author: Rene Ladan <rene@FreeBSD.org> 2020-05-05 15:38:11 +0000
committer: Rene Ladan <rene@FreeBSD.org> 2020-05-05 15:38:11 +0000
commit: 0786acb3155523a38d1442f3c16ca56750f1db04 (patch)
tree: 42843d6e23bc6be789c7f1284cdc61d43d3c0942 /biology
parent: e0510744daebb2bb9f73bf707c276e02e4c191fe (diff)
download: ports-0786acb3155523a38d1442f3c16ca56750f1db04.tar.gz
ports-0786acb3155523a38d1442f3c16ca56750f1db04.zip
35 files changed, 0 insertions, 2475 deletions
diff --git a/biology/Makefile b/biology/Makefile
index e113e4078e36..12be99b39569 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -21,7 +21,6 @@
     SUBDIR += checkm
     SUBDIR += clustal-omega
     SUBDIR += clustalw
-    SUBDIR += consed
     SUBDIR += cufflinks
     SUBDIR += cytoscape
     SUBDIR += ddocent
@@ -115,7 +114,6 @@
     SUBDIR += phylip
     SUBDIR += phyml
     SUBDIR += plink
-    SUBDIR += plinkseq
     SUBDIR += primer3
     SUBDIR += prodigal
     SUBDIR += prodigy-lig
@@ -151,7 +149,6 @@
     SUBDIR += seqan1
     SUBDIR += seqio
     SUBDIR += seqtk
-    SUBDIR += seqtools
     SUBDIR += sim4
     SUBDIR += slclust
     SUBDIR += smithwaterman
@@ -159,14 +156,12 @@
     SUBDIR += star
     SUBDIR += stringtie
     SUBDIR += tRNAscan-SE
-    SUBDIR += t_coffee
     SUBDIR += tabixpp
     SUBDIR += tophat
     SUBDIR += treekin
     SUBDIR += treepuzzle
     SUBDIR += trimadap
     SUBDIR += trimmomatic
-    SUBDIR += ugene
     SUBDIR += vcflib
     SUBDIR += vcftools
     SUBDIR += velvet
diff --git a/biology/consed/Makefile b/biology/consed/Makefile
deleted file mode 100644
index 2a0373ca0d4d..000000000000
--- a/biology/consed/Makefile
+++ /dev/null
@@ -1,86 +0,0 @@
-# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
-# $FreeBSD$
-
-PORTNAME=	consed
-PORTVERSION=	27.0
-CATEGORIES=	biology
-# MASTER_SITES=	http://www.phrap.org/consed/distributions/${PORTVERSION}/
-# MASTER_SITES=	http://bozeman.mbt.washington.edu/consed/distributions/${PORTVERSION}/
-DISTNAME=	${PORTNAME}_linux
-
-MAINTAINER=	mzaki@m.u-tokyo.ac.jp
-COMMENT=	Graphical tool for editing Phrap assemblies
-
-BROKEN=		unfetchable
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2020-05-05
-
-RUN_DEPENDS=	phred:biology/phred \
-		phrap:biology/phrap
-
-CONFLICTS_INSTALL=	phd2fasta-[0-9]*
-
-SUB_FILES=	pkg-message
-
-USES=		linux perl5 shebangfix
-USE_LINUX=	xorglibs
-ONLY_FOR_ARCHS=	i386 amd64
-MYSHEBANG=	bin/ace2Fasta.perl \
-		bin/tagRepeats.perl \
-		bin/selectRegions.perl \
-		bin/selectOneRegion.perl \
-		bin/revertToUneditedRead \
-		bin/removeReads \
-		bin/phredPhrap.orig \
-		bin/phredPhrap \
-		bin/phd2Ace.perl \
-		bin/orderPrimerPairs.perl \
-		bin/makeRegionsFile.perl \
-		bin/makePhdBall.perl \
-		bin/lib2Phd.perl \
-		bin/fixContigEnd.perl \
-		bin/findSequenceMatchesForConsed.perl \
-		bin/revert_fof \
-		bin/filter454Reads.perl \
-		bin/fastq2Phrap.perl \
-		bin/fasta2PhdBall.perl \
-		bin/fasta2Phd.perl \
-		bin/fasta2Ace.perl \
-		bin/determineReadTypes.perl \
-		bin/countEditedBases.perl \
-		bin/bam2Ace.perl \
-		bin/amplifyTranscripts.perl \
-		bin/alignSolexaReads2Refs.perl \
-		bin/alignRNA2Genomic.perl \
-		bin/addSolexaReads.perl \
-		bin/addSangerReads.perl \
-		bin/addReads2Consed.perl \
-		bin/add454Reads.perl \
-		bin/ace2Oligos.perl \
-		bin/transferConsensusTags.perl \
-		bin/ace2fof \
-		bin/ace2OligosWithComments.perl \
-		bin/sff2phd.perl \
-		bin/recover_consensus_tags \
-		bin/phredPhrapWithPhdBalls \
-		bin/cons.perl \
-		bin/acestatus.pl \
-		bin/aceContigs2Phds.perl \
-		bin/sff2phd_Samborskyy
-
-RESTRICTED=	Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use.
-.if defined(PACKAGE_BUILDING)
-IGNORE=		distribution files must be obtained via the authors
-.endif
-
-NO_WRKSUBDIR=	yes
-NO_BUILD=	yes
-
-do-install:
-	${MKDIR} ${STAGEDIR}${DATADIR}
-	${LN} -sf ../../bin ${STAGEDIR}${DATADIR}/bin
-	(cd ${WRKSRC}; ${SETENV} CC=${CC} ./installConsed.perl consed_linux32bit ${STAGEDIR}${DATADIR})
-	${LN} -sf ../../../etc/PhredPar/phredpar.dat ${STAGEDIR}${DATADIR}/lib/phredpar.dat
-	cd ${STAGEDIR}${PREFIX} && ${ECHO_CMD} ${MYSHEBANG} | ${XARGS} ${SED} -i '' ${_SHEBANG_REINPLACE_ARGS}
-
-.include <bsd.port.mk>
diff --git a/biology/consed/distinfo b/biology/consed/distinfo
deleted file mode 100644
index 828556d8cd5e..000000000000
--- a/biology/consed/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (consed_linux.tar.gz) = 8038d2b94078ba918e97785fc7497252139029281000f1c54ff9dd1ec70e05fc
-SIZE (consed_linux.tar.gz) = 34390726
diff --git a/biology/consed/files/patch-installConsed.perl b/biology/consed/files/patch-installConsed.perl
deleted file mode 100644
index 057ea5d13a90..000000000000
--- a/biology/consed/files/patch-installConsed.perl
+++ /dev/null
@@ -1,57 +0,0 @@
---- installConsed.perl.orig	2014-02-11 21:28:45.000000000 +0100
-+++ installConsed.perl	2014-08-23 19:27:23.000000000 +0200
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl -w
-+#!/usr/local/bin/perl -w
- 
- # installConsed.perl 
- 
-@@ -9,7 +9,7 @@
- # and this must be empty and must allow write access
- 
- # edit this if you are using a different compiler than gcc
--$CC = "gcc";
-+$CC = $ENV{'CC'};
- 
- $szVersion = "25.0";
- 
-@@ -78,9 +78,9 @@
- $szHowToStartOver = "if you have had an error in the midst of this script, you have a problem because some things have been done and others not done.  The cleanest solution is to go back to where nothing is done.  To do that, type:\nrm -rf $szConsedHome/bin\nrm -rf $szConsedHome/lib\nrm -rf $szConsedHome/examples";
- 
- 
--if ( -e "$szConsedHome/bin" ) {
--   die "$szConsedHome/bin already exists\n$szHowToStartOver\n";
--}
-+#if ( -e "$szConsedHome/bin" ) {
-+#   die "$szConsedHome/bin already exists\n$szHowToStartOver\n";
-+#}
- 
- if ( -e "$szConsedHome/lib" ) {
-    die "$szConsedHome/lib already exists\n$szHowToStartOver\n";
-@@ -91,7 +91,7 @@
- }
- 
- 
--&doCommand( "mkdir $szConsedHome/bin" );
-+#&doCommand( "mkdir $szConsedHome/bin" );
- &doCommand( "mkdir -p $szConsedHome/lib/screenLibs" );
- &doCommand( "mkdir $szConsedHome/examples" );
- &doCommand( "cp $szConsedExecutable $szConsedHome/bin" );
-@@ -101,7 +101,7 @@
- print "done\n";
- &doCommand( "cp README.txt $szConsedHome" );
- 
--&doCommand( "chmod -R a+w $szConsedHome/examples/*" );
-+#&doCommand( "chmod -R a+w $szConsedHome/examples/*" );
- 
- &doCommand( "cp $szDownloadDirectory/scripts/* $szConsedHome/bin" );
- 
-@@ -112,7 +112,7 @@
- @aScreenLibs = split(' ', $szScreenLibs );
- foreach $szScreenFile ( @aScreenLibs ) {
-    print "about to cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs\n";
--   &doCommand( "cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs" );
-+   &doCommand( "cp $szDownloadDirectory/misc/$szScreenFile $szConsedHome/lib/screenLibs/$szScreenFile.sample" );
- }
- 
- 
diff --git a/biology/consed/files/patch-misc_mktrace.c b/biology/consed/files/patch-misc_mktrace.c
deleted file mode 100644
index 99fa065b0bbf..000000000000
--- a/biology/consed/files/patch-misc_mktrace.c
+++ /dev/null
@@ -1,14 +0,0 @@
---- misc/mktrace/mktrace.c.orig	Tue Aug 31 03:14:17 2004
-+++ misc/mktrace/mktrace.c	Wed Jul 13 16:31:28 2005
-@@ -70,9 +70,9 @@
-   else
-   {
-     printf( "enter FASTA filename: " );
--    gets( ifnm );
-+    fgets( ifnm, sizeof(ifnm), stdin );
-     printf( "enter output filename: " );
--    gets( ofnm );
-+    fgets( ofnm, sizeof(ofnm), stdin );
-   }
- 
-   /*
diff --git a/biology/consed/files/patch-scripts_phredPhrap b/biology/consed/files/patch-scripts_phredPhrap
deleted file mode 100644
index b0543e7b5ed6..000000000000
--- a/biology/consed/files/patch-scripts_phredPhrap
+++ /dev/null
@@ -1,11 +0,0 @@
---- scripts/phredPhrap.orig	2014-02-12 05:28:45.000000000 +0900
-+++ scripts/phredPhrap	2014-06-22 03:07:33.000000000 +0900
-@@ -217,7 +217,7 @@
- #$solexaDirPath = "../solexa_dir";
- #$sffDirPath = "../sff_dir";
- 
--$niceExe = "/bin/nice";
-+$niceExe = "/usr/bin/nice";
- $mvExe = "/bin/mv";
- $lsExe = "/bin/ls";
- $pwdExe = "/bin/pwd";
diff --git a/biology/consed/files/pkg-message.in b/biology/consed/files/pkg-message.in
deleted file mode 100644
index 88635ec10cb2..000000000000
--- a/biology/consed/files/pkg-message.in
+++ /dev/null
@@ -1,16 +0,0 @@
-[
-{ type: install
-  message: <<EOM
-CONSED installation directory: %%PREFIX%%/share/consed
-
-  You must do either of following (see section 4.5 of README.txt):
-  1) set CONSED_HOME environment variable to the location above
-  2) make /usr/local/genome be a symlink targeting to the location above
-
-Example files are installed not as world writable, which README.txt assumes.
-So you must copy the files to anywhere you have writable permissions.
-
-Now you can follow README.txt from section 4.12
-EOM
-}
-]
diff --git a/biology/consed/pkg-descr b/biology/consed/pkg-descr
deleted file mode 100644
index f0c1defcddd8..000000000000
--- a/biology/consed/pkg-descr
+++ /dev/null
@@ -1,4 +0,0 @@
-Consed is a tool for viewing and editing sequence assemblies made by phrap,
-and includes Autofinish which will automatically choose finishing reads.
-
-WWW: http://www.phrap.org/consed/consed.html
diff --git a/biology/plinkseq/Makefile b/biology/plinkseq/Makefile
deleted file mode 100644
index 55c1f6274ecf..000000000000
--- a/biology/plinkseq/Makefile
+++ /dev/null
@@ -1,48 +0,0 @@
-# $FreeBSD$
-
-PORTNAME=	plinkseq
-PORTVERSION=	0.10
-PORTREVISION=	1
-CATEGORIES=	biology science
-MASTER_SITES=	http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/
-# Default DISTNAME is correct, so leave it alone.
-DISTFILES=	${PORTNAME}-src-${PORTVERSION}.tgz
-
-MAINTAINER=	jwb@FreeBSD.org
-COMMENT=	Toolset for working with human genetic variation data
-
-BROKEN=		unfetchable
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2020-05-05
-
-LICENSE=	GPLv2
-
-BROKEN_aarch64=		Does not build: Host architecture was not detected as supported by protobuf
-BROKEN_mips64=		Does not build: Host architecture was not detected as supported by protobuf
-BROKEN_powerpc64=	Does not build: atomicops.h: error: stray '\#' in program
-
-USES=		libtool gmake
-
-post-patch:
-	${REINPLACE_CMD} \
-		-e 's|PF_INET|AF_INET|g' \
-		${WRKSRC}/sources/mongoose/sources/lib/mongoose.c
-	${REINPLACE_CMD} \
-		-e 's|g++|${CXX}|g' \
-		-e 's|gcc|${CC}|g' \
-		-e 's|CXXFLAGS = -O3|CXXFLAGS = ${CXXFLAGS}|g' \
-		-e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = ${CFLAGS}|g' \
-		${WRKSRC}/config_defs.Makefile
-	${REINPLACE_CMD} \
-		-e 's| -ldl||g' \
-		-e 's| $$(STATIC_FLAG)||g' \
-		${WRKSRC}/Makefile
-
-do-install:
-.for f in behead browser gcol mm mongoose pdas pseq smp tab2vcf
-	${INSTALL_PROGRAM} ${WRKSRC}/build/execs/${f} ${STAGEDIR}${PREFIX}/bin
-.endfor
-	${INSTALL_DATA} ${WRKSRC}/sources/plinkseq/build/lib/libplinkseq.a \
-		${STAGEDIR}${PREFIX}/lib
-
-.include <bsd.port.mk>
diff --git a/biology/plinkseq/distinfo b/biology/plinkseq/distinfo
deleted file mode 100644
index 5bdc92e8a6bd..000000000000
--- a/biology/plinkseq/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (plinkseq-src-0.10.tgz) = e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58
-SIZE (plinkseq-src-0.10.tgz) = 6090698
diff --git a/biology/plinkseq/files/patch-sources_plinkseq_sources_lib_r8lib.cpp b/biology/plinkseq/files/patch-sources_plinkseq_sources_lib_r8lib.cpp
deleted file mode 100644
index 10d4005f15dc..000000000000
--- a/biology/plinkseq/files/patch-sources_plinkseq_sources_lib_r8lib.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- sources/plinkseq/sources/lib/r8lib.cpp.orig	2014-07-09 14:37:16 UTC
-+++ sources/plinkseq/sources/lib/r8lib.cpp
-@@ -31828,7 +31828,7 @@ void r8vec_index_sorted_range ( int n, d
-   if ( r_hi < r[indx[*i_hi]] )
-   {
-     *i_hi = *i_hi - 1;
--    if ( i_hi < 0 )
-+    if ( *i_hi < 0 )
-     {
-       *i_lo = *i_hi + 1;
-     }
diff --git a/biology/plinkseq/pkg-descr b/biology/plinkseq/pkg-descr
deleted file mode 100644
index 1d7356738a2a..000000000000
--- a/biology/plinkseq/pkg-descr
+++ /dev/null
@@ -1,8 +0,0 @@
-PLINK/SEQ is an open-source C/C++ library for working with human
-genetic variation data. The specific focus is to provide a platform
-for analytic tool development for variation data from large-scale
-resequencing and genotyping projects, particularly whole-exome and
-whole-genome studies. It is independent of (but designed to be
-complementary to) the existing PLINK package.
-
-WWW: http://atgu.mgh.harvard.edu/plinkseq/
diff --git a/biology/plinkseq/pkg-plist b/biology/plinkseq/pkg-plist
deleted file mode 100644
index d00aeaa028d8..000000000000
--- a/biology/plinkseq/pkg-plist
+++ /dev/null
@@ -1,10 +0,0 @@
-bin/behead
-bin/browser
-bin/gcol
-bin/mm
-bin/mongoose
-bin/pdas
-bin/pseq
-bin/smp
-bin/tab2vcf
-lib/libplinkseq.a
diff --git a/biology/seqtools/Makefile b/biology/seqtools/Makefile
deleted file mode 100644
index 382d2410701b..000000000000
--- a/biology/seqtools/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-# $FreeBSD$
-
-PORTNAME=	seqtools
-PORTVERSION=	4.44.1
-PORTREVISION=	4
-CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
-
-MAINTAINER=	pi@FreeBSD.org
-COMMENT=	Tools for visualising sequence alignments
-
-BROKEN=		unfetchable
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2020-05-05
-
-LICENSE=	GPLv3
-
-LIB_DEPENDS=	libcurl.so:ftp/curl \
-		libsqlite3.so:databases/sqlite3 \
-		libfontconfig.so:x11-fonts/fontconfig \
-		libfreetype.so:print/freetype2
-
-USES=		compiler:c++14-lang gettext gnome libtool pkgconfig xorg
-GNU_CONFIGURE=	yes
-USE_GNOME=	cairo gdkpixbuf2 gtk20
-USE_XORG=	x11
-CFLAGS+=	-I${LOCALBASE}/include
-LLD_UNSAFE=	yes
-LDFLAGS+=	-L${LOCALBASE}/lib -lexecinfo -lcurl -lsqlite3 -lm
-MAKE_JOBS_UNSAFE=	yes
-
-OPTIONS_DEFINE=	DOCS
-
-.include <bsd.port.mk>
diff --git a/biology/seqtools/distinfo b/biology/seqtools/distinfo
deleted file mode 100644
index 093df2f988da..000000000000
--- a/biology/seqtools/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-TIMESTAMP = 1478810582
-SHA256 (seqtools-4.44.1.tar.gz) = 0e1dd7087d1180e434f0ea1aac21b8dfb5261195581ec3ba012abf0d1e39daa9
-SIZE (seqtools-4.44.1.tar.gz) = 6922888
diff --git a/biology/seqtools/files/patch-gbtools_src_blatSrc_lib_gff3.c b/biology/seqtools/files/patch-gbtools_src_blatSrc_lib_gff3.c
deleted file mode 100644
index 9b2e58f66d57..000000000000
--- a/biology/seqtools/files/patch-gbtools_src_blatSrc_lib_gff3.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- gbtools/src/blatSrc/lib/gff3.c.orig	2016-11-10 21:14:27 UTC
-+++ gbtools/src/blatSrc/lib/gff3.c
-@@ -7,6 +7,7 @@
- /* Copyright (C) 2014 The Regents of the University of California 
-  * See README in this or parent directory for licensing information. */
- #include "common.h"
-+#include "dnaseq.h"
- #include "gff3.h"
- #include <limits.h>
- #include "errAbort.h"
diff --git a/biology/seqtools/pkg-descr b/biology/seqtools/pkg-descr
deleted file mode 100644
index 7b4688a5992e..000000000000
--- a/biology/seqtools/pkg-descr
+++ /dev/null
@@ -1,17 +0,0 @@
-A suite of tools for visualising sequence alignments.
-
-Blixem is an interactive browser of pairwise alignments that have
-been stacked up in a "master-slave" multiple alignment; it is not
-a 'true' multiple alignment but a 'one-to-many' alignment.
-
-Belvu is a multiple sequence alignment viewer and phylogenetic tool.
-It has an extensive set of user-configurable modes to color residues
-by conservation or by residue type, and some basic alignment editing
-capabilities.
-
-Dotter is a graphical dot-matrix program for detailed comparison
-of two sequences. Every residue in one sequence is compared to every
-residue in the other, with one sequence plotted on the x-axis and
-the other on the y-axis.
-
-WWW: http://www.sanger.ac.uk/science/tools/seqtools
diff --git a/biology/seqtools/pkg-plist b/biology/seqtools/pkg-plist
deleted file mode 100644
index a8e064fb6c53..000000000000
--- a/biology/seqtools/pkg-plist
+++ /dev/null
@@ -1,226 +0,0 @@
-%%PORTDOCS%%%%DOCSDIR%%/Belvu_manual.pdf
-%%PORTDOCS%%%%DOCSDIR%%/Blixem_manual.pdf
-%%PORTDOCS%%%%DOCSDIR%%/Dotter_manual.pdf
-%%PORTDOCS%%%%DOCSDIR%%/belvu_quick_start.html
-%%PORTDOCS%%%%DOCSDIR%%/belvu_usage.txt
-%%PORTDOCS%%%%DOCSDIR%%/blixem_quick_start.html
-%%PORTDOCS%%%%DOCSDIR%%/blixem_usage.txt
-%%PORTDOCS%%%%DOCSDIR%%/dotter_quick_start.html
-%%PORTDOCS%%%%DOCSDIR%%/dotter_usage.txt
-%%PORTDOCS%%%%DOCSDIR%%/release_notes.html
-%%PORTDOCS%%%%DOCSDIR%%/todo.html
-bin/belvu
-bin/blixem
-bin/blixemh
-bin/dotter
-include/blatSrc/ace.h
-include/blatSrc/aliType.h
-include/blatSrc/annoAssembly.h
-include/blatSrc/annoFilter.h
-include/blatSrc/annoFormatTab.h
-include/blatSrc/annoFormatter.h
-include/blatSrc/annoGrateWig.h
-include/blatSrc/annoGrator.h
-include/blatSrc/annoGratorQuery.h
-include/blatSrc/annoOption.h
-include/blatSrc/annoRow.h
-include/blatSrc/annoStreamBigBed.h
-include/blatSrc/annoStreamBigWig.h
-include/blatSrc/annoStreamTab.h
-include/blatSrc/annoStreamVcf.h
-include/blatSrc/annoStreamer.h
-include/blatSrc/apacheLog.h
-include/blatSrc/asParse.h
-include/blatSrc/axt.h
-include/blatSrc/bPlusTree.h
-include/blatSrc/bamFile.h
-include/blatSrc/bandExt.h
-include/blatSrc/base64.h
-include/blatSrc/basicBed.h
-include/blatSrc/bbiFile.h
-include/blatSrc/bigBed.h
-include/blatSrc/bigWig.h
-include/blatSrc/binRange.h
-include/blatSrc/bits.h
-include/blatSrc/blastParse.h
-include/blatSrc/boxClump.h
-include/blatSrc/boxLump.h
-include/blatSrc/bwgInternal.h
-include/blatSrc/cda.h
-include/blatSrc/cgi_build_rules.mk
-include/blatSrc/chain.h
-include/blatSrc/chainBlock.h
-include/blatSrc/chainConnect.h
-include/blatSrc/chainToAxt.h
-include/blatSrc/chainToPsl.h
-include/blatSrc/cheapcgi.h
-include/blatSrc/cirTree.h
-include/blatSrc/codebias.h
-include/blatSrc/common.h
-include/blatSrc/common.mk
-include/blatSrc/correlate.h
-include/blatSrc/crTree.h
-include/blatSrc/crudeali.h
-include/blatSrc/diGraph.h
-include/blatSrc/diGraph.h.97
-include/blatSrc/dlist.h
-include/blatSrc/dnaLoad.h
-include/blatSrc/dnaMarkov.h
-include/blatSrc/dnaMotif.h
-include/blatSrc/dnaseq.h
-include/blatSrc/dnautil.h
-include/blatSrc/dtdParse.h
-include/blatSrc/dyOut.h
-include/blatSrc/dystring.h
-include/blatSrc/elmTree.h
-include/blatSrc/emblParse.h
-include/blatSrc/ens.h
-include/blatSrc/errAbort.h
-include/blatSrc/errCatch.h
-include/blatSrc/fa.h
-include/blatSrc/fieldedTable.h
-include/blatSrc/filePath.h
-include/blatSrc/flydna.h
-include/blatSrc/fof.h
-include/blatSrc/fq.h
-include/blatSrc/fuzzyFind.h
-include/blatSrc/gapCalc.h
-include/blatSrc/gdf.h
-include/blatSrc/genoFind.h
-include/blatSrc/genomeRangeTree.h
-include/blatSrc/gfClientLib.h
-include/blatSrc/gfPcrLib.h
-include/blatSrc/gfWebLib.h
-include/blatSrc/gff.h
-include/blatSrc/gff3.h
-include/blatSrc/gfxPoly.h
-include/blatSrc/gifLabel.h
-include/blatSrc/hacTree.h
-include/blatSrc/hash.h
-include/blatSrc/hex.h
-include/blatSrc/hgGene.h
-include/blatSrc/hgap.h
-include/blatSrc/hgdb.h
-include/blatSrc/histogram.h
-include/blatSrc/hmac.h
-include/blatSrc/hmmPfamParse.h
-include/blatSrc/hmmstats.h
-include/blatSrc/htmlPage.h
-include/blatSrc/htmshell.h
-include/blatSrc/https.h
-include/blatSrc/intValTree.h
-include/blatSrc/internet.h
-include/blatSrc/itsa.h
-include/blatSrc/iupac.h
-include/blatSrc/jointalign.h
-include/blatSrc/jpegSize.h
-include/blatSrc/jsonParse.h
-include/blatSrc/jsonWrite.h
-include/blatSrc/keys.h
-include/blatSrc/knetUdc.h
-include/blatSrc/kxTok.h
-include/blatSrc/linefile.h
-include/blatSrc/localEnvironment.mk
-include/blatSrc/localmem.h
-include/blatSrc/log.h
-include/blatSrc/longToList.h
-include/blatSrc/maDbRep.h
-include/blatSrc/maToFf.h
-include/blatSrc/maf.h
-include/blatSrc/mailViaPipe.h
-include/blatSrc/md5.h
-include/blatSrc/memalloc.h
-include/blatSrc/memgfx.h
-include/blatSrc/meta.h
-include/blatSrc/metaWig.h
-include/blatSrc/mime.h
-include/blatSrc/net.h
-include/blatSrc/nib.h
-include/blatSrc/nibTwo.h
-include/blatSrc/nt4.h
-include/blatSrc/obscure.h
-include/blatSrc/oldGff.h
-include/blatSrc/oligoTm.h
-include/blatSrc/ooc.h
-include/blatSrc/options.h
-include/blatSrc/pairDistance.h
-include/blatSrc/pairHmm.h
-include/blatSrc/paraFetch.h
-include/blatSrc/patSpace.h
-include/blatSrc/peakCluster.h
-include/blatSrc/phyloTree.h
-include/blatSrc/pipeline.h
-include/blatSrc/portable.h
-include/blatSrc/psGfx.h
-include/blatSrc/psPoly.h
-include/blatSrc/pscmGfx.h
-include/blatSrc/psl.h
-include/blatSrc/pslTbl.h
-include/blatSrc/pslTransMap.h
-include/blatSrc/pthreadDoList.h
-include/blatSrc/pthreadWrap.h
-include/blatSrc/qa.h
-include/blatSrc/quickHeap.h
-include/blatSrc/quotedP.h
-include/blatSrc/ra.h
-include/blatSrc/raToStruct.h
-include/blatSrc/rainbow.h
-include/blatSrc/rangeTree.h
-include/blatSrc/rbTree.h
-include/blatSrc/regexHelper.h
-include/blatSrc/repMask.h
-include/blatSrc/rle.h
-include/blatSrc/rnautil.h
-include/blatSrc/rql.h
-include/blatSrc/rudp.h
-include/blatSrc/scoreWindow.h
-include/blatSrc/seg.h
-include/blatSrc/seqOut.h
-include/blatSrc/seqStats.h
-include/blatSrc/shaRes.h
-include/blatSrc/sig.h
-include/blatSrc/slog.h
-include/blatSrc/snof.h
-include/blatSrc/snofmake.h
-include/blatSrc/spaceSaver.h
-include/blatSrc/spacedColumn.h
-include/blatSrc/spacedSeed.h
-include/blatSrc/splatAli.h
-include/blatSrc/splix.h
-include/blatSrc/sqlList.h
-include/blatSrc/sqlNum.h
-include/blatSrc/subText.h
-include/blatSrc/sufa.h
-include/blatSrc/sufx.h
-include/blatSrc/supStitch.h
-include/blatSrc/synQueue.h
-include/blatSrc/tabRow.h
-include/blatSrc/textOut.h
-include/blatSrc/tokenizer.h
-include/blatSrc/trans3.h
-include/blatSrc/trix.h
-include/blatSrc/twoBit.h
-include/blatSrc/udc.h
-include/blatSrc/unfin.h
-include/blatSrc/userApp.mk
-include/blatSrc/vGfx.h
-include/blatSrc/vcf.h
-include/blatSrc/vcfBits.h
-include/blatSrc/verbose.h
-include/blatSrc/wormdna.h
-include/blatSrc/xAli.h
-include/blatSrc/xa.h
-include/blatSrc/xap.h
-include/blatSrc/xenalign.h
-include/blatSrc/xmlEscape.h
-include/blatSrc/xp.h
-include/blatSrc/zlibFace.h
-include/gbtools/gbtools.hpp
-include/gbtools/gbtoolsCurl.hpp
-include/gbtools/gbtoolsGUI.hpp
-include/gbtools/gbtoolsPfetch.hpp
-include/gbtools/gbtoolsTrackhub.hpp
-include/gbtools/gbtoolsUtils.hpp
-include/json/json-forwards.h
-include/json/json.h
-lib/libgbtools.a
diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
deleted file mode 100644
index af5beed604f1..000000000000
--- a/biology/t_coffee/Makefile
+++ /dev/null
@@ -1,41 +0,0 @@
-# Created by: Johann Visagie <wjv@FreeBSD.org>
-# $FreeBSD$
-
-PORTNAME=	t_coffee
-PORTVERSION=	9.03
-DISTVERSIONSUFFIX=	.r1318
-PORTREVISION=	11
-CATEGORIES=	biology
-MASTER_SITES=	http://www.tcoffee.org/Packages/Stable/Version_${PORTVERSION}${DISTVERSIONSUFFIX}/
-DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX}
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Multiple DNA or protein sequence alignment package
-
-BROKEN=		unfetchable
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2020-05-05
-
-LICENSE=	GPLv2
-
-RUN_DEPENDS=	clustalw:biology/clustalw
-
-OPTIONS_DEFINE=	EXAMPLES
-
-BUILD_WRKSRC=	${WRKSRC}/t_coffee_source
-
-USES=		fortran
-CFLAGS+=	-Wno-return-type
-MAKE_ENV=	FCC="${FC} ${FFLAGS}"
-MAKEFILE=	makefile
-
-PORTEXAMPLES=	*
-PLIST_FILES=	bin/TMalign bin/t_coffee
-
-do-install:
-	(cd ${BUILD_WRKSRC} \
-		&& ${INSTALL_PROGRAM} TMalign t_coffee ${STAGEDIR}${PREFIX}/bin)
-	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
-	(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
-
-.include <bsd.port.mk>
diff --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo
deleted file mode 100644
index 376d92c9077b..000000000000
--- a/biology/t_coffee/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c
-SIZE (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 3455629
diff --git a/biology/t_coffee/files/patch-dev3.c b/biology/t_coffee/files/patch-dev3.c
deleted file mode 100644
index 0b1335e5c5d9..000000000000
--- a/biology/t_coffee/files/patch-dev3.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- t_coffee_source/dev3.c.orig	2012-07-13 02:06:31.000000000 +0900
-+++ t_coffee_source/dev3.c	2012-10-04 22:14:10.000000000 +0900
-@@ -3,6 +3,7 @@
- #include <math.h>
- #include <stdarg.h>
- #include <string.h>
-+#include <sys/types.h>
- #include <sys/sysctl.h>
- #include "dev3_lib_header.h"
- /******************************COPYRIGHT NOTICE*******************************/
diff --git a/biology/t_coffee/pkg-descr b/biology/t_coffee/pkg-descr
deleted file mode 100644
index 2186686dd5e8..000000000000
--- a/biology/t_coffee/pkg-descr
+++ /dev/null
@@ -1,18 +0,0 @@
-From the website:
-
-  T-Coffee is a multiple sequence alignment package. Given a set of sequences
-  (Proteins or DNA), T-Coffee generates a multiple sequence alignment.
-
-  Related publications:
-  - 3DCoffee: Combining Protein Sequences and Structures within Multiple
-    Sequence Alignments.
-    O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame.
-    Journal of Molecular Biology, Vol 340, pp385-395, 2004
-  - T-Coffee: A novel method for multiple sequence alignments.  C.Notredame,
-    D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
-    pp205-217,2000
-  - COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
-    C.  Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
-    407-422,1998
-
-WWW: http://www.tcoffee.org/
diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
deleted file mode 100644
index e9e4e5b18cd9..000000000000
--- a/biology/ugene/Makefile
+++ /dev/null
@@ -1,76 +0,0 @@
-# Created by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
-# $FreeBSD$
-
-PORTNAME=	ugene
-DISTVERSION=	1.31.0
-PORTREVISION=	1
-CATEGORIES=	biology science
-MASTER_SITES=	http://ugene.unipro.ru/downloads/
-DISTFILES=	${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \
-		UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf
-DIST_SUBDIR=	${PORTNAME}
-EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
-
-MAINTAINER=	h2+fbsdports@fsfe.org
-COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
-
-BROKEN=		unfetchable
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2020-05-05
-
-LICENSE=	GPLv2+
-LICENSE_FILE=	${WRKSRC}/LICENSE.txt
-
-RUN_DEPENDS=	bash:shells/bash
-
-BROKEN_aarch64=	Fails to build: invokes x86 asm
-
-USES=		desktop-file-utils gl qmake qt:5 shared-mime-info xorg
-USE_GL=		gl glu
-USE_QT=		buildtools_build linguisttools_build \
-		core gui network opengl printsupport script scripttools \
-		sql svg testlib webkit widgets xml \
-		imageformats_run
-USE_XORG=	x11 xtst
-
-QMAKE_ARGS=	INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \
-		INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \
-		LUPDATE="${LUPDATE}"
-ALL_TARGET=	release
-
-DOCSDIR=	${DATADIR}/manuals
-
-OPTIONS_DEFINE=	DOCS OPENCL
-DOCS_DESC=	Install official UGENE documentation (PDF)
-
-OPENCL_QMAKE_ON=	UGENE_OPENCL_DETECTED=1
-
-.include <bsd.port.pre.mk>
-
-.if ${ARCH} == amd64
-# XXX: need to manually tell the build we are on x64
-QMAKE_ARGS+=	CONFIG+=x64
-.endif
-
-.if ${MACHINE_CPU:Msse2}
-QMAKE_ARGS+=	UGENE_SSE2_DETECTED=1
-.endif
-
-post-extract:
-	@${MKDIR} ${WRKSRC}/data/manuals
-	${CP} -p ${_DISTDIR}/*.pdf ${WRKSRC}/data/manuals
-
-post-patch:
-# yes, bash is required, stuff will not execute with sh
-	@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
-		${WRKSRC}/src/gen_bin_script.cmd \
-		${WRKSRC}/installer/_common_data/ugene
-	@${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \
-		${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp
-	@${REINPLACE_CMD} 's, -lbreakpad,,' \
-		${WRKSRC}/src/corelibs/U2Private/U2Private.pri \
-		${WRKSRC}/src/plugins_checker/plugins_checker.pri \
-		${WRKSRC}/src/ugenecl/ugenecl.pri \
-		${WRKSRC}/src/ugeneui/ugeneui.pri
-
-.include <bsd.port.post.mk>
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
deleted file mode 100644
index d85231b953aa..000000000000
--- a/biology/ugene/distinfo
+++ /dev/null
@@ -1,9 +0,0 @@
-TIMESTAMP = 1535840965
-SHA256 (ugene/ugene-1.31.0.tar.gz) = d1f46306834a292618cc54b31060b69da5b0b18da311a55bf82ab42f5a434320
-SIZE (ugene/ugene-1.31.0.tar.gz) = 20656562
-SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4
-SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662
-SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6
-SIZE (ugene/UniproUGENE_UserManual.pdf) = 13443754
-SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 8cc6630f62c82de42926c14c3d01ebc3c7d85ab7d9ec2a81e55a19740806735c
-SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29474484
diff --git a/biology/ugene/files/patch-git_578c949 b/biology/ugene/files/patch-git_578c949
deleted file mode 100644
index 8b11562770d1..000000000000
--- a/biology/ugene/files/patch-git_578c949
+++ /dev/null
@@ -1,25 +0,0 @@
-From 578c949ae7df017e23c3eda0293faa3db718c89f Mon Sep 17 00:00:00 2001
-From: Yuliya Algaer <yalgaer@gmail.com>
-Date: Fri, 24 Aug 2018 21:24:12 +0700
-Subject: [PATCH] Build fix for Fedora
-
---- src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp.orig	2018-08-16 13:58:58 UTC
-+++ src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
-@@ -20,6 +20,7 @@
-  */
- 
- #include <U2Core/U2SafePoints.h>
-+#include <QIntValidator>
- 
- #include "LengthSettingsWidget.h"
- #include "LineEditHighlighter.h"
---- src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp.orig	2018-08-16 13:58:58 UTC
-+++ src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
-@@ -19,6 +19,7 @@
-  * MA 02110-1301, USA.
-  */
- 
-+#include <QIntValidator>
- #include <U2Core/U2SafePoints.h>
- 
- #include "QualitySettingsWidget.h"
diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
deleted file mode 100644
index 73f2d4038887..000000000000
--- a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
+++ /dev/null
@@ -1,41 +0,0 @@
---- src/corelibs/U2Private/U2Private.pro.orig	2018-08-16 13:59:12 UTC
-+++ src/corelibs/U2Private/U2Private.pro
-@@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \
-            src/PluginSupportImpl.h \
-            src/ServiceRegistryImpl.h \
-            src/SettingsImpl.h \
--           src/TaskSchedulerImpl.h \
--           src/crash_handler/CrashHandler.h \
--           src/crash_handler/CrashHandlerArgsHelper.h \
--           src/crash_handler/CrashHandlerPrivate.h \
--           src/crash_handler/CrashLogCache.h \
--           src/crash_handler/StackWalker.h
-+           src/TaskSchedulerImpl.h
- 
- SOURCES += src/AppContextImpl.cpp \
-            src/AppSettingsImpl.cpp \
-@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \
-            src/PluginSupportImpl.cpp \
-            src/ServiceRegistryImpl.cpp \
-            src/SettingsImpl.cpp \
--           src/TaskSchedulerImpl.cpp \
--           src/crash_handler/CrashHandler.cpp \
--           src/crash_handler/CrashHandlerArgsHelper.cpp \
--           src/crash_handler/CrashHandlerPrivate.cpp \
--           src/crash_handler/CrashLogCache.cpp \
--           src/crash_handler/StackWalker.cpp
-+           src/TaskSchedulerImpl.cpp
- 
- TRANSLATIONS += transl/russian.ts
- 
- win32 {
-     HEADERS += src/crash_handler/CrashHandlerPrivateWin.h
-     SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp
--}
--
--unix_not_mac() {
--    HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h
--    SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp
- }
- 
- mac {
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
deleted file mode 100644
index cc2164cb1db0..000000000000
--- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
+++ /dev/null
@@ -1,22 +0,0 @@
-Use the Linux driver for FreeBSD as well. Fixes crash on startup.
-
---- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig	2018-09-02 00:22:54 UTC
-+++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
-@@ -22,7 +22,7 @@
- #include <cctype>
- #include "GTKeyboardDriver.h"
- 
--#if defined __linux__
-+#if defined(__linux__) || defined(__FreeBSD__)
-     #define XK_LATIN1      // for latin symbol
-     #define XK_MISCELLANY  // for action keys
-     #include <X11/keysymdef.h>
-@@ -31,7 +31,7 @@
- 
- namespace HI {
- 
--#if defined __linux__
-+#if defined(__linux__) || defined(__FreeBSD__)
- 
- #define GT_CLASS_NAME "GTKeyboardDriverLinux"
- 
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
deleted file mode 100644
index 8dfdd9b7d53f..000000000000
--- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
-Use the Linux driver for FreeBSD as well. Fixes crash on startup.
-
---- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig	2018-09-02 00:23:24 UTC
-+++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp
-@@ -22,13 +22,13 @@
- #include "GTMouseDriver.h"
- #include <QByteArray>
- 
--#ifdef __linux__
-+#if defined(__linux__) || defined(__FreeBSD__)
-     #include <X11/extensions/XTest.h>
- #endif
- 
- namespace HI {
- 
--#ifdef __linux__
-+#if defined(__linux__) || defined(__FreeBSD__)
- 
- #define GT_CLASS_NAME "GTMouseDriver Linux"
- QPoint GTMouseDriver::mousePos = QPoint(-1, -1);
diff --git a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
deleted file mode 100644
index bd0d64942c01..000000000000
--- a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
+++ /dev/null
@@ -1,31 +0,0 @@
---- src/plugins_checker/src/Main.cpp.orig	2018-08-16 13:59:06 UTC
-+++ src/plugins_checker/src/Main.cpp
-@@ -39,7 +39,7 @@
- #include <ServiceRegistryImpl.h>
- #include <SettingsImpl.h>
- #include <TaskSchedulerImpl.h>
--#include <crash_handler/CrashHandler.h>
-+//#include <crash_handler/CrashHandler.h>
- 
- #define TR_SETTINGS_ROOT QString("test_runner/")
- 
-@@ -55,8 +55,10 @@ static void registerCoreServices() {
- 
- int main(int argc, char **argv)
- {
-+#if 0
-     CrashHandler::setupHandler();
-     CrashHandler::setSendCrashReports(false);
-+#endif
- 
-     const char* build = QT_VERSION_STR, *runtime = qVersion();
-     if (strcmp(build, runtime) > 0){
-@@ -141,7 +143,7 @@ int main(int argc, char **argv)
-     delete cmdLineRegistry;
-     appContext->setCMDLineRegistry(NULL);
- 
--    CrashHandler::shutdown();
-+    //CrashHandler::shutdown();
- 
-     return rc;
- }
diff --git a/biology/ugene/files/patch-src_plugins_test__runner_src_Reporter.ui b/biology/ugene/files/patch-src_plugins_test__runner_src_Reporter.ui
deleted file mode 100644
index ea99ef35e76b..000000000000
--- a/biology/ugene/files/patch-src_plugins_test__runner_src_Reporter.ui
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/plugins/test_runner/src/Reporter.ui.orig	2018-12-11 15:24:12 UTC
-+++ src/plugins/test_runner/src/Reporter.ui
-@@ -36,7 +36,7 @@
-   <customwidget>
-    <class>QWebView</class>
-    <extends>QWidget</extends>
--   <header>QtWebKit/QWebView</header>
-+   <header>QtWebKitWidgets/QWebView</header>
-   </customwidget>
-  </customwidgets>
-  <resources/>
diff --git a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
deleted file mode 100644
index 917fc096b4c4..000000000000
--- a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
---- src/ugenecl/src/Main.cpp.orig	2018-08-16 13:59:20 UTC
-+++ src/ugenecl/src/Main.cpp
-@@ -93,7 +93,7 @@
- #include <ServiceRegistryImpl.h>
- #include <SettingsImpl.h>
- #include <TaskSchedulerImpl.h>
--#include <crash_handler/CrashHandler.h>
-+//#include <crash_handler/CrashHandler.h>
- 
- // local project imports
- #include "DumpHelpTask.h"
-@@ -191,6 +191,7 @@ static void setSearchPaths() {
- 
- int main(int argc, char **argv)
- {
-+#if 0
-     if (CrashHandler::isEnabled()) {
-         CrashHandler::setupHandler();
-     }
-@@ -198,6 +199,7 @@ int main(int argc, char **argv)
-     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
-         CrashHandler::setSendCrashReports(false);
-     }
-+#endif
- 
-     const char* build = QT_VERSION_STR, *runtime = qVersion();
-     if (strcmp(build, runtime) > 0){
-@@ -617,7 +619,7 @@ int main(int argc, char **argv)
-     delete pwr;
-     appContext->setAlignmentAlgorithmsRegistry(NULL);
- 
--    CrashHandler::shutdown();
-+    //CrashHandler::shutdown();
- 
-     return rc;
- }
diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
deleted file mode 100644
index e5dcadcdea21..000000000000
--- a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
---- src/ugeneui/src/Main.cpp.orig	2018-08-16 13:59:19 UTC
-+++ src/ugeneui/src/Main.cpp
-@@ -136,7 +136,7 @@
- #include <ServiceRegistryImpl.h>
- #include <SettingsImpl.h>
- #include <TaskSchedulerImpl.h>
--#include <crash_handler/CrashHandler.h>
-+//#include <crash_handler/CrashHandler.h>
- 
- #include "app_settings/AppSettingsGUIImpl.h"
- #include "app_settings/logview_settings/LogSettingsGUIController.h"
-@@ -353,6 +353,7 @@ void fixMacFonts() {
- 
- int main(int argc, char **argv)
- {
-+#if 0
-     if (CrashHandler::isEnabled()) {
-         CrashHandler::setupHandler();
-     }
-@@ -360,6 +361,7 @@ int main(int argc, char **argv)
-     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
-         CrashHandler::setSendCrashReports(false);
-     }
-+#endif
- 
-     QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR );
- 
-@@ -973,7 +975,7 @@ int main(int argc, char **argv)
-     }
- 
-     UgeneUpdater::onClose();
--    CrashHandler::shutdown();
-+    //CrashHandler::shutdown();
- 
-     return rc;
- }
diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro
deleted file mode 100644
index 8962a9edc02e..000000000000
--- a/biology/ugene/files/patch-ugene.pro
+++ /dev/null
@@ -1,29 +0,0 @@
---- ugene.pro.orig	2018-08-16 13:58:51 UTC
-+++ ugene.pro
-@@ -20,7 +20,6 @@ use_bundled_zlib() {
- }
- 
- SUBDIRS += \
--          src/libs_3rdparty/breakpad \
-           src/libs_3rdparty/qscore \
-           src/libs_3rdparty/sqlite3 \
-           src/libs_3rdparty/samtools \
-@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
- win32 : UGENE_DEV_NULL = nul
- unix : UGENE_DEV_NULL = /dev/null
- 
--UGENE_LRELEASE =
--UGENE_LUPDATE =
--message(Using QT from $$[QT_INSTALL_BINS])
--system($$[QT_INSTALL_BINS]/lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
--    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease-qt5
--    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate-qt5
--} else : system($$[QT_INSTALL_BINS]/lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
--    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
--    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate
--}
-+UGENE_LRELEASE = $$LRELEASE
-+UGENE_LUPDATE = $$LUPDATE
- 
- #foreach 'language'
- for( i, UGENE_TRANSL_IDX ) {
diff --git a/biology/ugene/pkg-descr b/biology/ugene/pkg-descr
deleted file mode 100644
index a5e84919dfc2..000000000000
--- a/biology/ugene/pkg-descr
+++ /dev/null
@@ -1,12 +0,0 @@
-Unipro UGENE is multiplatform, open-source software with the main goal of
-assisting molecular biologists without much expertise in bioinformatics to
-manage, analyze, and visualize their data.  UGENE integrates widely used
-bioinformatics tools within one common user interface.
-
-UGENE toolkit supports multiple biological data formats and allows the
-retrieval of data from remote data sources.  It provides visualization
-modules for biological objects such as annotated genome sequences, Next
-Generation Sequencing (NGS) assembly data, multiple sequence alignments,
-phylogenetic trees, and 3D structures.
-
-WWW: http://ugene.unipro.ru/
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
deleted file mode 100644
index 08b3c7f508f3..000000000000
--- a/biology/ugene/pkg-plist
+++ /dev/null
@@ -1,1492 +0,0 @@
-bin/ugene
-lib/ugene/libQSpec.so
-lib/ugene/libQSpec.so.1
-lib/ugene/libQSpec.so.1.0
-lib/ugene/libQSpec.so.1.0.0
-lib/ugene/libU2Algorithm.so
-lib/ugene/libU2Algorithm.so.1
-lib/ugene/libU2Algorithm.so.1.0
-lib/ugene/libU2Algorithm.so.1.0.0
-lib/ugene/libU2Core.so
-lib/ugene/libU2Core.so.1
-lib/ugene/libU2Core.so.1.0
-lib/ugene/libU2Core.so.1.0.0
-lib/ugene/libU2Designer.so
-lib/ugene/libU2Designer.so.1
-lib/ugene/libU2Designer.so.1.0
-lib/ugene/libU2Designer.so.1.0.0
-lib/ugene/libU2Formats.so
-lib/ugene/libU2Formats.so.1
-lib/ugene/libU2Formats.so.1.0
-lib/ugene/libU2Formats.so.1.0.0
-lib/ugene/libU2Gui.so
-lib/ugene/libU2Gui.so.1
-lib/ugene/libU2Gui.so.1.0
-lib/ugene/libU2Gui.so.1.0.0
-lib/ugene/libU2Lang.so
-lib/ugene/libU2Lang.so.1
-lib/ugene/libU2Lang.so.1.0
-lib/ugene/libU2Lang.so.1.0.0
-lib/ugene/libU2Private.so
-lib/ugene/libU2Private.so.1
-lib/ugene/libU2Private.so.1.0
-lib/ugene/libU2Private.so.1.0.0
-lib/ugene/libU2Script.so
-lib/ugene/libU2Script.so.1
-lib/ugene/libU2Script.so.1.0
-lib/ugene/libU2Script.so.1.0.0
-lib/ugene/libU2Test.so
-lib/ugene/libU2Test.so.1
-lib/ugene/libU2Test.so.1.0
-lib/ugene/libU2Test.so.1.0.0
-lib/ugene/libU2View.so
-lib/ugene/libU2View.so.1
-lib/ugene/libU2View.so.1.0
-lib/ugene/libU2View.so.1.0.0
-lib/ugene/libugenedb.so
-lib/ugene/libugenedb.so.1
-lib/ugene/libugenedb.so.1.0
-lib/ugene/libugenedb.so.1.0.0
-lib/ugene/plugins/CoreTests.license
-lib/ugene/plugins/CoreTests.plugin
-lib/ugene/plugins/GUITestBase.license
-lib/ugene/plugins/GUITestBase.plugin
-lib/ugene/plugins/annotator.license
-lib/ugene/plugins/annotator.plugin
-lib/ugene/plugins/api_tests.license
-lib/ugene/plugins/api_tests.plugin
-lib/ugene/plugins/ball.license
-lib/ugene/plugins/ball.plugin
-lib/ugene/plugins/biostruct3d_view.license
-lib/ugene/plugins/biostruct3d_view.plugin
-lib/ugene/plugins/browser_support.license
-lib/ugene/plugins/browser_support.plugin
-lib/ugene/plugins/chroma_view.license
-lib/ugene/plugins/chroma_view.plugin
-lib/ugene/plugins/circular_view.license
-lib/ugene/plugins/circular_view.plugin
-lib/ugene/plugins/clark_support.license
-lib/ugene/plugins/clark_support.plugin
-lib/ugene/plugins/dbi_bam.license
-lib/ugene/plugins/dbi_bam.plugin
-lib/ugene/plugins/diamond_support.license
-lib/ugene/plugins/diamond_support.plugin
-lib/ugene/plugins/dna_export.license
-lib/ugene/plugins/dna_export.plugin
-lib/ugene/plugins/dna_flexibility.license
-lib/ugene/plugins/dna_flexibility.plugin
-lib/ugene/plugins/dna_graphpack.license
-lib/ugene/plugins/dna_graphpack.plugin
-lib/ugene/plugins/dna_stat.license
-lib/ugene/plugins/dna_stat.plugin
-lib/ugene/plugins/dotplot.license
-lib/ugene/plugins/dotplot.plugin
-lib/ugene/plugins/enzymes.license
-lib/ugene/plugins/enzymes.plugin
-lib/ugene/plugins/external_tool_support.license
-lib/ugene/plugins/external_tool_support.plugin
-lib/ugene/plugins/genome_aligner.license
-lib/ugene/plugins/genome_aligner.plugin
-lib/ugene/plugins/gor4.license
-lib/ugene/plugins/gor4.plugin
-lib/ugene/plugins/hmm2.license
-lib/ugene/plugins/hmm2.plugin
-lib/ugene/plugins/kalign.license
-lib/ugene/plugins/kalign.plugin
-lib/ugene/plugins/kraken_support.license
-lib/ugene/plugins/kraken_support.plugin
-lib/ugene/plugins/libCoreTests.so
-lib/ugene/plugins/libCoreTests.so.1
-lib/ugene/plugins/libCoreTests.so.1.0
-lib/ugene/plugins/libCoreTests.so.1.0.0
-lib/ugene/plugins/libGUITestBase.so
-lib/ugene/plugins/libGUITestBase.so.1
-lib/ugene/plugins/libGUITestBase.so.1.0
-lib/ugene/plugins/libGUITestBase.so.1.0.0
-lib/ugene/plugins/libannotator.so
-lib/ugene/plugins/libannotator.so.1
-lib/ugene/plugins/libannotator.so.1.0
-lib/ugene/plugins/libannotator.so.1.0.0
-lib/ugene/plugins/libapi_tests.so
-lib/ugene/plugins/libapi_tests.so.1
-lib/ugene/plugins/libapi_tests.so.1.0
-lib/ugene/plugins/libapi_tests.so.1.0.0
-lib/ugene/plugins/libball.so
-lib/ugene/plugins/libball.so.1
-lib/ugene/plugins/libball.so.1.0
-lib/ugene/plugins/libball.so.1.0.0
-lib/ugene/plugins/libbiostruct3d_view.so
-lib/ugene/plugins/libbiostruct3d_view.so.1
-lib/ugene/plugins/libbiostruct3d_view.so.1.0
-lib/ugene/plugins/libbiostruct3d_view.so.1.0.0
-lib/ugene/plugins/libbrowser_support.so
-lib/ugene/plugins/libbrowser_support.so.1
-lib/ugene/plugins/libbrowser_support.so.1.0
-lib/ugene/plugins/libbrowser_support.so.1.0.0
-lib/ugene/plugins/libchroma_view.so
-lib/ugene/plugins/libchroma_view.so.1
-lib/ugene/plugins/libchroma_view.so.1.0
-lib/ugene/plugins/libchroma_view.so.1.0.0
-lib/ugene/plugins/libcircular_view.so
-lib/ugene/plugins/libcircular_view.so.1
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-lib/ugene/plugins/libcircular_view.so.1.0.0
-lib/ugene/plugins/libclark_support.so
-lib/ugene/plugins/libclark_support.so.1
-lib/ugene/plugins/libclark_support.so.1.0
-lib/ugene/plugins/libclark_support.so.1.0.0
-lib/ugene/plugins/libdbi_bam.so
-lib/ugene/plugins/libdbi_bam.so.1
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-lib/ugene/plugins/libdbi_bam.so.1.0.0
-lib/ugene/plugins/libdiamond_support.so
-lib/ugene/plugins/libdiamond_support.so.1
-lib/ugene/plugins/libdiamond_support.so.1.0
-lib/ugene/plugins/libdiamond_support.so.1.0.0
-lib/ugene/plugins/libdna_export.so
-lib/ugene/plugins/libdna_export.so.1
-lib/ugene/plugins/libdna_export.so.1.0
-lib/ugene/plugins/libdna_export.so.1.0.0
-lib/ugene/plugins/libdna_flexibility.so
-lib/ugene/plugins/libdna_flexibility.so.1
-lib/ugene/plugins/libdna_flexibility.so.1.0
-lib/ugene/plugins/libdna_flexibility.so.1.0.0
-lib/ugene/plugins/libdna_graphpack.so
-lib/ugene/plugins/libdna_graphpack.so.1
-lib/ugene/plugins/libdna_graphpack.so.1.0
-lib/ugene/plugins/libdna_graphpack.so.1.0.0
-lib/ugene/plugins/libdna_stat.so
-lib/ugene/plugins/libdna_stat.so.1
-lib/ugene/plugins/libdna_stat.so.1.0
-lib/ugene/plugins/libdna_stat.so.1.0.0
-lib/ugene/plugins/libdotplot.so
-lib/ugene/plugins/libdotplot.so.1
-lib/ugene/plugins/libdotplot.so.1.0
-lib/ugene/plugins/libdotplot.so.1.0.0
-lib/ugene/plugins/libenzymes.so
-lib/ugene/plugins/libenzymes.so.1
-lib/ugene/plugins/libenzymes.so.1.0
-lib/ugene/plugins/libenzymes.so.1.0.0
-lib/ugene/plugins/libexternal_tool_support.so
-lib/ugene/plugins/libexternal_tool_support.so.1
-lib/ugene/plugins/libexternal_tool_support.so.1.0
-lib/ugene/plugins/libexternal_tool_support.so.1.0.0
-lib/ugene/plugins/libgenome_aligner.so
-lib/ugene/plugins/libgenome_aligner.so.1
-lib/ugene/plugins/libgenome_aligner.so.1.0
-lib/ugene/plugins/libgenome_aligner.so.1.0.0
-lib/ugene/plugins/libgor4.so
-lib/ugene/plugins/libgor4.so.1
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-lib/ugene/plugins/libgor4.so.1.0.0
-lib/ugene/plugins/libhmm2.so
-lib/ugene/plugins/libhmm2.so.1
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-lib/ugene/plugins/libkalign.so
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-lib/ugene/plugins/libkraken_support.so
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-lib/ugene/plugins/libkraken_support.so.1.0.0
-lib/ugene/plugins/liblinkdata_support.so
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-lib/ugene/plugins/liblinkdata_support.so.1.0.0
-lib/ugene/plugins/libngs_reads_classification.so
-lib/ugene/plugins/libngs_reads_classification.so.1
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-lib/ugene/plugins/libopencl_support.so
-lib/ugene/plugins/libopencl_support.so.1
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-lib/ugene/plugins/libopencl_support.so.1.0.0
-lib/ugene/plugins/liborf_marker.so
-lib/ugene/plugins/liborf_marker.so.1
-lib/ugene/plugins/liborf_marker.so.1.0
-lib/ugene/plugins/liborf_marker.so.1.0.0
-lib/ugene/plugins/libpcr.so
-lib/ugene/plugins/libpcr.so.1
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-lib/ugene/plugins/libpcr.so.1.0.0
-lib/ugene/plugins/libperf_monitor.so
-lib/ugene/plugins/libperf_monitor.so.1
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-lib/ugene/plugins/libperf_monitor.so.1.0.0
-lib/ugene/plugins/libphylip.so
-lib/ugene/plugins/libphylip.so.1
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-lib/ugene/plugins/libptools.so
-lib/ugene/plugins/libptools.so.1
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-lib/ugene/plugins/libquery_designer.so
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-lib/ugene/plugins/libremote_blast.so
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-lib/ugene/plugins/opencl_support.license
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-lib/ugene/plugins/orf_marker.plugin
-lib/ugene/plugins/pcr.license
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-lib/ugene/plugins/perf_monitor.license
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-lib/ugene/plugins/primer3.license
-lib/ugene/plugins/primer3.plugin
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-lib/ugene/plugins/query_designer.license
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-lib/ugene/plugins/remote_blast.plugin
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-lib/ugene/plugins/sitecon.license
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-%%DATADIR%%/DBXRefRegistry.txt
-%%DATADIR%%/adapters/adapters.fasta
-%%DATADIR%%/adapters/illumina/NexteraPE-PE.fa
-%%DATADIR%%/adapters/illumina/TruSeq2-PE.fa
-%%DATADIR%%/adapters/illumina/TruSeq2-SE.fa
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-%%DATADIR%%/adapters/illumina/TruSeq3-SE.fa
-%%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
-%%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut
-%%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut
-%%DATADIR%%/back_translation/Bacteria/Haemophilus_influenzae.cut
-%%DATADIR%%/back_translation/Bacteria/Helicobacter_pylori.cut
-%%DATADIR%%/back_translation/Bacteria/Listeria_monocytogenes.cut
-%%DATADIR%%/back_translation/Bacteria/Neisseria_meningitidis.cut
-%%DATADIR%%/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut
-%%DATADIR%%/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut
-%%DATADIR%%/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut
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-%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut
-%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut
-%%DATADIR%%/back_translation/Mammalia/Bos_taurus_(cow).cut
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-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx4_3488.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx5_3419.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dmbx1_2277.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dobox4_3956.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dobox5_3493.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Duxl_1286.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Emx2_3420.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/En1_3123.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/En2_0952.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Esx1_3124.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Evx1_3952.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Evx2_2645.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gbx1_2883.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gbx2_3110.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gsc_2327.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gsh2_3990.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hdx_3845.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlx1_2350.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlxb9_3422.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmbox1_2674.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx1_3423.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx2_3424.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx3_3490.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Homez_1063.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa10_2318.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa11_2218.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa13_3126.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa1_3425.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa2_3079.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa3_2783.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa4_3426.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa5_3415.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa6_1040.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_2668.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_3750.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa9_2622.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb13_3479.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb3_1720.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb4_2627.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb5_3122.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb6_3428.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb7_3953.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb8_3780.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb9_3413.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc10_2779.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc11_3718.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc12_3480.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc13_3127.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc4_3491.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc5_2630.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc6_3954.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc8_3429.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc9_2367.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd10_2368.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd11_3873.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd12_3481.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd13_2356.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd1_3448.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd3_1742.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd8_2644.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Ipf1_3815.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx2_0900.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_0920.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_2226.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx4_2242.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx5_2385.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx6_2623.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isl2_3430.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isx_3445.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lbx2_3869.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx1_2240.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx2_0953.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx3_3431.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx4_1719.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx5_2279.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_2272.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_3432.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx8_2247.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx9_3492.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1a_2238.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1b_3433.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meis1_2335.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meox1_2310.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg1_2246.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg2_2302.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx1_3031.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx2_3449.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx3_3206.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-1_3856.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-2_3214.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-2_2823.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-3_3435.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-4_3074.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-5_3436.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-6_3437.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-9_3082.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx3-1_2923.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-3_3446.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox1_3970.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox2_3438.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox3_3439.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_2284.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_3963.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox6_3440.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Og2x_3719.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otp_3496.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx1_2325.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx2_3441.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax4_3989.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax6_3838.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax7_3783.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pbx1_3203.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2a_3947.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2b_3948.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx1_2312.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx2_2274.3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx3_3497.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox1_2364.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox2_3077.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou1f1_3818.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f1_3081.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f2_3748.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f3_3986.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f1_3819.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f2_2824.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f3_3235.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f4_3773.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou4f3_2791.1.pwm
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-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx1_3442.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx2_3072.1.pwm
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-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_2205.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox6_4251.1.pwm
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-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six2_2307.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six3_1732.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six4_2860.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.5.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf1_2666.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf2_0913.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif1_2342.2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif2_3451.1.pwm
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-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax2_3500.1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vsx1_1728.1.pwm
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-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Asg1.pwm
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-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cbf1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cep3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cha4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cup9.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ecm22.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fhl1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gal4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gcn4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gln3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gsm1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gzf3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Hal9.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Leu3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Lys14.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Matalpha2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mbp1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mcm1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Met32.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mga1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ndt80.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6a.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6b.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nrg1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Oaf1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pdr1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Phd1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Put3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rap1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rdr1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rgt1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rph1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rpn4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfl1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sip4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Skn7.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Smp1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Spt15.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Srd1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stb3.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp4.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sum1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sut2.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbf1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tbs1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tea1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tec1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tye7.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ume6.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Usv1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Xbp1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap6.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ybr239c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ydr520c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yer130c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ygr067c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ykl222c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yll054c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yml081w.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ynr063w.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yox1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr013c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm
-%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm
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author	Rene Ladan <rene@FreeBSD.org>	2020-05-05 15:38:11 +0000
committer	Rene Ladan <rene@FreeBSD.org>	2020-05-05 15:38:11 +0000
commit	0786acb3155523a38d1442f3c16ca56750f1db04 (patch)
tree	42843d6e23bc6be789c7f1284cdc61d43d3c0942 /biology
parent	e0510744daebb2bb9f73bf707c276e02e4c191fe (diff)
download	ports-0786acb3155523a38d1442f3c16ca56750f1db04.tar.gz ports-0786acb3155523a38d1442f3c16ca56750f1db04.zip