gentoo resync : 22.05.2018

25 files changed, 48 insertions, 116 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 978a218d0c8a..4f957c1a1f3e 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 90848bfe1f68..587682895717 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,4 +1,4 @@
 AUX fasta-36.3.5e-ldflags.patch 2781 BLAKE2B e6d4e0984b4dadfc9d38504ab215d769084edc6c79cfe641b6b3fba8264a40add1665027295ec4afa19d26277036bfe1a5103ecdf72ef91a1139542ac8272954 SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7
 DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812
-EBUILD fasta-36.3.5e.ebuild 1625 BLAKE2B 20dd1cc003b8ae7a1cabbbcfa06f6968d6486f86751d08d791dca74e4365358f456f88a398b98e65a4bfa85d7220c6e64e91998d57c2b0c4d422c7d3533cb20d SHA512 618aa434a8271332dc1042c731d6f19d99f08eb90cc156af3b855d8df9664d5efa62a40a043c031205a03e768cf8251d246e4e7b14d7ca14deb47678399e5797
+EBUILD fasta-36.3.5e.ebuild 1626 BLAKE2B 0227b1f5b986e3155ef64637ed8dcac75bf92e9ec0e36320a0c43e89cd160fec87f59c16796bc4621f96b2df68082d3ebb2a2b33fb024c10544c45fd9680e358 SHA512 06ebb5136e78c0cf34ba2145aeda1a21e979b09ac53acfa8ad91c161dea363791d5e9b9b4a26b02111e7e6f1131c03fdd7a12e66ddcbf16e360540893abcf721
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
index 96494b79aa34..30fda7e9ae00 100644
--- a/sci-biology/fasta/fasta-36.3.5e.ebuild
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -6,7 +6,7 @@ EAPI=5
 inherit eutils flag-o-matic toolchain-funcs
 
 DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
 SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
 
 LICENSE="fasta"
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
index 71c8e3c2054d..6455e2a011b1 100644
--- a/sci-biology/glimmer/Manifest
+++ b/sci-biology/glimmer/Manifest
@@ -6,6 +6,6 @@ AUX glimmer-3.02b-ldflags.patch 2057 BLAKE2B 1333aa5d94d218dfd7f986cdea3f7e5c448
 AUX glimmer-3.02b-rename_extract.patch 9286 BLAKE2B ce955f8f721f8043fe2beed82b7676e6503da20bd9a4cc556e1e29fcfcd9ffdfab1a430a98ece99f13a03241771f7b393d7c7290bf1d5c6652e67bdc5905950c SHA512 b5c08ba7ac973e723aeb8bc8808f69eded90b1e59c9d14804519d1d689e820193bf71860026642b3aed049881289c651f9cfd45bc05d53d73a2e9ab891f9b342
 DIST glimmer302.tar.gz 5637075 BLAKE2B 07fc22a9192644c42291bd305a24bd7c40881cf5e8b668885ffdd5695100a2370b9cdbb275956e36df9007b1cb7bbfba84ab84863f26b70e68638fdf35e608d0 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c
 DIST glimmer302b.tar.gz 5637975 BLAKE2B 76c0b19fe08e9ece3e930fe3e53444a2b620e565ac3c83db484294627403e34c3ab77165e4b82176282df340fe47672bf28e5694edbcea9e17a57b61a502ae11 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6
-EBUILD glimmer-3.02-r3.ebuild 1354 BLAKE2B 593b846736ca9232a924646b4955c59031f4a8c4c883164ab4b5769d4ad1007b38087f355228984339df5f4b4fca398b209754433d3a9eb57634debb105c9ab3 SHA512 c2930627e031436d36b87ac8ec80f672700faa91db3aba175e428e9190ae8129a66288c08f10e501e4c4de98fb6a9aebdb46c7300c0ad6b17768a6d1e53161ea
-EBUILD glimmer-3.02b.ebuild 1700 BLAKE2B 4ad4f1678ec05064d3f80bc68a65cf6f6b642085c89f56dafee4f3f5c7bcfc69372b131648207ace2c2e836166b122c9d24fa63604fab905f43dff147f298218 SHA512 f66d205a926c198c92a8798cd7cdf20bc9620225fc67a20d097b70e08db995c05c2ebf9e7d760d123e5e9dee8c11b862070547ed1a751508d7b07d86ae983062
+EBUILD glimmer-3.02-r3.ebuild 1361 BLAKE2B e493ff1e9f6237b23f3d2a010385d955b1dcc1fc4668a16be7325711ed03d7444388b67a3e187bc7f18930dee933d770dc86eb3cd47dcf068a96e7f1170fd3a8 SHA512 0fd7e98d14981ea15c9b19d1a8a3af7ee316c9038d82956f232c9842ef476f2a5636ff87339dbcf1eb935448788fb3fd45caaefd90ce73d00c1bef05b17f0ad5
+EBUILD glimmer-3.02b.ebuild 1714 BLAKE2B d737bc73c36fd390c5b9235323f738a740c008571d37b87c74372a9ec7f1492bbbeb6a4c16b9a6cabee70a06ea76f2607406453307e98068e463cbde5656646b SHA512 df03f729fa5b0dd6b1e0121701e58d0c6a60b4e8d70d02bdebf6bd7ddd10523a7429c3e13ff4267e4835220cac3a15970565fbcac7979b400ff87707cbaca29c
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
index 992a6d327fcb..9a32e3dbf895 100644
--- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="5"
@@ -8,7 +8,7 @@ inherit eutils toolchain-funcs
 MY_PV=${PV//./}
 
 DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
-HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
+HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml"
 SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
 
 LICENSE="Artistic"
diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
index 9653024a1de2..4318b60ff949 100644
--- a/sci-biology/glimmer/glimmer-3.02b.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02b.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="5"
@@ -8,8 +8,8 @@ inherit eutils toolchain-funcs
 MY_PV=${PV//./}
 
 DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
-HOMEPAGE="http://ccb.jhu.edu/software/glimmer"
-SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml"
+SRC_URI="https://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 5ae34b3cecc5..b5bb9dcd4893 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -2,7 +2,7 @@ AUX mafft-7.037-respect.patch 7463 BLAKE2B a7218e21a08452aab65ea544cfff91a0a88f3
 DIST mafft-7.050-without-extensions-src.tgz 380375 BLAKE2B 86b5813c3cc9897a4f52e4dd3d7317d96b78e5f39530d1d5a34c3493965ba12f80e95fbecbc61a58738913132541a2b7265cd928327019dfdbeafcb10c060351 SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e
 DIST mafft-7.215-without-extensions-src.tgz 393239 BLAKE2B a8aad83a004d468c5723a15c20b30745f6edb47157d545622b0cb1904d8663d1ce64a1a4d067ce96a150e58bfacb90db933967ad4dda61f14f29b68bc1c4d4a4 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada
 DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9
-EBUILD mafft-7.050.ebuild 1794 BLAKE2B 01645a61932c32fdc9f7394b5a59ff548dddddc99a4bca57e0dbfde10a4a71408635db5285940efb526a4d2c91506f87bfa5cd68f6730dcffe701631e6abcf03 SHA512 b908836f2024be4a6315333a84708379e5f4213b179b4c104365f4d0c5878f90602548e9a38d3f11330513f15522094c34aa5cd0e6bc60250c68d18a9d2dd09f
-EBUILD mafft-7.215.ebuild 1974 BLAKE2B a115ccd3488e9786f8b34ef2bfa68f0f283fecfe78b9b94e48d803eed3f88f70d2044797d96f4ee591d03b91405a23e9dcbe41ae8f1bd059456c7e8c1f453c71 SHA512 787a8bf04c3a5d894328331a5908aeb1c1b0850602d145345965cb740beef75be90bf464a9b8519fb93c691253c05665e62a099b72b39ca7081685755c2c1a8b
-EBUILD mafft-7.305.ebuild 2013 BLAKE2B a48c0d9f9ea5cfdb951a84c97003b9faf048f6b658f66b9aa1ca5a45a6dff2a7081a989d33ed5509f01f4ccfdcea12d029c2b97d9ce6bb74014cb6951da1d4c7 SHA512 557a10cb6c9dd0690b7d4979661780597dbcfa110df924250d2b9e6a3943a6f0876c73e803e99c5733fa223c79760fc9e37ef45879a75b2b934452cb86c1615b
+EBUILD mafft-7.050.ebuild 1796 BLAKE2B 7377a5d75e2c0d61e9502e16c8a61d5031f12adcbfb53ba58e1ec0ef7a7eab730aa0bbfbc1c7f6da77b185e5eb429300bd8c997e31dea9927738fc2b31c764cd SHA512 2c5e8078a76c44ccc8151b6493f74038ed2e7bdff336fdebe4171d87c34a3664d2b794030198f798606231c13d3b4b0dabc101c429b438c3675f3909d93a1c1e
+EBUILD mafft-7.215.ebuild 1976 BLAKE2B e490252063bc448db647d0de765c49c468bc2b395b06c2fa26b6368d8d5e26eceb99204f879f0d3104930881393e3f99ecfc9a915b936f299863750cfceb656d SHA512 f297da061416bdbbb3d7ebcaa4efe62b88cb7ca8eedcf0eeaf61fcfb8af42f7dd8b1cbec270ae247efd7a4c7c95ee04a44903d26116e4b73e87ea9fe349d38fa
+EBUILD mafft-7.305.ebuild 2015 BLAKE2B baae93bd674fc22dcbdc14c728c1bd30216f6d94aaceef3b0889ced8fb5b9f55114d03f9a84679f8dfcb54db630a4ff70df538af46b33da2251345b657bdab89 SHA512 c5102f225b1bbe7b89d497e14a78c742f05e873c73a9947669c125bda951d59806da697a29134b639043fef49375a1bb73aeb935445a1e698124fdb78ddb6004
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild
index 685d78005c73..5da5d12d1b31 100644
--- a/sci-biology/mafft/mafft-7.050.ebuild
+++ b/sci-biology/mafft/mafft-7.050.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -8,8 +8,8 @@ inherit eutils flag-o-matic multilib toolchain-funcs
 EXTENSIONS="-without-extensions"
 
 DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
 
 LICENSE="BSD"
 SLOT="0"
diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild
index 21761f1378e4..05c3d8d52399 100644
--- a/sci-biology/mafft/mafft-7.215.ebuild
+++ b/sci-biology/mafft/mafft-7.215.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -8,8 +8,8 @@ inherit eutils flag-o-matic multilib toolchain-funcs
 EXTENSIONS="-without-extensions"
 
 DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
 
 LICENSE="BSD"
 SLOT="0"
diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild
index 92925d8342b2..9f9f631416b2 100644
--- a/sci-biology/mafft/mafft-7.305.ebuild
+++ b/sci-biology/mafft/mafft-7.305.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -8,8 +8,8 @@ inherit flag-o-matic toolchain-funcs
 EXTENSIONS="-without-extensions"
 
 DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
 
 LICENSE="BSD"
 SLOT="0"
diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
index dd69742981e7..a28de67ee118 100644
--- a/sci-biology/mothur/Manifest
+++ b/sci-biology/mothur/Manifest
@@ -1,5 +1,5 @@
 AUX mothur-1.27.0-makefile.patch 1196 BLAKE2B dbe053a5f5629eadae57bd09545ef46106741204050d0c888532388fe0b7f8f2fe4d5f311163e95812d0d828aae2228a2f72b7f0c861f5a3d42a41e17b6ba4f3 SHA512 8a78ddbc926d4e116deed440fda8431ccbca3299ac182fc84850259187dc130cc43fb6f23845d055d998293fa43f94cbe35930242c5f6aa049f8275ad3e42adf
 AUX mothur-1.27.0-overflows.patch 4894 BLAKE2B a9de0276a9ccbb5e86d6cf208f86414ea8c0befdf80807e05b40bee0c6f685cb40a608005e69eb3f77b85990424a36cde14971044cb6a1136a50d85078eb9f1f SHA512 aa392b2060cecc38006a7ac50aaa8e4249a020029234ac2abdc33441b12a09faabb0335144ff4d888e55a1da1838a45347981f49f6658f3546a54a30b5e2133a
 DIST mothur-1.27.0.zip 7095054 BLAKE2B 96a6410d36f64ff50591955aa22bfddf6217c7568022c8c7f70ab70c65d57af2217477de56b6f9ceaf11237cdc5380bd354cf6564002357546539585d0f58221 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5
-EBUILD mothur-1.27.0-r1.ebuild 881 BLAKE2B 41d5d2bdb5dac6704982d6635febbbc565bec0bfba545bf70c85555f8bbf614cc91c4afb471c3cee49e59539906077b33cde0c7940818304bfbb3b7c1da1f3fc SHA512 6f2fcb2d296ef3ef33786b579106f14ee0dfe05a50b53f5e0225c477598da1171cbd88e84f0fc7df5a973c221319a2fa23fb5cbddb339e7ede4e54b34b223be2
+EBUILD mothur-1.27.0-r1.ebuild 883 BLAKE2B dbdda281b6c7a79e4c3202add586f038011502e1c5bf7cc386a4a5c5f90b1926fb16fa3202d6266db77ef5350bad0f56722adb69f1ac7faa50a73a1ae0f5f558 SHA512 c0d22ad5dbe6290f6aed0d055f2ad57b8b25bb33fcb1166c154e604d7337a367beb23f9acc61487ed969e6698ca6f115f8c8d36dc14863a36d08e3f8dd08cf1d
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
index d12d3c9b4399..9e9bf2160310 100644
--- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild
+++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -6,8 +6,8 @@ EAPI=5
 inherit eutils flag-o-matic fortran-2 toolchain-funcs
 
 DESCRIPTION="A suite of algorithms for ecological bioinformatics"
-HOMEPAGE="http://www.mothur.org/"
-SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
+HOMEPAGE="https://www.mothur.org/"
+SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip"
 
 LICENSE="GPL-3"
 SLOT="0"
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index fe65928e9093..25ed4df38bd1 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -6,5 +6,5 @@ AUX ncbi-tools-extra_vib.patch 1393 BLAKE2B 3c9e0ffa614e7baccf87beea601561a8f6e1
 AUX ncbi-tools-lop.patch 701 BLAKE2B 9df2fd3ba86bc9a4f52d3c1809b4d795392666c601aa607d2377129c42562a99087387eaa69d9e9ae07545ea91808902db65718ccf3d671ca88f7255119b1028 SHA512 706dfb29f9b1eff1fcc7dc1df1d533563d9d12ead5b930930121ad92a3e8c159d1d7cf30acd9f4462772e8f27e6dcf45cd6125f2fa077b3902145f6faf1c8352
 AUX ncbirc 57 BLAKE2B 140c208cf1c7dbb6a204e58632c576e4edf0cd71d151b69f70839f1b06ae19db0d74d49179d2f0bc1320a40fabad49bed18a98a8bd2a75f6ecf068e647382c60 SHA512 0b9b68116b362ccc625623abf4e959abfb8555c31117216eefe3093fe2dd122c3ce508fe389c07a069d6f4322d889718e455de65dd3ab7d55a16d947ecb07cfd
 DIST ncbi-tools-2.2.26.tar.gz 68691452 BLAKE2B 21444227c6896c387f46a5490db1e4cf3ac437f94029c68f11ee3c5438bf2c34584d4b1b0ab18d3996f9c4e423a7e17fece510a96a1aa8be5dea6c5a2688f24c SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014
-EBUILD ncbi-tools-2.2.26-r2.ebuild 4648 BLAKE2B a8b9407caac66f67f117696dccd630e7516f939300c9a5c70e9f7ef49e5b5598fc1363f74b7ba956b89397fb13ef19b4eb5258c649bab7db3f1a577fb76c4145 SHA512 c2a72119bb087fb210723fbc6ef88e397a2144b7256801ec382c251c1e5355481e0e17b8e6aa0c76e6ed45244c838a2ef9fa26761ffa40be114f241e115b6bde
+EBUILD ncbi-tools-2.2.26-r2.ebuild 4649 BLAKE2B 856db3d5f76ab1d246c8d67eb71b0c9c06f227cb88212ceafc0863370d52adc379135397dd8978cc57b2803f2cb8d36d53603dad5a8921616b8f236e9b47ff1e SHA512 c6611b3458c0369599c0027d9206d3dab72e52decae655d1f2b3394008d2dc96236c121754526c0f358bb3ed512ca7c485add1784bcd80e208f710330a3a208a
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
index cc0e8e3b5472..1d3b5784a3a1 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -6,7 +6,7 @@ EAPI=5
 inherit eutils flag-o-matic prefix toolchain-funcs
 
 DESCRIPTION="Development toolkit and applications for computational biology, including BLAST"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/"
 SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
 
 SLOT="0"
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
index edaa0919bf69..b51fe5eea178 100644
--- a/sci-biology/phylip/Manifest
+++ b/sci-biology/phylip/Manifest
@@ -1,7 +1,7 @@
 AUX README.Gentoo 643 BLAKE2B 95193d4c9c8fc8fb5796bb0a8ca470f440ac66eb1da9b9ed4784494a6a4c9bb12a451223c0ff81ae3ba80da81f4d8d3a00a21cad557f575a81325a180a819c0e SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a
 DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d
 DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be
-EBUILD phylip-3.69-r1.ebuild 1142 BLAKE2B 314baf63e3cf102ebe7d524fb1795ff9e1a85a4e5b0c2d54a11e7bb85d8cd0500a2e55c3c9ad46c74bdc0fbd0242afb2f7086ddb84891eb94918faf786e99d06 SHA512 b7d6638ddc1a035132507918dd49e82e41e450ca31b8e6afbf646e69ce29690b5be74795a108a03eaf79399bc909031d844f664e072861f4cc656aaa0b8946c7
-EBUILD phylip-3.696-r1.ebuild 1134 BLAKE2B 4c7dd5c2f3c4d3a6df4f0894c7c59b962d7289ff720887e97e51410722c43949dca349f7b6b49407975fa53e149a919f9009799a9f30d6fb5a2043b51fff7955 SHA512 ef7196f540a1bf981dd1d2489fc2cba31fd0ea3135f060331f8f1ba43ce585ae4c6d33cc76f53d561c1c36059c631303caeaa20c28ada2c02ce218119a202872
-EBUILD phylip-3.696-r2.ebuild 1208 BLAKE2B 708b9651012a28d5f1d7b425364144cb6bbaf278245d4c46a9932b86020199d327456f62e57ba791dc39221d66e993166d6e39bb7a990c02ebbb7d97772ed4ce SHA512 e84c5b74d63d51d4151c097eaaea814d2ba0e25ea16aee1f30f9cf57d4ff3207a4090b942ca09f835f5fc81fd460b04623c8d49e2406f0f9ef7c210178be8dda
+EBUILD phylip-3.69-r1.ebuild 1145 BLAKE2B 55565e21aa748ede76c7c37fbc4cef8849707c1f7500ef283485f461ffc99282fca1316af634bf24abdb1ee33005d26e6dce1f2fe30d52c224882dbf3313ae8e SHA512 2f591f9616ab7ba831ea63eb02b8a83ab3ae0ed63221c02a59ad63f5d05475e2b51a4adccb47532740c809ee832cb0dd02e3389208d095c930e68070974e3fb3
+EBUILD phylip-3.696-r1.ebuild 1137 BLAKE2B 46e27a695491b597ccb6ee4f3e5fa33e44cfd322dc9a05856de06b9997dd698ae91ec6629eabe5684b17394c1026535d548da99d1ae76277bf5421dc505f426a SHA512 2c1141ada9169a1e399bd29c9ed8bea1ae1bca067dcdc557fbbecbd8f92695a1af5fd4299600cf7511971d2015da3156da180dc56d507e0ad2a9d445bb2ff1f4
+EBUILD phylip-3.696-r2.ebuild 1211 BLAKE2B ab783c32ca07e6b0a49696babc9527585277ab110138aecfde70e3d321b1de389580f4303a9ade1d4f379ee10dd75d4d6c0f5cc3193e99136321872ac1020150 SHA512 65347aa28dcb75f520030be9b0ab3ed349e01079b1ea3fcf5680f9a1da1fda08fc3464f099ecf6c05b9ef73b5f33f41e8d678eeaf4ce226585a7c186a6ba9a06
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild
index 658c92e785c2..12f007810806 100644
--- a/sci-biology/phylip/phylip-3.69-r1.ebuild
+++ b/sci-biology/phylip/phylip-3.69-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -16,7 +16,7 @@ KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
 RDEPEND="x11-libs/libXaw"
 DEPEND="${RDEPEND}
-	x11-proto/xproto"
+	x11-base/xorg-proto"
 
 S="${WORKDIR}/${P}/src"
 
diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild
index 03b33b303805..3943d3637946 100644
--- a/sci-biology/phylip/phylip-3.696-r1.ebuild
+++ b/sci-biology/phylip/phylip-3.696-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
 RDEPEND="x11-libs/libXaw"
 DEPEND="${RDEPEND}
-	x11-proto/xproto"
+	x11-base/xorg-proto"
 
 S="${WORKDIR}/${P}/src"
 
diff --git a/sci-biology/phylip/phylip-3.696-r2.ebuild b/sci-biology/phylip/phylip-3.696-r2.ebuild
index c19085ed6cfe..b3488d65421c 100644
--- a/sci-biology/phylip/phylip-3.696-r2.ebuild
+++ b/sci-biology/phylip/phylip-3.696-r2.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 RDEPEND="x11-libs/libXaw
 	!!dev-lang/elixir"
 DEPEND="${RDEPEND}
-	x11-proto/xproto"
+	x11-base/xorg-proto"
 
 S="${WORKDIR}/${P}/src"
 
diff --git a/sci-biology/prosite/Manifest b/sci-biology/prosite/Manifest
index 46868c97f0b1..8b6172bf4160 100644
--- a/sci-biology/prosite/Manifest
+++ b/sci-biology/prosite/Manifest
@@ -1,3 +1,3 @@
 DIST prosite2017_02.tar.bz2 9234253 BLAKE2B e818ba766a0761336b3f06b173fe98133e3c6fd9ee21198234fdfaf711ac2bf6ee68513c073a09765b050ffdcfe8c8d83a2ae91b89558db18ac6039798201c68 SHA512 2b8a26a44d62d17108afc43a3ab65d024f76e41ea9c9f477024700621323d2606fcaec54411e1d3f4ddad40717ad9ce3a1989ffd92220e0d3c2acf70400d2e43
-EBUILD prosite-2017.02.ebuild 980 BLAKE2B c9f2ac051576b919e9877798bc0e0f19fe483d3d7b4ead717c27555501a841f5e5856da69ead2af90087fe0dc893feb5fee3934e81ea6e0c4d768df2ef7c5b02 SHA512 5911898bd4cb41283277dbb4cf9ada173f29bd0378af4b7f679d5415a368085d00826ee0c709195605a03b3fc4cdd96a8d9b1613e152ea0347d9ac0d8dfdef14
+EBUILD prosite-2017.02.ebuild 981 BLAKE2B 6ec1b47ed30ef51891901ea2f67ec0e0729903672437824d0b06f05a8fed9083a750336190b5d396c91c7f5bcfb2fcec849889475a12dfd186351ac711122df9 SHA512 0f0c805052daa587cd8699965230fc36dd118b53855fe13ad8127b7556192778dfd05e21145b0ac13922cc84c3cab88c758f0f8fb874d90a3221e41e1169568b
 MISC metadata.xml 817 BLAKE2B e6b944c3a297b0eaedfd5e3eca09e4c27f4f4b6f1dc7a93d66b5ab265f465c326b6cc1c26f167b41eb57c43f8c7835415dc91b6fa6f0a4b389b2a99582e435cb SHA512 28b74af20192bc861cf78d43e55264e84473e471ce6dcdc63f30c3b64d4727cd3e8db5b4934d79ece4a3d732263393264d9085e0e53ce16649a6269a3c40f8e9
diff --git a/sci-biology/prosite/prosite-2017.02.ebuild b/sci-biology/prosite/prosite-2017.02.ebuild
index b3d9ef2335fd..6003b17cff85 100644
--- a/sci-biology/prosite/prosite-2017.02.ebuild
+++ b/sci-biology/prosite/prosite-2017.02.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
 DESCRIPTION="A protein families and domains database"
-HOMEPAGE="http://prosite.expasy.org/"
+HOMEPAGE="https://prosite.expasy.org/"
 SRC_URI="ftp://ftp.expasy.org/databases/prosite/old_releases/prosite${PV//./_}.tar.bz2"
 
 LICENSE="swiss-prot"
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index 90cc4da57424..88cc05d2f45e 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,6 +1,6 @@
 AUX velvet-1.0.18-gentoo-r1.diff 7879 BLAKE2B a1aaa683c82d7c69669c815b2b3351ba115fddb600fe0eea46d2cc002b75b752565ed9e289c2f0143550e5ffcea13587bb8f8cb31227d38ed63a769da3b05b88 SHA512 7aa112850c1d83220e1545ef29aa3e445ce55bc4334d062c353a5c5681723a3492c8dec52aeb58cfb5d464d1c748b721dc6400509fa872a48c428a2e0f9cdbf0
 DIST velvet_1.0.18.tgz 7598196 BLAKE2B acaee0fef39afe34d80a6be0bcb0069fd2daab396741034fc9d298a3a828303dcba50f2cd40d94f2b97f5066b281df810716f548cd88a64ae2c661ad3e012c1f SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad
 DIST velvet_1.2.10.tgz 18818559 BLAKE2B 5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874
-EBUILD velvet-1.0.18-r1.ebuild 1504 BLAKE2B f1d7be13ac57ab98eb3d74fc94d070e80b9d9e9422bf822bcada8c3417322df2956ca9c110b98b19d62ec6ebf2a309518062616c0e070e4c83de136737d8643f SHA512 fe13e66f7d8eab941ba7fcd900967a13bd1f7279a63068275be1bdbcbd29aa29d6acf8b29ac8b9690936d8e95440c8eaec88c99a2da40270654dee2a29748ac0
-EBUILD velvet-1.2.10.ebuild 2104 BLAKE2B 10cba35da08d85298fdfd8c0d5e34f9ab1edcf4c0ee9d938f958126cec002a66561ac843d21492688a19fc83fbe16beed9dc6405f1e7cc9bda3d7adc6c6b977e SHA512 5176ce7dd9ff4f2bdd272333081a91e7e8441eedf49b5eb81ed0aaddddb21d60c02b1927168894cda0c48ae520b685d92446ccea28fbc151dc0a8aa61b6eabbc
+EBUILD velvet-1.0.18-r1.ebuild 1506 BLAKE2B 53b3c71ae3cf401f5626215b418c15ac4dbc96817bbadf127dbc2739d6686a8a227ec61f5112a0aff444d4fee53ed5513042c78c28c3a8086158c249f43040f4 SHA512 13551819ee7eb7a86dd388a31cd48688fabced7cd42cfbdb536615c314ea9da5a94fb1fd4a52695c8a931c62407991592948f53a2d191133a6d394d15c2708c2
+EBUILD velvet-1.2.10.ebuild 2106 BLAKE2B d7ea6a576303cffaf8785fc125b6848d3dde0775756867c952d196f0f1e55959e5d7a3b29c0096108208db043658d5f7e382e3ef701b20c4c6a383cc3f561934 SHA512 6c02607cd77b12cd2a64a92cc2a469994aba906823b3acf5c36537749a6268e8766bbc4e319d057430204af1ae36c9351f68ff579d4065048851fac9e12ccc3b
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
index 4b7d1958cee6..a8ec87b6625a 100644
--- a/sci-biology/velvet/velvet-1.0.18-r1.ebuild
+++ b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=4
@@ -8,8 +8,8 @@ inherit eutils toolchain-funcs flag-o-matic
 MY_P=${PN}_${PV}
 
 DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
-SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
 
 LICENSE="GPL-2"
 SLOT="0"
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
index d5a93f2f3e48..3de28bdb7481 100644
--- a/sci-biology/velvet/velvet-1.2.10.ebuild
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -8,8 +8,8 @@ inherit eutils flag-o-matic toolchain-funcs
 MY_P=${PN}_${PV}
 
 DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
-SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
 
 LICENSE="GPL-2"
 SLOT="0"
diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
index 80eddbef357e..1cb622926ec9 100644
--- a/sci-biology/wgs-assembler/Manifest
+++ b/sci-biology/wgs-assembler/Manifest
@@ -1,6 +1,5 @@
 AUX wgs-assembler-7.0-build.patch 10279 BLAKE2B 9fd4a113d4ea3b07570c39e32892b535a0ed7d0e958602ca891c75fa3aa73a44d205fe43580e43d98cdafa1d431c12f68d5fe55e52aca82e451d5aae3ea2c551 SHA512 77e432319cb279d188ab74edda822f6b4dda127f1e5f1d75febb6fe0533b66d5bfd066781f1ff5d4d0d8f832c491d31ec470653b9c36b29d8280b5786783c5b9
 AUX wgs-assembler-7.0-libtirpc.patch 516 BLAKE2B 1ee7876f767e559a008d86b8f6ccdbf70763646b782ea23d2bc9f74edab84ff633270ff15d0cd5b888674c5ee0d0bdcd3b73a48bf040f06f2a56bf4e366125cf SHA512 b2a29b2dc0578d4e8544dce258327a34ac4a5ca6bea3e901bee06d89618e9cba7f569fd54da6148372826d053829bc991db7c4cfd5a8564dd81545566698c947
 DIST wgs-7.0.tar.bz2 1952253 BLAKE2B 2dbff6ffb9f4310d3d1301405e74476b7b7bbed4359c1701b5100d9597db46cc9956ccbe467bb37f8976d176ab9f92bfabcd5d1210b1e10675cff9a87ff379b9 SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba
-EBUILD wgs-assembler-7.0-r1.ebuild 1597 BLAKE2B 046fee583f335d5554069c0b9d489af94fa78d98b9d41cfbee518ff124e06c0f603afb6494c50bb6958f6f92c63957e6fefc6357eb358a950a71db8396753c07 SHA512 d874b917c4b86cfb56681473c4c99ec38bd9a681b7e0832a0e9240f2a1c20a754be30316ca4b64f579cbd8c3bb50cad18e874664f5e51e41194e6941088bcb86
 EBUILD wgs-assembler-7.0-r2.ebuild 1662 BLAKE2B 1c542685f8667e1901eb3950c084ad386e29a077d280e5c3ed24ae84fed71e4876a5c8bed80ea33c4b7b4c3b0c0720f0229d3efc1e2f1654548cdfeb32383e5b SHA512 ad0f1a44e14c9c714b7b6d00dda05bb9b16b9bdde29989d2fd4d785294053aae94d85d0b5ab92faeb2574e99f18a6c566c2c8cc01c5d920632a480aae6f88a4e
 MISC metadata.xml 354 BLAKE2B eaf844f74ea3b2a51cba2f00ebc0a3cc895312e04a995000e93426fa0e2f9d8601edb2011ff6c837f85b3a5755b819dc7ce517d3787c2e7bd37e097e144fb156 SHA512 b46f437eb224dbc7d7cec21941565ab48055f1d7b787fae7e66b135a8abeff0ea55dc191643d1e5f6212012001d98e4b7e8a7a655c9a66c9f3124bf7e700e193
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
deleted file mode 100644
index 066654dcfb92..000000000000
--- a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
-HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
-SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="static-libs"
-
-DEPEND="
-	x11-libs/libXt
-	!x11-terms/terminator"
-RDEPEND="${DEPEND}
-	app-shells/tcsh
-	dev-perl/Log-Log4perl"
-
-S="${WORKDIR}/wgs-${PV}"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-build.patch
-	tc-export CC CXX
-}
-
-src_configure() {
-	cd "${S}/kmer"
-	./configure.sh || die
-}
-
-src_compile() {
-	# not really an install target
-	emake -C kmer -j1 install
-	emake -C src -j1 SITE_NAME=LOCAL
-}
-
-src_install() {
-	OSTYPE=$(uname)
-	MACHTYPE=$(uname -m)
-	MACHTYPE=${MACHTYPE/x86_64/amd64}
-	MY_S="${OSTYPE}-${MACHTYPE}"
-	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
-
-	sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
-	sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
-	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
-
-	dobin kmer/${MY_S}/bin/*
-	insinto /usr/$(get_libdir)/${PN}
-	use static-libs && doins kmer/${MY_S}/lib/*
-
-	insinto /usr/include/${PN}
-	doins kmer/${MY_S}/include/*
-
-	insinto /usr/share/${PN}/lib
-	doins -r ${MY_S}/bin/TIGR
-	rm -rf ${MY_S}/bin/TIGR || die
-	dobin ${MY_S}/bin/*
-	use static-libs && dolib.a ${MY_S}/lib/*
-	dodoc README
-}