Revert "sci-biology/blue: Initial ebuild, does not install the *.exe.so files. Do we need them?"

This reverts commit b79af8f82794f511181ab43aa0c20871a4d39723.

33 files changed, 0 insertions, 623 deletions

diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
deleted file mode 100644
index 84008208e..000000000
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Atlas Whole Genome Assembly Suite"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"
-# https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/Atlas/Manifest b/sci-biology/Atlas/Manifest
deleted file mode 100644
index 176b0e2fb..000000000
--- a/sci-biology/Atlas/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST atlas-src.tgz 645758 SHA256 d157d4ea77101925b648dd0ad8a22b9d58944df1ea5be19c9627ac200b344978 SHA512 12d31642fbab52ae06a681dda8a3aae675f8898f357e2ffa9a5d37933ad327bef157784fbe936076cba17d774187296b0b8b516eced48a45914bba879165b8d9 WHIRLPOOL 459a57ba1178e5a8df9506da1d6dc6e8a7afea4a3c67977804e066ef0453e434019c9cf10b16526c6e7cfb5b8b5a687d3f85cb84588c952eb9a7a30f66bbbcba
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
deleted file mode 100644
index b918714f7..000000000
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Close gaps using BWA-identified reads and reassemble using Phrap, Newbler, Velvet, compare by cross_match"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill"
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2"
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# is there an ebuild for newbler?
-DEPEND="dev-lang/perl
-	(sys-cluster/torque || sys/cluster/openpbs)
-	sci-biology/phrap
-	sci-biology/bwa
-	sci-biology/velvet"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/CAutils/CAutils-20120126.ebuild b/sci-biology/CAutils/CAutils-20120126.ebuild
deleted file mode 100644
index 7b1ca7b97..000000000
--- a/sci-biology/CAutils/CAutils-20120126.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION="Additional utilities for Celera assembler (wgs-assembler) from UMD"
-HOMEPAGE="http://www.cbcb.umd.edu/research/CeleraAssembler.shtml"
-SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/CAutils.tar.gz"
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-lang/perl"
-
-# is partially included in amos-3.1.0
diff --git a/sci-biology/CAutils/Manifest b/sci-biology/CAutils/Manifest
deleted file mode 100644
index 5f12e80e2..000000000
--- a/sci-biology/CAutils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST CAutils.tar.gz 16800 SHA256 d772b338ade65ac59c6190885219053fd8c613c1b53a024df7899ef187a929e6 SHA512 382578957510f8bab3688510a1ec37c864ff48de2e94cbbd532cbe4b318a3a286ce2a456704f48055e4d27aac972748a61944c061b22b35c76402f5d58f20a83 WHIRLPOOL 141e3b46d7373fed27239493adb124a913c1b2693923959b2a4d53543a637847b492a22b21bd719cbbf4a40de3c782956692114cd73f5743b6d62a00f0f5dc4e
diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild b/sci-biology/InterMine/InterMine-0.98.ebuild
deleted file mode 100644
index a06fba722..000000000
--- a/sci-biology/InterMine/InterMine-0.98.ebuild
+++ /dev/null
@@ -1,3 +0,0 @@
-http://intermine.org/
-svn co svn://subversion.flymine.org/branches/intermine_0_98
-LGPL-3
diff --git a/sci-biology/MochiView/MochiView-1.45.ebuild b/sci-biology/MochiView/MochiView-1.45.ebuild
deleted file mode 100644
index 5e9344a1f..000000000
--- a/sci-biology/MochiView/MochiView-1.45.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-DESCRIPTION=""
-HOMEPAGE=""
-SRC_URI=""
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
deleted file mode 100644
index 984b7a643..000000000
--- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-DESCRIPTION="Noise removal from pyrosequenced amplicons"
-HOMEPAGE="http://code.google.com/p/ampliconnoise/"
-SRC_URI="http://ampliconnoise.googlecode.com/files/AmpliconNoiseV"${PV}".tar.gz
-	http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz
-	http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz"
-
-LICENSE="LGPL"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
deleted file mode 100644
index 2dfb766c2..000000000
--- a/sci-biology/bioperl/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST BioPerl-1.6.901.tar.gz 12284856 RMD160 d852438ab4720501b8bd62fa5df4ba302981b410 SHA1 d0650c5e16895c13798003dd3a57bced23e7a9ce SHA256 8c74bde900222ce3926491ee103997c841c8755148c8dcaf0be1abfd61c5ac01
-EBUILD bioperl-1.6.901.ebuild 2210 RMD160 d22a323e95ee934455d87312837bd9caeb0d6b76 SHA1 3b0381ea010716cfd2f7ce6d8eefc43fe31723de SHA256 eb1f8606548377497f3c4b270c9cb3ed76f61093c9b7c88b3114fc0604f4e167
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
diff --git a/sci-biology/bioperl/bioperl-1.6.901.ebuild b/sci-biology/bioperl/bioperl-1.6.901.ebuild
deleted file mode 100644
index 98d0763c1..000000000
--- a/sci-biology/bioperl/bioperl-1.6.901.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.1.ebuild,v 1.3 2009/10/02 14:51:51 weaver Exp $
-
-EAPI="2"
-
-inherit perl-module
-
-SUBPROJECTS="+db +network +run"
-MIN_PV="1.6"
-
-DESCRIPTION="Perl tools for bioinformatics - Core modules"
-HOMEPAGE="http://www.bioperl.org/"
-# SRC_URI="http://www.bioperl.org/DIST/BioPerl-${PV}.tar.bz2"
-SRC_URI="http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-${PV}.tar.gz"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="-minimal graphviz sqlite ${SUBPROJECTS}"
-
-CDEPEND=">=perl-core/Module-Build-0.380.0
-	dev-perl/Data-Stag
-	dev-perl/libwww-perl
-	!minimal? (
-		dev-perl/Ace
-		dev-perl/Spreadsheet-ParseExcel
-		dev-perl/Spreadsheet-WriteExcel
-		>=dev-perl/XML-SAX-0.15
-		dev-perl/Graph
-		dev-perl/SOAP-Lite
-		dev-perl/Array-Compare
-		dev-perl/SVG
-		dev-perl/XML-Simple
-		dev-perl/XML-Parser
-		dev-perl/XML-Twig
-		>=dev-perl/HTML-Parser-3.60
-		>=dev-perl/XML-Writer-0.4
-		dev-perl/Clone
-		dev-perl/XML-DOM
-		dev-perl/set-scalar
-		dev-perl/XML-XPath
-		dev-perl/XML-DOM-XPath
-		dev-perl/Algorithm-Munkres
-		dev-perl/Data-Stag
-		dev-perl/Math-Random
-		dev-perl/PostScript
-		dev-perl/Convert-Binary-C
-		dev-perl/SVG-Graph
-		dev-perl/IO-String
-		dev-perl/Class-Inspector
-		dev-perl/Sort-Naturally
-	)
-	graphviz? ( dev-perl/GraphViz )
-	sqlite? ( dev-perl/DBD-SQLite )"
-DEPEND="virtual/perl-Module-Build
-	${CDEPEND}"
-# In perl-overlay
-#	>=virtual/perl-ExtUtils-Manifest-1.52 (to CDEPEND?)
-#	>=perl-CPAN/perl-CPAN-1.81
-RDEPEND="${CDEPEND}"
-PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene )
-	db? ( >=sci-biology/bioperl-db-${MIN_PV} )
-	network? ( >=sci-biology/bioperl-network-${MIN_PV} )
-	run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
-
-S="${WORKDIR}/BioPerl-${PV}"
-
-src_configure() {
-	sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
-		-e "/'CPAN' *=> *1.81/d" \
-		-e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" || die
-
-	if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi
-	perl-module_src_configure
-}
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
deleted file mode 100644
index d4648212c..000000000
--- a/sci-biology/bioperl/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-biology</herd>
-</pkgmetadata>
diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog
deleted file mode 100644
index 7c7456378..000000000
--- a/sci-biology/blue/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for sci-biology/blue
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*blue-1.1.2 (07 Jan 2015)
-
-  07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.2.ebuild,
-  +metadata.xml:
-  Initial ebuild, does not install the *.exe.so files. Do we need them?
-
diff --git a/sci-biology/blue/Manifest b/sci-biology/blue/Manifest
deleted file mode 100644
index eaacef198..000000000
--- a/sci-biology/blue/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST Correcting_reads_with_Blue.pdf 821286 SHA256 b20cf2524740a2fbacee6bf0dbb652c06a00a3a1b112d448114cebe900bc970d SHA512 73906f2844d89dbf7dcf6a163d8763b8995669871082abf362c4cc4fa8b21fa180cad0c4f024ea4d82a32a0fcda8d4e85a563d58cc7fd2b49dc63c09c88ef714 WHIRLPOOL 754b77f034f1df878f8b942f6985212a3da0f57576a6a5bbd06564591ac41c40396c147a91a2792ab226a7c30a23179e3118724f72ee289bd2133b61c14a2ec1
-DIST blue-1.1.2.tar.gz 658544 SHA256 c038fa9fd76330cb70059cd47979327708368e2d6b6d7edae00825ba39dc23bd SHA512 933b2a8bb1e1f3fed241cff2eac9566d49d77c3f97b2f22f4a8194f3cdf25c09ae474b4d681ff65914d695598579fded6433f6a47ad06b78879c36d58402ea4b WHIRLPOOL 32c89ae39cfadab9beae038afd530cf85d8c8775a84bd5e2c29a2e67246d9b09d5c872492c1836dfab6fe20e9f59a1b0aaddc5dc051393030ccff39bb08fec8e
diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
deleted file mode 100644
index 52ca61484..000000000
--- a/sci-biology/blue/blue-1.1.2.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions"
-HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx"
-SRC_URI="http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> "${P}".tar.gz
-	http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx -> Correcting_reads_with_Blue.pdf"
-
-LICENSE="GPL"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="dev-lang/mono"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/Linux
-
-src_compile(){
-	Blue/compile.sh || die
-	Tessel/compile.sh || die
-	GenerateMerPairs/compile.sh || die
-}
-
-src_install(){
-	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
-	# BUG: probably have to install also the *.exe.so files
-}
diff --git a/sci-biology/blue/metadata.xml b/sci-biology/blue/metadata.xml
deleted file mode 100644
index 2bc893037..000000000
--- a/sci-biology/blue/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-  <maintainer>
-    <email>mmokrejs@fold.natur.cuni.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/ePCR/Manifest b/sci-biology/ePCR/Manifest
deleted file mode 100644
index 15ae9cb05..000000000
--- a/sci-biology/ePCR/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST e-PCR-2.3.12-src.tar.gz 76391 SHA256 c53887b3b5e07bfb902f9717a737ed5a093402384b859724a525feb86111764f SHA512 d943b4f1f7173d517c09a98aa61649864b74362741192b52cbe9bbc40d12a7318bb9ce3753f99231cf953d8838c076378af187b4eb2404707669457709b5a412 WHIRLPOOL 756385f519a3a301e308e0cdf37ea83cc983ed736d28b9bb481b49242ccd12d31be7ce00e4680912cdd93637548b235eb5a8bb30a4b257079001be5f70c5864b
diff --git a/sci-biology/ePCR/ePCR-2.3.12.ebuild b/sci-biology/ePCR/ePCR-2.3.12.ebuild
deleted file mode 100644
index 8e71c90be..000000000
--- a/sci-biology/ePCR/ePCR-2.3.12.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit eutils
-
-DESCRIPTION="Search for sub-sequences matching PCR primers with correct order, orientation, and spacing"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/e-pcr/"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-"${PV}"-src.tar.gz"
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}"/e-PCR-"${PV}
-
-src_prepare(){
-	epatch ${FILESDIR}"/config.mk.patch"
-}
-
-src_compile(){
-	make -j1 srcdir=${S} objdir=${S} || die "make -j1 failed"
-}
-
-src_install(){
-	dobin e-PCR famap fahash re-PCR
-	dodoc README.TXT
-}
diff --git a/sci-biology/ePCR/files/config.mk.patch b/sci-biology/ePCR/files/config.mk.patch
deleted file mode 100644
index 1960b43f7..000000000
--- a/sci-biology/ePCR/files/config.mk.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- stand/config.mk.ori	2012-01-16 17:38:11.000000000 +0100
-+++ stand/config.mk	2012-01-16 17:39:12.000000000 +0100
-@@ -52,11 +52,11 @@
- 
- #########################################################################
- # GNU compiler flags
--CC = gcc
--CXX = g++
--CXXFLAGS = -I$(srcdir) -I$(INCDIR) $(CC_FLAGS) $(PART_CXXFLAGS) \
-+#CC = gcc
-+#CXX = g++
-+CXXFLAGS = -I$(srcdir) -I$(INCDIR) -I`pwd` \
- 	-DDEALLOCATE=0 $(LF64CCFLAGS) $(VERSION_FLAGS) -DSTANDALONE=1
--LDFLAGS = $(LD_FLAGS) $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR) $(PART_LDFLAGS) 
-+LDFLAGS = $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR) 
- #	$(PART_PRELIBS) $(LIBS:%=-l%) $(PART_POSTLIBS)
- 
- LF64CCFLAGS = `getconf LFS_CFLAGS` 
diff --git a/sci-biology/est2assembly/Manifest b/sci-biology/est2assembly/Manifest
deleted file mode 100644
index 51f8a3d58..000000000
--- a/sci-biology/est2assembly/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST est2assembly_1.08.tar.gz 5643052 RMD160 703e30be0d16791c3454d4842445927d0977c3ed SHA1 03308472afe3d12960308282c65e65c533368ab6 SHA256 fc16fe362398502786a581c68e710933f91f7a03c7466d808b786f46f7c7d336
-EBUILD est2assembly-1.08.ebuild 605 RMD160 358fd35029cf9d65607453fef82526f3c492a52c SHA1 5f8a8cd88a3460853a25b00464fb38bd809aca4f SHA256 48176e0518299793375027587858a5574991ae61883c74492b13b7a8acfdcc31
diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild
deleted file mode 100644
index 72fcd5d31..000000000
--- a/sci-biology/est2assembly/est2assembly-1.08.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
-HOMEPAGE="http://code.google.com/p/est2assembly/"
-SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz"
-
-LICENSE="GPL-v3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl
-		app-portage/g-cpan
-		perl-gcpan/Time-Progress
-		sci-biology/fasta
-		sci-biology/ssaha2
-		sci-biology/mira
-		sci-biology/emboss
-		sci-biology/bioperl
-		app-arch/pbzip2"
-RDEPEND="${DEPEND}"
-
diff --git a/sci-biology/jigsaw/jigsaw-3.2.10.ebuild b/sci-biology/jigsaw/jigsaw-3.2.10.ebuild
deleted file mode 100644
index 5f85fbf7c..000000000
--- a/sci-biology/jigsaw/jigsaw-3.2.10.ebuild
+++ /dev/null
@@ -1,2 +0,0 @@
-http://www.cbcb.umd.edu/software/jigsaw/
-http://cbcb.umd.edu/software/jigsaw/jigsaw-3.2.10.tar.gz
diff --git a/sci-biology/pb-honey/Manifest b/sci-biology/pb-honey/Manifest
deleted file mode 100644
index 897d384b2..000000000
--- a/sci-biology/pb-honey/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST PBHoney_14.1.15.tgz 1277165 SHA256 5b709ec9a4951abf2c9df6b01fb9856e4bc4e1b50c7c10f5c777779657cb2a8f SHA512 05214e3299ec508523cdb63ecc17f518f493bf809a23febee5dec1ebe44c46c086c92c9633de9ad48d57ca8e062f09ccf8e97a064d73fd9ffd7d9163af2c3294 WHIRLPOOL 6ab0ef2ad8fa05e5cc96ab6509262a812969d54c768f9ed1f0ffc909a92416e533ecef48b729345424a72f97df1b9a1e7806128b1aabf06c5cf1b643c547736a
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
deleted file mode 100644
index 2ba4b1a6e..000000000
--- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Structural variant identification (SNV) using long reads (over 10kbp)"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/honey"
-SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBHoney/PBHoney_14.1.15.tgz"
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="sci-biology/samtools
-	sci-biology/blasr
-	sci-biology/pysam
-	dev-python/h5py
-	dev-python/numpy"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild b/sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild
deleted file mode 100644
index 0c659156f..000000000
--- a/sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Close gaps using PacBio RS or 454 FLX+ reads"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/jelly"
-SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBJelly/PBJelly_14.1.14.tgz"
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="sci-biology/blasr
-	dev-python/networkx-1.1" # upstream says "Versions past v1.1 have been shown to have many issues."
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild
deleted file mode 100644
index 764d69877..000000000
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ /dev/null
@@ -1,3 +0,0 @@
-"A program to design denegerate primer pairs"
-http://mblab.wustl.edu/software.html
-http://mblab.wustl.edu/software/download/primerD.tar.gz
diff --git a/sci-biology/pvmsx/Manifest b/sci-biology/pvmsx/Manifest
deleted file mode 100644
index 835da12eb..000000000
--- a/sci-biology/pvmsx/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c
-DIST pvmsx.tar.gz 10963 RMD160 1d14cb6e25a533f8a9879b04c5eb9e04532874e5 SHA1 562ea8628e47739ec7b98c622c894fe45e210c98 SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230
-EBUILD pvmsx-0.1.ebuild 1393 RMD160 61f01e960c18303d5511cdbf8129b3399091c17d SHA1 207c5c590b34df60454e0fb936ca8dd9da3f4432 SHA256 470fb9373cf0bc23dbaf9bcb24b9f0509881f4dde0e0e75b7b5de297247f52e3
diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
deleted file mode 100644
index 07b525505..000000000
--- a/sci-biology/pvmsx/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
deleted file mode 100644
index 1983f6b49..000000000
--- a/sci-biology/pvmsx/pvmsx-0.1.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR Gene Indices project tools, an alternative to psx"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
-		ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="pvm"
-
-DEPEND="pvm? ( sys-cluster/pvm )"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_unpack(){
-	mkdir ${PN} || die
-	cd ${PN} || die "Failed to chdir"
-	unpack ${PN}.tar.gz || die
-}
-
-src_prepare() {
-	# we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
-	sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed"
-	sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die
-	sed -i "s#-I-#-iquote#" ${S}/${PN}/Makefile
-	cd ${PN} || die
-	ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
-}
-
-src_compile() {
-	cd ${PN} || die
-	emake || die "emake failed in "${S}"/${PN}"
-}
-
-src_install() {
-	cd ${PN} || die
-	dobin ${PN} || die "Failed to install ${PN} binary"
-	newdoc README README.${PN}
-}
diff --git a/sci-biology/tigr-closure/Manifest b/sci-biology/tigr-closure/Manifest
deleted file mode 100644
index 1b2d852e5..000000000
--- a/sci-biology/tigr-closure/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST tigr-closure-svn-20080106.tar.gz 25760145 RMD160 e099cef993c01ae8a94838c0a26f855ed4574a2e SHA1 4ed2b052f40bafb5665d14bc74848079d61d8a71 SHA256 60e474beb7e408c3c47633b2bf029ff9fde05840a10b01c875164e68811b6c5f
-EBUILD tigr-closure-20080106.ebuild 1361 RMD160 9dc3c7585f14dd78dd0c397a434023aed1183244 SHA1 932992744169a782f3c7b9caf8a84abc1cd74fc4 SHA256 308c8b4c4a46501e16fa07709ff4bfe8e69f5aa0f5ca7d943e8cee4d81e46e82
diff --git a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
deleted file mode 100644
index e4a242118..000000000
--- a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit perl-module
-
-DESCRIPTION="TIGR closure tools for the assembly/finishing stage of DNA sequencing projects"
-HOMEPAGE="http://tigr-closure.sourceforge.net/"
-# http://tigr-closure.svn.sourceforge.net/tigr-closure/
-SRC_URI="tigr-closure-svn-20080106.tar.gz"
-
-LICENSE=""
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND=""
-
-src_compile() {
-	cd TIGR
-	# install the two *.pm files into our perl path?
-	cd ..
-
-	# Closure Work Order Processing (CWP - CLOVER)
-	# clover and oats
-	cd ${WORKDIR}/CWPSystem/trunk/
-	# needs TIGR/EUIDService.pm in PERL paths
-	make dist
-	# how to install the files from install/ ?
-	cd ../..
-	
-	# 
-	cd ScaffoldMgmt/trunk
-	make dist
-	# FIXME: unpack the .tar file into image during src_install()
-	cd ../..
-
-	# awfull
-	cd ClosureQC/trunk/
-	mkdir sandbox
-	${SANDBOX}=${WORKDIR}/sandbox
-	# have ./src/, ./doc, ./install, ./test/work/drivers, ./test/work/getqc, ./test/tmp
-	cd test
-	# ...
-	cd ../../..
-
-	# 
-	cd ClosureReactionSystem/trunk
-	make BUILD=true
-	cd ../..
-
-	# some Java servlet?
-	cd AserverConsoleEJB3Hibernate
-	# huh?
-	cd ../..
-}
-
-src_install() {
-	cd ${WORKDIR}/SequenceTiling
-	dobin trunk/src/*.pl
-	cd trunk/src/TIGR/SequenceTiling/
-	myinst="DESTDIR=${D}"
-	perl-module_src_install
-	#
-}
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
deleted file mode 100644
index 3cf6c6051..000000000
--- a/sci-biology/ucsc-genome-browser/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jksrc.v260.zip 59090224 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 WHIRLPOOL 669b0f342a97f84164b32707a3b2bb51f64219168beceb8f9d46211749351b2c65b21ffe830f82620e7112a332e88ca271d4327739d8f93afbe14e399e45e248
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
deleted file mode 100644
index 18137f66a..000000000
--- a/sci-biology/ucsc-genome-browser/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-	<use>
-		<flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
deleted file mode 100644
index ae00dd8df..000000000
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild,v 1.1 2011/12/27 09:39:04 jlec Exp $
-
-EAPI=4
-
-inherit toolchain-funcs flag-o-matic webapp
-
-DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
-HOMEPAGE="http://genome.ucsc.edu/"
-SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"
-
-LICENSE="blat"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+mysql +server +static-libs"
-
-REQUIRED_USE="server? ( mysql )"
-
-WEBAPP_MANUAL_SLOT="yes"
-
-DEPEND="
-	app-arch/unzip
-	!<sci-biology/ucsc-genome-browser-223
-	mysql? ( virtual/mysql )
-	server? ( virtual/httpd-cgi )" # TODO: test with other webservers
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/kent"
-
-src_prepare() {
-	use server && webapp_src_preinst
-	sed \
-		-e 's/-Werror//' \
-		-e "/COPT/s:=.*$:=${LDFLAGS}:g" \
-		-e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \
-		-e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \
-		-i src/inc/common.mk src/hg/lib/makefile || die
-	find -name makefile -or -name cgi_build_rules.mk \
-		| xargs sed -i \
-			-e 's/-${USER}//g' \
-			-e 's/-$(USER)//g' \
-			-e 's:-O2::g' \
-			-e 's:-ggdb::g' \
-			-e 's:-pipe::g' || die
-	sed \
-		-e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \
-		-i src/hg/genePredToMafFrames/makefile || die
-}
-
-src_compile() {
-	export MACHTYPE=${MACHTYPE/-*/} \
-		BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \
-		SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \
-		ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \
-		PATH="${BINDIR}:${PATH}" \
-		STRIP="echo 'skipping strip' "
-
-	export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
-
-	use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
-		MYSQLINC="${ROOT}usr/include/mysql"
-
-	use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
-		CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
-
-	mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die
-	use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT"
-
-	emake -C src clean
-	emake -C src/lib
-	emake -C src/jkOwnLib
-	emake -C src/utils/stringify
-	emake -C src blatSuite
-	if use mysql; then
-		emake -j1 -C src/hg utils
-		emake -j1 -C src utils
-		emake -C src libs userApps
-		if use server; then
-			emake -j1 -C src/hg
-			emake -j1 -C src
-		fi
-	fi
-}
-
-src_install() {
-	use server && webapp_src_preinst
-	cp -ad "${WORKDIR}"/destdir/* "${D}" || die
-	use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a
-	echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}"
-	doenvd "${S}/98${PN}"
-
-	use server && webapp_postinst_txt en src/product/README.QuickStart
-	use server && webapp_src_install
-
-	insinto "/usr/include/${PN}"
-	doins src/inc/*.h
-	insinto "/usr/share/${PN}"
-	doins -r src/product
-	keepdir "/usr/share/doc/${PF}"
-	find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die
-}
-
-pkg_postinst() {
-	use server && webapp_pkg_postinst
-}