gentoo resync : 10.02.2020

8 files changed, 26 insertions, 11 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 2c9928c841fc..f9edb0bfb762 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 2c0602a79c08..09afec5ba291 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,8 +1,9 @@
 AUX bcftools-1.5-buildsystem.patch 376 BLAKE2B 384bf91c3af4f98c76c0ab6fecdfe0ec9483b77c54517df0ad2703441def7a7a6982ee792ae1775414ab8cec43d0e65ff6d2187be7cb85bb42eb5af8f9b7283e SHA512 c8ede2be5205ab287843662e7b97ecae8d4fc7d2aaf09e0b9fa67f5a3168149b15457e73c2c9d8b74fcfada08ec5c1bbe61013a2ef434ee50acf56eccabf6723
 AUX bcftools-1.5-fix-shebangs.patch 594 BLAKE2B 28d0a58627dcc1b1eb8f546c73a88f76e3277c82772f8a7af814d9ff3bcb116751b065166661c486e8c6b1708a54de227a5ef65d18a8527b38f5119d744539d2 SHA512 e00cc0de35ad5866f7321408a7995f054f80e37e642b6c3097c5e786635dc61baefa7ea8847f2222d32196825e3e44209d63fdfd219c54b09421a4bb310067f5
+AUX bcftools-1.9-buildsystem.patch 380 BLAKE2B b71567ad14d96b85bf449db473b38cd9ff2a32420d9c4d1b606cad0e09a478fd0946b589c62405aceacf234db7abde3fcf180eed7fbf0d8db73565b4424f86b8 SHA512 f0124734e6309eda73e5f32a9832e8c35de1929c6503627564346f097415bc76294371eda1886100ce2f1ed8e0de695e978a720dd4517e8411dcd041797af2b5
 AUX bcftools-1.9-fix-shebangs.patch 198 BLAKE2B 9d6c365c7193c7815216be4f8034c00e0048f7352e15ee24b4359828bf0906755ab9524fb10ad185754652b74007dc2c756b2260f64a263f696cf0f737ff25d7 SHA512 65eecc5e0d5cf3df1538b078c7606b38451e13f4f359ecf9287a9e03721c7c7ba1cd8bd517a98dd34842db22624fbdc570e9707d13f2e2fb82b16b3ca41ca71e
 DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
 DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c
 EBUILD bcftools-1.5.ebuild 868 BLAKE2B acfd6758e27cb9ade023d91074724affd0fa3016af565c809819fae615be61ca8af90edf6b38eaf0a4ed5f3e9eaaa19451096b8d7c27a58c6ed0540bf7260784 SHA512 e0aacba5fc54cbf7a8d64db84e52f28baf8df36fa01c63fc167998c6ec5ef65a040c0725f445970f32888ae947b89d50d92dc2fc704fdf63a8a900762ec367e6
-EBUILD bcftools-1.9.ebuild 927 BLAKE2B 3e9c712316fa510ddc7be30c398565e3fa4e435fe58cf4263ba3c69dca34b4c227fc80ea23c52e70437a3b9058645f02505a17831c04a23e97086175ed8ee383 SHA512 0cbb0d08596819f7769d23ade97627b6ac9362140904609a2ea0603b8285e94ea2472721a49f298e7aae9a97d3495c3816e8229620a1a11225d2fcd881504cf8
+EBUILD bcftools-1.9-r2.ebuild 996 BLAKE2B 27af6e1f88f2501f6b4c2a627a755e82024130f1e0b884a517322fa7181d18f00a1323fe0477f914d80c25aa0dc81152d930689e1e18870af69d8dbeb1daaeb8 SHA512 f9e052edd07c6cd9bafa338913954729bbcf0302d418426d3077685acc15128cd19991361a2737c8f56fca4069123d58446633e0ca7c881b3996a65f33fd7d0b
 MISC metadata.xml 452 BLAKE2B 53a356b0569d9db1377bc1881d58b4b354d4861eb21b2c602df59b7923b175a20623cf3369695416eb08d44fabe32036f5a5ec3119c765c8f85347d3b094918a SHA512 eb656430c9ee5ffee5ec5f9f8f3c69e8b0d1ae124cd720ae4af6c3c160da5dc261838744f75e838a85935bbc9bd5201b038ee11cb41a0e1209c9df58aa85fc1a
diff --git a/sci-biology/bcftools/bcftools-1.9.ebuild b/sci-biology/bcftools/bcftools-1.9-r2.ebuild
index 53e47bc01a81..eafe63a1ee54 100644
--- a/sci-biology/bcftools/bcftools-1.9.ebuild
+++ b/sci-biology/bcftools/bcftools-1.9-r2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_6 )
 
 inherit python-single-r1
 
@@ -14,18 +14,20 @@ SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
 	dev-lang/perl
+	$(python_gen_cond_dep '
+		dev-python/matplotlib[${PYTHON_MULTI_USEDEP}]
+	')
 	=sci-libs/htslib-${PV}*:=
 	sys-libs/zlib:=
 	${PYTHON_DEPS}"
 DEPEND="${RDEPEND}"
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-1.5-buildsystem.patch
+	"${FILESDIR}"/${PN}-1.9-buildsystem.patch
 	"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
 )
 
diff --git a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
new file mode 100644
index 000000000000..a0df4b917bcb
--- /dev/null
+++ b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
@@ -0,0 +1,10 @@
+--- a/Makefile
++++ b/Makefile
+@@ -282,7 +282,6 @@
+ 	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
+ 	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
+ 	$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
+-	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
+ 
+ clean: testclean clean-plugins
+ 	-rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 8dd3860d13c8..9c73c14bcb7b 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,4 +1,4 @@
 DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
 DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
-EBUILD bedtools-2.26.0.ebuild 965 BLAKE2B d7bd87cd069734c20c2ead2fbe6ce889f0e348e35406f390eb7b6826a993f3866968599006c2dd918e017c17550005d630c3e843b15fe28f5a9ca140adcb0178 SHA512 a32f895d9fe683be0d62176eff4dc800cc5d4a32b6c3fe749062f96fd4183f97217781e171434ddb87e9b958135e6b8f980529a8aa6514b9d6aae69c0325f9a8
+EBUILD bedtools-2.26.0.ebuild 959 BLAKE2B c3d42f033913e18a9bd1f0b6f669a4000bc6b6892bbd5986a33a99ed496ae4af11b690f1c7c350644b62e77baef80a9eb52f15e87818a74b684d4fac816a2512 SHA512 a3914d04806fa4b3f14f83d91717d00fd183e1f6d4a39690ae04e7767791605a8e90d86cefc4deaa50327651c64125808658de4471f05df936c19e46768bf988
 MISC metadata.xml 761 BLAKE2B 35d57919e32a4b8bd6070ab5a513f62578394d43098d9e7b9b0765fd57d684c049dad9ec1b315044518bf01535d505e9d9d3fee540308df40c0b70886db8e49f SHA512 2d98b9559ef00bee2b741f9e7d22645442ba161f3cadb32c6366b39fcd71b6eac52afd210f59ae709a15cba36a2d0a47341345740e0cab6a1f6bfdffed064770
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index 0ad6f3eb354d..b062a6fef84d 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=6
 
-PYTHON_COMPAT=( python{2_7,3_6} )
+PYTHON_COMPAT=( python3_6 )
 
 inherit flag-o-matic python-any-r1 toolchain-funcs
 
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 3ae47ce22cb9..391b7baa196a 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -2,5 +2,5 @@ AUX tophat-2.1.1-fix-c++14.patch 655 BLAKE2B 760f2d371e6467340d31c688187a62b0266
 AUX tophat-2.1.1-python2-shebangs.patch 758 BLAKE2B 83bda360dc36d3eaa890adee00bdb58698fb5eaaa29255c85b3b63f61536921386115662051a4938d21079a3eb1a103dce752f0320fe1990535d35ae74480fcc SHA512 887e5a8b02c2e43a7fa35c9f98670dd722527c45454ca24d5e2f9d2f372267905d7e0142317769b14830706cf82868cb83ede970ffe527f736d71df794fd6342
 AUX tophat-2.1.1-unbundle-seqan-samtools.patch 5224 BLAKE2B acdf26085b6eab54f478f5e31e2f180a008b9a05b853253f8f161759dc79a0fb5ea0c54bbf3a0f4ebf79da71988c60d17899aaa1ff6e927a308eca01edccbdf1 SHA512 d920cee92a0a694a34d6ac5b949e5b883bf9dcff338f36e227cb014732231b96461c02e75418972c85880169751a96c2367f6a4be6ce8c91f310b4b4f6858248
 DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
-EBUILD tophat-2.1.1-r4.ebuild 2182 BLAKE2B 31ab114249ef61d7e8fc6d47538483676bb106c9ebebada91236dbb2cfbd9e17aea36d7f480b552ca8a204cae7d6bd10f201ea1ccef7bd23ada5a1758a78b968 SHA512 b97690d43bc89aaafe2df3091602e3509cc1ef4ed2323a58aeb734329f587872325bf73ad69b899d467591bb7be5f685ebeb87376e5fab4b867831b3858c92f0
+EBUILD tophat-2.1.1-r5.ebuild 2222 BLAKE2B 6495a600bb9986ecb5fb2eb09a7c0a5066cc1e28bea0c40df319294dde84a4d08f4eb9e784492f4f416fde4c981d2b6881182439af1a80320eef0ab567a70d7f SHA512 b07baa1225df5a2dbe8d6b031249ab212f815c8710a6d5e74d4a5a9ea8af149e76c045fc1fc943d09b10f7e0e035c899a7a79d7386c73381a0c13f57d6d58e44
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/tophat/tophat-2.1.1-r4.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild
index 590f6eb2d20f..84f3d82b39d0 100644
--- a/sci-biology/tophat/tophat-2.1.1-r4.ebuild
+++ b/sci-biology/tophat/tophat-2.1.1-r5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -19,8 +19,10 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="${PYTHON_DEPS}
 	dev-libs/boost:=[threads]
-	dev-python/intervaltree[${PYTHON_USEDEP}]
-	dev-python/sortedcontainers[${PYTHON_USEDEP}]
+	$(python_gen_cond_dep '
+		dev-python/intervaltree[${PYTHON_MULTI_USEDEP}]
+		dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}]
+	')
 	sci-biology/samtools:0.1-legacy
 	sci-biology/bowtie:2"
 DEPEND="${RDEPEND}