13 files changed, 94 insertions, 240 deletions
diff --git a/sci-biology/bioperl-db/ChangeLog b/sci-biology/bioperl-db/ChangeLog
index e86d0ff22816..f9dfa92bd846 100644
--- a/sci-biology/bioperl-db/ChangeLog
+++ b/sci-biology/bioperl-db/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/bioperl-db
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-db/ChangeLog,v 1.13 2015/05/27 10:14:31 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-db/ChangeLog,v 1.14 2015/05/27 16:28:25 jlec Exp $
+
+  27 May 2015; Justin Lecher <jlec@gentoo.org> -bioperl-db-1.6.0.ebuild:
+  Drop old
 
   27 May 2015; Agostino Sarubbo <ago@gentoo.org> bioperl-db-1.6.9.ebuild:
   Stable for amd64, wrt bug #539426
diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest
index e557d7f7005d..7b32a134d9d4 100644
--- a/sci-biology/bioperl-db/Manifest
+++ b/sci-biology/bioperl-db/Manifest
@@ -1,27 +1,27 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 DIST BioPerl-DB-1.006900.tar.gz 492799 SHA256 50df2447b7f3e26aebcf02ed7344d3ef562c3f5393c1584a8ae086185c8c9139 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 WHIRLPOOL b484ce9f464a7189e5b2fffd6facdd426e8b9009ffca5e1661986490bc45dc0269faec5e9eeebdb23ec5c706f62a670fbb6bfc5a60b11c268c7e6f34bf1f03f2
-DIST BioPerl-db-1.6.0.tar.bz2 296041 SHA256 81710b9c6d021511b8ad19d106309f76ef3111015873a56af9b109902d24a699
-EBUILD bioperl-db-1.6.0.ebuild 935 SHA256 67841aed2cdc99f42d9596dbdafbac980594d71a455ddbd370167095704ac657 SHA512 7ec3027c834c1a0704ba8e101da080ef1416da68ae0eabe089231889806eb15fc7a0b6f4f533a120b9b88ea5a3b47c24b4f21d7abe00d0ed8c4d21af087e47c3 WHIRLPOOL 4934f5410d82387bdb115a2ecc018f08b3eaf9f26c094ee78d909fc20484bdaa915f71e9dcc6f624688476e7ed3c0f460c62a91fda01b56c5c26decde2e15765
 EBUILD bioperl-db-1.6.9.ebuild 756 SHA256 e847714cab8f2dfb41f479f35ea19d824bbdc40b0e9c27ef7de963f984f65b79 SHA512 fd11cf66e4c6d8de8fb4bda44169786f2d3cb4ee3fe780b59c3edccc8c24d2761bbaf79cfd7c6c07dbde22a6a40dbb7d79e20e8d3ad4dbd9602ab012df7cbf51 WHIRLPOOL 038110f8043bb64a7ae43e4f1af65b9494f1a3a5508b3f5d880280eed80dc94d45c11a3551ddbcfceb1062465106ad9353896da66b5a5fe80b24c95bee6a45d4
 EBUILD bioperl-db-9999-r1.ebuild 975 SHA256 b6e138022894860c8b40bb8c1341dd8d031c41b43305f8bab9f3261c72b8bebb SHA512 582954d290ee5b6eb8decad3d2f18f95e2ee9280f909be1ca4222f12fe016d03e47841b5ce66bd1c12c85a64b46e9cf19836b8501d23e6157a909daabcbc9945 WHIRLPOOL 2500389084e7ae3937de7d2676f823f61793cc86849acb91c678e2623723bde36d6cb84c42dccde2a95352291515dcc499b37311e0b47fd67eeb34be824bf94b
-MISC ChangeLog 2038 SHA256 4264a6c1c100f7a45c3beddd855d55c55a6ab61137e7804e9650f5274acf51f8 SHA512 83933e58dc2c1a4cca7227d400347c3bb36ee3db7ef6f2feaddfdf3fc4f5108420396de10c507cce7538c71edab9028bc8d4f2785c000e592371dd739f834e5f WHIRLPOOL 15ffb7ab3e4b69555bb52ca3440520774e7e82e33de35727c64bfa18da91aac468c1ad612f763f9fe9785feab5b8239d668c9953ceef425c7ef6b29001db5d4d
+MISC ChangeLog 2124 SHA256 40d7ea8d6fa77f96dc6524056b81095a02eb5179c2b20fbaa15e4e7f34e80b23 SHA512 cbf5bfe096f3268147b8e71fa6976a23b731fe0adb893dced44555461dbfc697794d95cc03caf732b2b61aa688ce9ec24ce77a60ac9c293e5792cf06d2e68641 WHIRLPOOL 256d943291404df636510480de61f47feb771a1351b5b74d90cd32c8b7aa8eadc7d5ec2306b19d11d90d45c4ac5caaac7e1819ca3d0fb527923cb9d9e3dbc365
 MISC metadata.xml 243 SHA256 caaade52752dd9332b4b9a7d233b1ea13357b98591091b09297f57407d9bf55d SHA512 43432ecd4c8101878bf4f42adf279128df74e0d0129c0f178658104d5c60e9938f270cbdd8760d0e000b95a11fcf7d1cba8a58ac0af7a1e595bdfd4761e84dac WHIRLPOOL 7de11b5857df86f15986efd61327090d4112ee9b975680dde9db7c716e760623e2ca114d781205f978aa175657ad4e54ad26a1e15d820c43b479b4957d9030c9
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diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.0.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.0.ebuild
deleted file mode 100644
index 9a3a22f0470b..000000000000
--- a/sci-biology/bioperl-db/bioperl-db-1.6.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-db/bioperl-db-1.6.0.ebuild,v 1.5 2014/08/09 22:47:12 zlogene Exp $
-
-EAPI="5"
-
-inherit perl-module
-
-DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://bioperl.org/DIST/BioPerl-db-${PV}.tar.bz2"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-CDEPEND=">=sci-biology/bioperl-${PV}
-	dev-perl/DBI
-	sci-biology/biosql"
-DEPEND="virtual/perl-Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-S="${WORKDIR}/BioPerl-db-${PV}"
-
-src_configure() {
-	# This disables tests. TODO: Enable tests
-	sed -i -e '/biosql_conf();/d' \
-		-e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die
-	perl-module_src_configure
-}
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}
diff --git a/sci-biology/bioperl-network/ChangeLog b/sci-biology/bioperl-network/ChangeLog
index e1b55ee0a94e..d477aed1e78b 100644
--- a/sci-biology/bioperl-network/ChangeLog
+++ b/sci-biology/bioperl-network/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/bioperl-network
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-network/ChangeLog,v 1.12 2015/05/27 10:14:27 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-network/ChangeLog,v 1.13 2015/05/27 16:30:54 jlec Exp $
+
+  27 May 2015; Justin Lecher <jlec@gentoo.org> -bioperl-network-1.6.0.ebuild:
+  Drop old
 
   27 May 2015; Agostino Sarubbo <ago@gentoo.org> bioperl-network-1.6.9.ebuild:
   Stable for amd64, wrt bug #539426
diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest
index b5fc80327c41..c28e2c6f2640 100644
--- a/sci-biology/bioperl-network/Manifest
+++ b/sci-biology/bioperl-network/Manifest
@@ -1,27 +1,27 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 DIST BioPerl-Network-1.006900.tar.gz 2198089 SHA256 5b31ab7d048ee8e7bd6ba933f96b904d7ee06b46ab29c00276eca3513a77c32a SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842 WHIRLPOOL 65ff9e2509c0136232b7cff1aa5e8ad55f26241f51e70e6d34f9383c0af4bfdb0c5358b1a69075d480e9e1fdfa19342058fbe33ea4d4a633220ef3a80d6ed984
-DIST BioPerl-network-1.6.0.tar.bz2 902029 SHA256 1f9e48d7bf1b563fef235eede9524f8446a0374b65c6bf522f3203ed61164cb3
-EBUILD bioperl-network-1.6.0.ebuild 781 SHA256 bf65f52817faa3460e1ce45574f5ec9c7b5407ae38ec60953f895bc5cad75282 SHA512 f7f34ddea8ae1ddcff267082bfb0b358184d03dc1c719d4d817b715236389a4f02a5f08286518a3dadf499f0e4be40ef4221216e7d7f022f61d1b0b93cafb515 WHIRLPOOL ea2068203160bc4c3631490edf824d08b313ab3dd4433b1c7196249b1cb644858c0652b7db44fce114d8e8cb9933194ab5f7a298ceb8454f0257cef315c86bca
 EBUILD bioperl-network-1.6.9.ebuild 742 SHA256 7576beb479b94865d9bad4fa2f31427c03abe83b5ca328659428f17f02585745 SHA512 9536b87418c314c84aa9b8351ce27c5e413fb428c9b350a89c11da884313529893f863deaa297bfd60239fe1fe841e919dba6891aaf4fab3743ea91e1ec4d7c2 WHIRLPOOL 6b87f34a977db3a0a73a60435fb34f3bc3abeda0758b69019f0a8421e51b7c0494225763e6448067610aac1533cd5ef22ff22971259fcfd740d61f883849c7a3
 EBUILD bioperl-network-9999-r1.ebuild 816 SHA256 eb951e17bcd4981414298a748f987260565ce555e691b4b84659811eac15c325 SHA512 2bbab52c65518b555fd50c0a0d0d7e4881559813c2c46e3f361d38ceda9c507d124c448e1aaf139941cb5e2a24e6c97bd103df3880c248c621161b4656b398ba WHIRLPOOL 1772b353b306f21fb7184affe99dbf8afc54c456fb36be05b19c12ad57387bb8d8ade6e794a45c9f56af83ccd7c25cfdcba8d03e61122d6a7a0d28013ff95904
-MISC ChangeLog 2027 SHA256 96897ba1c523021f72df7a2978183ad8b75675806e4ee4766ffff3bf562186e5 SHA512 4e9a7a1fe0222b4555afb460b812c599f3a0ca9097637af077dc725376324561df3dfd2fa5ed06db209acfb205bfce628d5b890cfd5cb61d782c94dc4c96e4c2 WHIRLPOOL 22e54f96fca01301452798ba10d80fc737f2e0d2c80f8b4242119a98cf7d38dfb7e30d2f17ebed949e02ae41c861eb136ce1b58abe31d8bc941c2cfdff5aa75c
+MISC ChangeLog 2118 SHA256 f936ebb3f34f236b3369ee0850f842fa6452ffab50058e3c530e25cbfb6ba3f0 SHA512 35d306f3a7907cc8324cb6d870bb558f9d5f64f76bc5a7e33a3660d86a3842aa43d933e24da9ec7b545ddc18985901404c3760b3dc11712abd7a9aef3b24f81f WHIRLPOOL 52fbb99de39a45d316e56be6a7feaf0a860d543afa0545b4715b0ef97ed9b0466dc56871fb05bc2dea720cde8623e9324fe678225bef47ba371f42dde4369c7b
 MISC metadata.xml 248 SHA256 dbfd5f643fae0df4baa7271ae0029203db6b1c3a3ab9774ec1b9cba26ab3c2cd SHA512 13b45d68789a04b4253bcbd9d10883c1eb3256657a67df00827c7c6e9e4853dbf8a670eb88e674d84a2790bc8c9aa4f5ce55ff7478eb7d261011bf6f573719b9 WHIRLPOOL 684409333d8a43c27c5c86816e1def48384ecd85353f381cc98122477a4e91bfae7e071cf3754727651b70adc6a5f9258e2d78f3689bdf6e2db2db8e72c30859
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diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.0.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.0.ebuild
deleted file mode 100644
index 20f9c5ac0a90..000000000000
--- a/sci-biology/bioperl-network/bioperl-network-1.6.0.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-network/bioperl-network-1.6.0.ebuild,v 1.5 2014/08/09 22:48:22 zlogene Exp $
-
-EAPI="5"
-
-inherit perl-module
-
-DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://bioperl.org/DIST/BioPerl-network-${PV}.tar.bz2"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="test"
-SRC_TEST="do"
-
-CDEPEND=">=sci-biology/bioperl-${PV}
-	>=dev-perl/Graph-0.86"
-DEPEND="virtual/perl-Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-S="${WORKDIR}/BioPerl-network-${PV}"
-
-src_install() {
-	mydoc="AUTHORS BUGS"
-	perl-module_src_install
-}
diff --git a/sci-biology/bioperl-run/ChangeLog b/sci-biology/bioperl-run/ChangeLog
index e3cb982136d2..e4f5a620f95c 100644
--- a/sci-biology/bioperl-run/ChangeLog
+++ b/sci-biology/bioperl-run/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/bioperl-run
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.27 2015/05/27 10:14:23 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.28 2015/05/27 16:26:34 jlec Exp $
+
+  27 May 2015; Justin Lecher <jlec@gentoo.org> -bioperl-run-1.6.1.ebuild,
+  metadata.xml:
+  Drop old
 
   27 May 2015; Agostino Sarubbo <ago@gentoo.org> bioperl-run-1.6.9.ebuild:
   Stable for amd64, wrt bug #539426
diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest
index 47bce99a4226..bfca7606a260 100644
--- a/sci-biology/bioperl-run/Manifest
+++ b/sci-biology/bioperl-run/Manifest
@@ -1,28 +1,28 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX bioperl-run-Pise-test-patch.diff 722 SHA256 84c8280f8d3af311b53c8b6edd4e6ffa9acc0824528d96d7f1c2537404d3e30f SHA512 75aca2b0faa198e923673f4f0e4c40c04179881dbe33ad4ae7f831ff7eb633d26baa44dd983dcf8e3edef672b4dbd92d3d46983ecc8419cca1beb3acdbdf2111 WHIRLPOOL 54367c5bf97f72adce7ae21dfd554c9ddafdc2b176a2ac1529aa3c8cd7dfda0d961b1249d025c3a810458aebc28e42365434c633cd30ead0348141804de3c5b4
 DIST BioPerl-Run-1.006900.tar.gz 14546677 SHA256 6eddca8aae38a139caaa0b28505e2ff3e919e8ed39b7539a662b0145f1f08d96 SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c WHIRLPOOL a671180b3680d94683e771ba661e0f86430814200efcd8df1552dbc3c30228d90ea8be1b47cc36603cbfc6eadacb276414ae6d79e30ec80495fd836eb1732cca
-DIST BioPerl-run-1.6.1.tar.bz2 3968370 SHA256 16f406d196b6e6d063f4ef518161571ea27909c5b47184d9eddf1eb9da147f53
-EBUILD bioperl-run-1.6.1.ebuild 1106 SHA256 2640705edf4ed4473de5ae43acabf8316db7bc51baf7b4fe350ead210cc5ab8e SHA512 8060992e922dbc0e689eab2ec36360e956782f4a5677ae3f87a2b39861f01f6c02cbbbbf2e89d895fe0eeade68ddc44cc571d878198ffe3533ab941baabf1467 WHIRLPOOL 89327927791fd8f932f347375b27c3c292ba34d503f6724c362f19a73b2722a8e21437d1187a98bc45a4ab38172165c149255b06847f6c5ed6ab2dae13166831
 EBUILD bioperl-run-1.6.9.ebuild 1085 SHA256 f521b2beebd86c5c2693be2eca730fded712d0fc9ba0a102523bafc8569fb4a7 SHA512 7f3c54542c40f71dcfcc19ea8026609ef2f8dfbc84e7170f868ab9e02cd12fc4589626acf542e6f944a36d06856f786ed5066305e044d5fa43dae841f6632d0d WHIRLPOOL 45362ca256f94068e7c9375b0362d221cd193988e5635cf2e17d63b6046edbf7bda9a2f00f5144ebe3681ed204a22ba4161a9554b3ea749be8212f05d7ed502a
 EBUILD bioperl-run-9999-r1.ebuild 1124 SHA256 ae3731d4ac16ba293b0a9e04e85e11d8d577f7dbdf395de2058fe61fa8699afb SHA512 9892d3db721583a055e8e684b95bebcdc4bf04bb179d6707b009afb8195a0b5535d02ff1a4ffb5cf506fdbff8706a6f5cb2fccb936254f327350e64a9904eaa2 WHIRLPOOL 2ccdf58b4090114df96d3bb594453e27b5ce56c65166b8a0c3b64692bcfab25f6846af7e144d65b7ffbf3d43c2a5c0ae7c1efb2112048fe1d7e664ebf9ba8d87
-MISC ChangeLog 4622 SHA256 6850ec0dc445883cd38e45f600ab1316ebefe4759673edbf2b56c327a954f64d SHA512 be8bf58dcaa4b560f9fa37c880814f4a29f922b6fc110e7131a74c4517b5f67adaee44dadbc2761371894583f6804143bdf3396a14cbac11734ffef3e38155c7 WHIRLPOOL 6d74cfa37756be244be3aba96a077452ba0559643d37b4d855bc6cec8ab8cc3b466cbff747870afdbed60a7f30a434f0eea8e661a70148db0f0752cccb136d04
-MISC metadata.xml 239 SHA256 60082888c0555ed9bf001256819cf779438504bbc38afac272bc4bb696eed6a4 SHA512 e25122619624257aa7caf3c4a456c9f404dae487091dc1e250425463a4cf8ad8eabc259f607e49362de3906eabcd0ded1aa5861126d35c08ff8a6cd65b87c3d4 WHIRLPOOL 85438f199a1834d64deebd761b736accedc8ca6788b808affd1d9f8f278ec8e80251c4e1d500aaf69639d4601aa695d4cf733b8b1e59951683c8c86aa2146dc6
+MISC ChangeLog 4725 SHA256 2a40cb2f9909594daac499b7bab9983c2f76db006446f1323f2c5775d38bfd70 SHA512 c22b133def33e6e505b7fb73d1f40c104dcf11ea99e94cbef477fe8a1526969fe6d523b8e2dfc445eed1e2aff402c82907225a58f06b448d5aa9c3eff797d97b WHIRLPOOL 93d9d0374349156458c7a82d8074866310d4141c1bcc8dc180f7b3882c35116d4c63dadd4416d9f6ec67782b11fdcf7896445c8f0b4a528785e92e06a917b020
+MISC metadata.xml 244 SHA256 25b9b30a7e01909ac80d0d3a4d22ff39057d8a7de30446571e88bdc8a276e2b7 SHA512 b609ea3873cb8765079a83583f436e0af9d1fdb9262c3f2c231d13c2294901dad5ab563df3570bf06043d7bedc76b23e4470c51d88a9861045e8883e72fc77f5 WHIRLPOOL 298d3100a1a62e9b653e62345e227856994c306e6aa641dda8f676c4bef5e3ae83993baf3e1c2b8505921c0a84956122792503d83b2497989143862efcde48ec
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2
+Version: GnuPG v2.0
 
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diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.1.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.1.ebuild
deleted file mode 100644
index 2cad02c05ca7..000000000000
--- a/sci-biology/bioperl-run/bioperl-run-1.6.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.6.1.ebuild,v 1.7 2014/08/09 22:49:45 zlogene Exp $
-
-EAPI="5"
-
-inherit perl-module
-
-MY_PV="1.6.0"
-
-DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://bioperl.org/DIST/BioPerl-run-${PV}.tar.bz2"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="-minimal test"
-#SRC_TEST="do"
-
-RESTRICT="test"
-
-CDEPEND=">=sci-biology/bioperl-${MY_PV}
-	!minimal? (
-		dev-perl/Algorithm-Diff
-		dev-perl/XML-Twig
-		dev-perl/IO-String
-		dev-perl/IPC-Run
-	)"
-DEPEND="virtual/perl-Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-S="${WORKDIR}/BioPerl-run-${MY_PV}"
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-	# TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file)
-	# with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D
-	find "${D}" -name '*ConfigData*' -print -delete
-}
diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml
index bdb3c86c7218..f8c7078a2813 100644
--- a/sci-biology/bioperl-run/metadata.xml
+++ b/sci-biology/bioperl-run/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<upstream>
-		<remote-id type="cpan">BioPerl-Run</remote-id>
-	</upstream>
+  <herd>sci-biology</herd>
+  <upstream>
+    <remote-id type="cpan">BioPerl-Run</remote-id>
+  </upstream>
 </pkgmetadata>
diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index ba89882f6ee7..9ce25e185b42 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/glimmer
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.13 2015/05/27 11:01:14 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.14 2015/05/27 16:32:11 jlec Exp $
+
+  27 May 2015; Justin Lecher <jlec@gentoo.org> -glimmer-3.02-r2.ebuild:
+  Drop old
 
   27 May 2015; Agostino Sarubbo <ago@gentoo.org> glimmer-3.02-r3.ebuild:
   Stable for x86, wrt bug #550436
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
index 3153adf1f967..8cb0bc25e7fb 100644
--- a/sci-biology/glimmer/Manifest
+++ b/sci-biology/glimmer/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX glimmer-3.02-glibc210.patch 799 SHA256 6b0655e796a938990c29070950b36e861bdb6dd3ee1a0ae962590585976e7c5b SHA512 7a6b05a9b626dbefdabf4535026077b6259747cd2603847e6aa7fed991d456d87bc658ca923959fbdd2ceb4e43e096d46925946ffc135277794a1a6399433a1b WHIRLPOOL 797232ac343731e37800495a50bbdb4c254d04c52ec9ad5b3e57b2ad623bb93c4024fe150f7d8bc2dc4f0d0a83cd75d511d985a62bf4a02bcb04ec813528c606
 AUX glimmer-3.02-jobserver-fix.patch 433 SHA256 19f45973fa230874274d779b03aba73abbecf1344d4a0d795d70256a82036e15 SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d WHIRLPOOL a93193e48512a0cd8c6996d77ee8f1fd91b18cf00e6c99ec6c59dc9953bcb5ee5a90180b317ffb99337666e451da91f77f14a805f43026c1819ec596bb1268c1
@@ -9,25 +9,26 @@ AUX glimmer-3.02b-ldflags.patch 2057 SHA256 95d391acdbf6d84440c2f3d96791e9f97776
 AUX glimmer-3.02b-rename_extract.patch 9286 SHA256 275f783f675729e5b39bea26e9a506dd2a1b675ef20f9a611ca50cb94b1ad272 SHA512 b5c08ba7ac973e723aeb8bc8808f69eded90b1e59c9d14804519d1d689e820193bf71860026642b3aed049881289c651f9cfd45bc05d53d73a2e9ab891f9b342 WHIRLPOOL b5cc7d1d3734fc373c2a96d82bbcbb2a531bdc8040a7543d0ffdfcc9f4889ba9c89854ba4f99f9b4c1be30eb7a477530ee707bfadcc4ef180b1d6fcda26e7334
 DIST glimmer302.tar.gz 5637075 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c WHIRLPOOL c3eedb4a3a65043a69d632360608f04382117b8f7f3718eae328a1aa14f9f5d6d9ae6f05e0a83a09af5eb9e6b0c7b0ae26cb820813341aa5d7fa3f6002938ce8
 DIST glimmer302b.tar.gz 5637975 SHA256 ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6 WHIRLPOOL bbce6f57546e6cc77801ac7f5e783510feafc2e120a8727e848a95dd9e2d966538e56cb7be597c2a463d9b372c8586a389d639e1377708a27bd56f81b37fea1f
-EBUILD glimmer-3.02-r2.ebuild 1322 SHA256 6ab8d0b9d4552eaa86d0172350bf107bfa7395fde5a0930b0f3b2b8f53f3c9f3 SHA512 02429bade2542dcd9acb27f6fac7cb392a76bb490df655c8bb2d6065fd9f77848ad3579c331fa63194d6527134d80148fa2aef2b407eb1ebec8a217e057e86bd WHIRLPOOL 81d6e280bc9cfe9301758e68b3e07810b828b1900117112a9087689167109739eb417cefb71e65b27c5983afd96bdb0990d173255263a96609300b1fefca0be2
 EBUILD glimmer-3.02-r3.ebuild 1468 SHA256 a1db2201b88dc82ba9c04af9fc479a2dc80108c3c631b8769d4e77e2596c5e7d SHA512 18a0e08a613428de6a9cfae98b6432b5dca0e68b76e162ce97e9ee0f6dceaab1db01383724971658c22e3f8dcdf189924845380c3f10f3bd0e450dae00788edd WHIRLPOOL b1386471e128c807fae4ec3426e0ea8b2411949fc1cc1a7e31a210a6fb09c2ee39858d988c9e447eed8655867dd14a800e5b54774760071d63c82494dc0ef5d3
 EBUILD glimmer-3.02b.ebuild 1813 SHA256 9a12cfb1ff260933b83d87335521fd21c9ff3d076c4377005ad73010c65a47fc SHA512 8e52bbbc4317691461a8e83e7861e8191249a371e54ddf5f3cff28f4856e98caa57c4f0f79fa95f3dcdabbeca7a23d3ccfef919cbf1417f726258c8723eb1b29 WHIRLPOOL 0878a4568342cff4c9d21044e441a8fff868b22af9963b89769ff6b53c31554adf18a6fb72f82b9f6a7550e5dce14e8e05135ac4541ff4835c54630ab0b4985f
-MISC ChangeLog 2219 SHA256 725fdbd18f7724093b6efd87f76befaf002230f80723420d22d8a4e91e531470 SHA512 4c8172a9bc637ee9e22c205aae21d4882942a159ac8939a7e5b7df0fb4e96da940dc7890d50c71784bbd8afed71fd596cfb58a4f5c1b9772e0f2d5ee46d23480 WHIRLPOOL adce5bd86095ee046690e79cd402e6b9669ca35c0ddc4e62e884434a636b2883bb8e343cffb6e4d6afe00230ceed81884e107c305804c49b9455a58eeceb25e5
+MISC ChangeLog 2304 SHA256 d33edc8f014290bdadb5508d59dd3a3b9fe115aba78d667bee1312034dc168da SHA512 ed293293a8875e5c31a515e8ee1c1bb1c73774201325280382fbb618cb6c6b86095715c6c126e1aa5de6b6a8bd55709e3a473b5750b4bf8ee081047aa90e2572 WHIRLPOOL fae3fb2318dbdf875c4c507b18d7c0016aa3cfded21f16236804ddb012e14053fb52b4541dad3e744c4336dbec2951e70682897d6b10cc922a80cc82a566dbd9
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+=GrC2
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/glimmer/glimmer-3.02-r2.ebuild b/sci-biology/glimmer/glimmer-3.02-r2.ebuild
deleted file mode 100644
index e0ebb19b6adb..000000000000
--- a/sci-biology/glimmer/glimmer-3.02-r2.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r2.ebuild,v 1.3 2010/07/16 17:29:32 hwoarang Exp $
-
-EAPI="2"
-
-inherit eutils
-
-MY_PV=${PV//./}
-
-DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
-HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
-SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="app-shells/tcsh
-	!app-crypt/pkcrack
-	!media-libs/libextractor"
-
-S="${WORKDIR}/${PN}${PV}"
-
-src_prepare() {
-	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
-		-e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
-	# Fix Makefile to die on failure
-	sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
-	# GCC 4.3 include fix
-	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
-	epatch "${FILESDIR}/${P}-glibc210.patch"
-	epatch "${FILESDIR}/${P}-jobserver-fix.patch"
-	epatch "${FILESDIR}/${P}-ldflags.patch"
-}
-
-src_compile() {
-	emake -C src || die
-}
-
-src_install() {
-	rm bin/test
-	dobin bin/* || die
-
-	insinto /usr/share/${PN}/scripts
-	doins scripts/* || die
-
-	dodoc glim302notes.pdf
-}