0.tar.gz) = 450102
-MD5 (emboss/MSE-1.0.0.tar.gz) = 3122000020565077a421a53cf114127a
-SHA256 (emboss/MSE-1.0.0.tar.gz) = 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90
-SIZE (emboss/MSE-1.0.0.tar.gz) = 445562
-MD5 (emboss/PHYLIPNEW-3.67.tar.gz) = cbd539fb39673cc362d827fa731f03f3
-SHA256 (emboss/PHYLIPNEW-3.67.tar.gz) = efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945
-SIZE (emboss/PHYLIPNEW-3.67.tar.gz) = 1624802
-MD5 (emboss/TOPO-1.0.0.tar.gz) = 03ea6cf067db1f673ec27195076b0e4a
-SHA256 (emboss/TOPO-1.0.0.tar.gz) = a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16
-SIZE (emboss/TOPO-1.0.0.tar.gz) = 379929
-MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 58dff4731762bef6248b163bf2d160bd
-SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a
-SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 462156
-MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = e862f6b4f02f4640f9729862efab5a0a
-SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95
-SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 470537
-MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = cc7c707c41156b6681ddca7b76ff009d
-SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f
-SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 574940
-MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 7df40530fd15f441c531f5dbd5c10fff
-SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23
-SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 532035
-MD5 (emboss/MYEMBOSS-6.0.0.tar.gz) = 5f51d49558131a518ac40220dd7fa0c3
-SHA256 (emboss/MYEMBOSS-6.0.0.tar.gz) = 7f24d800044b0957006c8550de74ca621301f6de1c724980fe90e8a6093b6048
-SIZE (emboss/MYEMBOSS-6.0.0.tar.gz) = 343305
-MD5 (emboss/VIENNA-1.7.2.tar.gz) = f6ec2092de41dafdb6cf302dd5412498
-SHA256 (emboss/VIENNA-1.7.2.tar.gz) = 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db
-SIZE (emboss/VIENNA-1.7.2.tar.gz) = 682200
-MD5 (emboss/MIRA-2.8.2.tar.gz) = c74a63e10ce983c39389593693c851e7
-SHA256 (emboss/MIRA-2.8.2.tar.gz) = 33d756bd50fe26c04aff862f34230feaad831cbe538096e4d8e5c8e0b6784fe1
-SIZE (emboss/MIRA-2.8.2.tar.gz) = 365566
-MD5 (emboss/IPRSCAN-4.3.1.tar.gz) = 8164a9b8392d29ba3bc723c1bc5da2ff
-SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a
-SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 339939
-MD5 (emboss/CBSTOOLS-1.0.0.tar.gz) = 9352c924a8c86233fbf6dc80c58cc481
-SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693
-SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 343812
+MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = fae63eaa478c0864451e969793949499
+SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 53b1633d8a4fec4335ffe96fff309ef2e61b38140dad916b042522e1a48d5e02
+SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 407290
+MD5 (emboss/EMNU-1.05.tar.gz) = f43feb89e7cf68fe37375a19a2dd971b
+SHA256 (emboss/EMNU-1.05.tar.gz) = ccad2f9572b2667b2522e47aa8256b2f17e33a31f74f75991424af0c49ca651d
+SIZE (emboss/EMNU-1.05.tar.gz) = 368599
+MD5 (emboss/ESIM4-1.0.0.tar.gz) = 16f732db3f64e702b8030a41f806e50d
+SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 8c02b53105f9bb95fd0acda15133ad4ac736e720df93c06ffaa6fe54b9baad10
+SIZE (emboss/ESIM4-1.0.0.tar.gz) = 406757
+MD5 (emboss/HMMER-2.3.2.tar.gz) = e83a34abdcd4ed1419db3b4a1a7bf2ff
+SHA256 (emboss/HMMER-2.3.2.tar.gz) = fd60908ffe8fea41259480701d64c3442a6a469945dbe03fdfa5677b1a3dc6a6
+SIZE (emboss/HMMER-2.3.2.tar.gz) = 559938
+MD5 (emboss/MEMENEW-4.0.0.tar.gz) = c9256d7dfebb309533369aecdbe53667
+SHA256 (emboss/MEMENEW-4.0.0.tar.gz) = f5dab1527612e060e6230f579b3243e0da2da086df7ba0e280d0efbb99d5d973
+SIZE (emboss/MEMENEW-4.0.0.tar.gz) = 507901
+MD5 (emboss/MSE-3.0.0.tar.gz) = abb377c097b841308e50a60991ad4b62
+SHA256 (emboss/MSE-3.0.0.tar.gz) = 1fc5f5313cede53ad95122afeb69b4b588f3b564567bff9855a9691b92eea701
+SIZE (emboss/MSE-3.0.0.tar.gz) = 425691
+MD5 (emboss/PHYLIPNEW-3.69.tar.gz) = af08b628e433a0561f830b21412c2969
+SHA256 (emboss/PHYLIPNEW-3.69.tar.gz) = ae0fd57a5b87961d12df8579298d5ec02a147d6678ead4b561dff2c57c5dba67
+SIZE (emboss/PHYLIPNEW-3.69.tar.gz) = 1652212
+MD5 (emboss/TOPO-2.0.0.tar.gz) = 735b6d53e6644b4033ce32f0a2591248
+SHA256 (emboss/TOPO-2.0.0.tar.gz) = 15f1106800ba803e2c5d79dbfa79b5d521e9ed0ca9da0ceaa77e15366613e915
+SIZE (emboss/TOPO-2.0.0.tar.gz) = 377565
+MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = d369817f082da807ca82e8953f04c128
+SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = 33a12d28c16039663467f34d930b2a0a6ab2ef7d987db94fd8ed4abd02b1bf9f
+SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 430542
+MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = dd9d7c6be07c254c6d5487aa5678a74a
+SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = af2e408dcd29b9330df7c310d64c888f53d225ebb0bb5402237891fdcdea7ce3
+SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 447445
+MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 49cfa31d0a42e31e1141cec704bf8ac9
+SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = e24bda9ff60ef9940f603f4c65b7e5673d6b81ef0c19d53b294197e98bb2497c
+SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 559082
+MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6edce4e40a17a6ea836f2e13620c1f86
+SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = c555e1fc16b377109a1bef21116bfe0907709fb2f629d7cbb4add455bc871050
+SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 521708
+MD5 (emboss/MYEMBOSS-6.2.0.tar.gz) = f302aafbe22d0f3e1ca6cd4280f91d21
+SHA256 (emboss/MYEMBOSS-6.2.0.tar.gz) = 13edbea0d11a14f67631a4cf6c69985f42c97383d8182f8815e294be03c5ebae
+SIZE (emboss/MYEMBOSS-6.2.0.tar.gz) = 322935
+MD5 (emboss/VIENNA-1.7.2.tar.gz) = 90bc38801dfe2d4967ed7b35070856e0
+SHA256 (emboss/VIENNA-1.7.2.tar.gz) = e2288e6a2f4538cce916033208ab12f0ffb8a92bb1d3ab89fae302b785171fb7
+SIZE (emboss/VIENNA-1.7.2.tar.gz) = 649028
+MD5 (emboss/MIRA-2.8.2.tar.gz) = f59b73667f3d212d7dbd43fed6117bd9
+SHA256 (emboss/MIRA-2.8.2.tar.gz) = 9d2a64fdb1b95bb6e2ac280be3352740e9b5f498f2ff17157374a2ca9744601d
+SIZE (emboss/MIRA-2.8.2.tar.gz) = 347282
+MD5 (emboss/IPRSCAN-4.3.1.tar.gz) = ac921ebe9555e7f939bd8a06aa524994
+SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = 179513e2473dc31e5b6153c29670773e7bceaaf84315156961baf8f1e292a289
+SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 345907
+MD5 (emboss/CBSTOOLS-1.0.0.tar.gz) = c2405d865148cdcfdccdf5623f5fa784
+SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = 100131d86d4efeafbd63fc712c82bf493e9d174f0bc505e37bdd35ffb56182ff
+SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 385340
diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist
index 3badc2e6a7d9..ff9b9963614d 100644
--- a/biology/embassy/pkg-plist
+++ b/biology/embassy/pkg-plist
@@ -188,14 +188,18 @@
 %%PLIST_HMMER%%bin/ehmmsearch
 %%PLIST_MEMENEW%%share/EMBOSS/acd/emast.acd
 %%PLIST_MEMENEW%%share/EMBOSS/acd/ememe.acd
+%%PLIST_MEMENEW%%share/EMBOSS/acd/ememetext.acd
 %%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/emast.txt
 %%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememe.txt
+%%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememetext.txt
 %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/index.html
 %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/emast.html
 %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememe.html
+%%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememetext.html
 %%PLIST_MEMENEW%%@dirrm share/EMBOSS/doc/html/embassy/memenew
 %%PLIST_MEMENEW%%bin/emast
 %%PLIST_MEMENEW%%bin/ememe
+%%PLIST_MEMENEW%%bin/ememetext
 %%PLIST_MSE%%share/EMBOSS/acd/mse.acd
 %%PLIST_MSE%%share/EMBOSS/doc/programs/text/mse.txt
 %%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/index.html
@@ -251,11 +255,14 @@
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fcontml.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fcontrast.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdiscboot.txt
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdolmove.txt
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/frestdist.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnacomp.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnadist.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnainvar.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnaml.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnamlk.txt
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnamove.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnapars.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnapenny.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdollop.txt
@@ -289,6 +296,9 @@
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fcontml.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fcontrast.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdiscboot.html
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnamove.html
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdolmove.html
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/frestdist.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnacomp.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnadist.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnainvar.html
@@ -374,6 +384,7 @@
 %%PLIST_TOPO%%share/EMBOSS/doc/programs/text/topo.txt
 %%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/index.html
 %%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.html
+%%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.1.topo.gif
 %%PLIST_TOPO%%@dirrm share/EMBOSS/doc/html/embassy/topo
 %%PLIST_TOPO%%bin/topo
 %%PLIST_VIENNA%%share/EMBOSS/acd/vrnaalifold.acd
@@ -451,8 +462,34 @@
 %%PLIST_MIRA%%share/EMBOSS/acd/emiraest.acd
 %%PLIST_MIRA%%bin/emira
 %%PLIST_MIRA%%bin/emiraest
+%%PLIST_MYEMBOSS%%share/EMBOSS/doc/html/embassy/myemboss/index.html
+%%PLIST_MYEMBOSS%%@dirrm share/EMBOSS/doc/html/embassy/myemboss
 %%PLIST_IPRSCAN%%share/EMBOSS/acd/eiprscan.acd
+%%PLIST_IPRSCAN%%share/EMBOSS/doc/html/embassy/iprscan/eiprscan.html
+%%PLIST_IPRSCAN%%share/EMBOSS/doc/html/embassy/iprscan/index.html
 %%PLIST_IPRSCAN%%bin/eiprscan
+%%PLIST_IPRSCAN%%@dirrm share/EMBOSS/doc/html/embassy/iprscan
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/elipop.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eiprscan.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/echlorop.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetnglyc.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetoglyc.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetphos.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eprop.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/esignalp.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/etmhmm.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eyinoyang.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/index.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/echlorop.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/elipop.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetnglyc.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetoglyc.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetphos.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/eprop.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/esignalp.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/etmhmm.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/eyinoyang.html
+%%PLIST_CBSTOOLS%%@dirrm share/EMBOSS/doc/html/embassy/cbstools
 %%PLIST_CBSTOOLS%%share/EMBOSS/acd/echlorop.acd
 %%PLIST_CBSTOOLS%%share/EMBOSS/acd/elipop.acd
 %%PLIST_CBSTOOLS%%share/EMBOSS/acd/enetnglyc.acd
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