gentoo resync : 16.01.2018

7 files changed, 13 insertions, 8 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 63826002c21f..e15ec4201e57 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
index 5d9e4c7935f9..cf9af10bddd2 100644
--- a/sci-biology/amos/Manifest
+++ b/sci-biology/amos/Manifest
@@ -4,5 +4,5 @@ AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 BLAKE2B fde1011da76275
 AUX amos-3.1.0-qa-Wformat.patch 4511 BLAKE2B 64064175db625a098a528f0c8036196968c58dae445edd3c98fc5627e3a84d593abc438958573ef7a28193d0d2fc76db30fe16a180a383dec9bae5084305505d SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe
 DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634
 DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491
-EBUILD amos-3.1.0-r3.ebuild 1089 BLAKE2B 7ee83b8e948e16f3fdc486ed8896c6fb57496e982859ca18cedb1e0e8a2bebd9125fccd2d13602edc137a6fd6d62d003ab4f9dbe0ac517937b76690d87769253 SHA512 5eaebe166daa11142d77e0d1623a46a0736a1d1180c6bc80ad246f67c684ad38ceba0cf179ea2a7af83c8c2785f24ed12f54c2a71d6a10fe7174f852e649ded8
+EBUILD amos-3.1.0-r3.ebuild 1189 BLAKE2B d0e36265d14eb3b3c0da7e21edc63bc75e3176d52ec0a117fefa394d234f29954809626bd0517a9210b7fa104dae9c72f962b3cde12386da04890f039a5af8a2 SHA512 b2e0386fc5bd65884f4f9ccbdb74ec0f42c37c157cf52c17195fbf390156f242f9c77780323b40fa33e6f5be52863fb0beddd23048695c3e40a65f2272dce7c7
 MISC metadata.xml 345 BLAKE2B 750928cf3e96c24e2af8e84d5889100c1954eb140596368dc00d479f63898c82e3bb0e07a9e970c6c12eb36ed3ae84c6bcc7913cf3ed56e2d71120185d24a4f0 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497
diff --git a/sci-biology/amos/amos-3.1.0-r3.ebuild b/sci-biology/amos/amos-3.1.0-r3.ebuild
index ab383a3b95a0..33c30995b11b 100644
--- a/sci-biology/amos/amos-3.1.0-r3.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r3.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit autotools flag-o-matic python-single-r1
+inherit autotools flag-o-matic python-single-r1 qmake-utils
 
 DESCRIPTION="A Modular, Open-Source whole genome assembler"
 HOMEPAGE="http://amos.sourceforge.net/"
@@ -42,6 +42,11 @@ src_prepare() {
 	append-cxxflags -Wno-cpp
 }
 
+src_configure() {
+	econf \
+		--with-qmake-qt4=$(usex qt4 $(qt4_get_bindir)/qmake no)
+}
+
 src_install() {
 	default
 	python_fix_shebang "${ED%/}"/usr/bin/goBambus2
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
index 7738d880d777..ee33e813846f 100644
--- a/sci-biology/consed/Manifest
+++ b/sci-biology/consed/Manifest
@@ -2,7 +2,7 @@ AUX consed-29-fix-build-system.patch 5614 BLAKE2B 8b145d01e5fa6935715e7775d8e415
 AUX consed-29-fix-c++14.patch 9261 BLAKE2B ff70814b39780dbbabc70eb7555359e8aee2ef72b40b7e149e2f63ccaeedfe7e0dc8822cb2b5c79d57c33e621a59e0e1cd273e49a0976daef0bdeb52f4f46569 SHA512 be5cd76d36cf437c1113d09e540d98d0eb92b7e2e732f4a5a308066b8046b5628048203e791a0fa316e44a4cc127d027418a7f038406df22c3f60552f5b87789
 AUX consed-29-fix-perl-shebang.patch 17375 BLAKE2B e34a358569d594f4ab60fc3745a6a84cab781cbad860421f5ac322154df9635e13b2e2349c92f4271b0ca161eda87285ba89bf0801992954fecaa11575c8baf9 SHA512 4caed1ab7229e2b3e367f03a8d650cafed2974232fcd6daa08e62c90512d49e09caceb34c5bb65c67a588bab314165d72d8c1687393549d4107425df78e3218d
 AUX consed-29-fix-qa.patch 11168 BLAKE2B 139b52d402f27c8121a43f933a181aabf150c0c8836f2facc7b42909db3808fab1ceede30956d6b3c2462ad31b43e054c0bbf8552e57e6e41479d25eb111738b SHA512 088d774159b421666bf75f6f9f17ee83d488625d482d8d404bde12671025b1f03322bee5c50e792fbbd822c223fa5ee697cf99c7efc9fcbebc119314d02df604
-DIST consed-29-linux.tar.gz 36172715 SHA256 98354e2507ef9026b82c89db199ff1de7e4ec3686fccd691d215acdcde34ce39 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd WHIRLPOOL 26ebc1ee7114b0c609fd36c2c46b71c399bacb61f7db285ab36f296902964c14518c058e814a166b20a36c2d320280aeed0ca18b7104c6b503324bf27d4b57af
-DIST consed-29-sources.tar.gz 3258845 SHA256 e7d3c2bf60e0bb22025e0416d16cf9864fec8091811ec285a39db4cb46bc3fc6 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 WHIRLPOOL 5ac363f049b6b40554112f830e812e7ab7d334a0f6707ea4da981ed1e468109f3bd7669382aa77e93cf12c78cc95fb1085711dcc972c7ff22ffe6b73056bb2c2
+DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd
+DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93
 EBUILD consed-29.ebuild 2701 BLAKE2B 0eaed4ffca6daa9921ab782b00e34f207ff235e94ed2cff0147921c037667d30af200141b61ca91c9e386f5f9672566ba92e3dbeb8c2bef965f9ab72cbf2c27d SHA512 56d73a2d4ed207924c2a7676bfca84b8c0cc4f80d1a2a1b94fa2b3d644a6583f15e32ee81b9892122e051f17a1eda56d63ffb8d650283a9bee5c61bca6faf1d3
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
index 8c05c3f368bb..0905e1e9256c 100644
--- a/sci-biology/phrap/Manifest
+++ b/sci-biology/phrap/Manifest
@@ -1,4 +1,4 @@
 AUX phrap-1.080812-fix-build-system.patch 3600 BLAKE2B 29a7846cd6394d17b35e525220b8ead461a22ab0f1301ae5668da36605649c07f23040c4c134424802d4da6e0c3b48fbbb05ec5708de50b33f024e4ba702ac49 SHA512 536ad862b9b8ce0fbc7ab67bc48db597e7d4b8c66018a5abefe5a59f4fbc30a4a76c94f4c13f5af7d42a422a22f5181d8f015b797d37f175238c3d4170adf21c
-DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052 SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca WHIRLPOOL e516561804620ba8c96ed0e5c5d791f3fe1e7984e08f646e6fd7c30042f2550f5d1c9b2f800e8a853e42b049b92418ed9d0121e77bf4e9aa895974bce5e73717
+DIST phrap-1.080812-distrib.tar.gz 317350 BLAKE2B 9cc53d05184b4a55a9a80e6112498f91a622b98a853b255daedd57c892b7c2bb8ef3091ed3d141e297864c158b7e03d02313a272448d2e0fb80e1c51a906e00a SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca
 EBUILD phrap-1.080812-r2.ebuild 950 BLAKE2B bf8ecd534bd6f9dc99eb815e17196a23fbfd5a3caae7fc3ff024f188e73d061787f140350fd4bff042d5aa5663f52ea91e62b3e95eb56387eb225335181e6bb5 SHA512 4857f1fe337f24ee33618e3dac40a5edb7210d1353c058b57a1263a4ccdd8213270827c2c2f902d454226fc65368a1588d497dcdcf2eb9c15af406d1d5cac3fe
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest
index dfd40b35f024..5c9b996c45e9 100644
--- a/sci-biology/phred/Manifest
+++ b/sci-biology/phred/Manifest
@@ -1,5 +1,5 @@
 AUX phred-071220-fix-build-system.patch 1981 BLAKE2B 0c9ae75ecf54eadd1d6cd3cfeed5d2f949f234b77d4f329133e2c176207410e93a35341c43636c5b2f742a2ee2d20825cf79bb65d5dac43ba28fc07f7c6bb69b SHA512 7647f6f6e9a1ae51cbf1aa3e39b337288e22fc26a95fdd88f92ce43fc6c0ef6ff59ec26919d14dfefff70be48e4a5604ddefef98bddf5d1d14d1e656665c878d
 AUX phred-071220-fix-qa.patch 787 BLAKE2B 79f687dc1e51dd51e9f97886e0ada9b515d7e4255dff0ec3e81dccb2103ba8b4bee691c8a5b9a321cbdde5576fe8d80dbadafdb740c2cdee81fe9748255084ab SHA512 27811a834358d0e1bf8281882e0420e0eb6bd9586871c8c72a4de79badc9539ea8e9258b9c3a3bf8ca1d3f6924d61abce2dcc0c0ed3b64e5fa53d4548109f5bc
-DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975 SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276 WHIRLPOOL 9b14cfb1ca970a14ef613ca17efb82955c0ecec414dfad8835c883650f306b3a79846b7a410a9359cbd9ca953d890673366b6f865a2a357e81213d34b3327d3e
+DIST phred-dist-071220.b-acd.tar.gz 357767 BLAKE2B ae1180f54eaa3631a4e32c2ffe388b35745302e3d014c8fa893119e7e488d4bb4316f7ee0588cd12db5cbbc23033f689f4a0a487cdc7fe42e8c7a67ceb3c43ae SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276
 EBUILD phred-071220-r1.ebuild 966 BLAKE2B 1d01310018b354843d7650a15f70b6ae5005f4ffa70fcbd270f88e02e9dea837e972c28d771a8926eb7c68faca87d475c2e79fc0332007214b37ce88d9817479 SHA512 203ced3280f1c1bced57a1cb514533b71df1c2c9eefc94e594f61d45300da32617ff6023196d47cab7a1ca21bef61392760f5a12f25815ac5d78b9a8c58e7e91
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest
index 55328cbe57b4..75681cc74b2a 100644
--- a/sci-biology/repeatmasker-libraries/Manifest
+++ b/sci-biology/repeatmasker-libraries/Manifest
@@ -1,3 +1,3 @@
-DIST repeatmaskerlibraries-20120418.tar.gz 28059668 SHA256 7bd44a70ee33ef60ab829b4cb84a2a82a6fa923e2992071f374b7a473e4dac62 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32 WHIRLPOOL 1da932f84c591221c61177116d734d00c36c52d588bcdab73ed63e8128b9c90a63f855bf4e8e603167e059f98465460b5b2e7e00e4a724bec230d27b1b32a31a
+DIST repeatmaskerlibraries-20120418.tar.gz 28059668 BLAKE2B 0683305f0d3045ff1bcb9f1c952d3c12e92a3003f79ba18a16334805049a64e0b307fac2cf7fad236c9b0cab80e3317ebb1d93bf6487bafd9d45de2455565879 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32
 EBUILD repeatmasker-libraries-20120418.ebuild 760 BLAKE2B 3e4019a480811b8cfd18a5bb822e3f7061b8c49a3361f1db2bc2b8f9c7e610442a3924a0ddea1b7cefe55353dca39edd433cfda0feaa32da5416805ddc7d8b65 SHA512 ceb9b66624d509e9c6f3750d7a51d707e7b626dc3c15fe09d84be632f68ca8d0bcbde25b9b5dde4919af2449ea25877931f751f5934e2fbe7f1db0b394ef5cc0
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403