gentoo resync : 25.08.2020

author: V3n3RiX <venerix@redcorelinux.org> 2020-08-25 10:45:55 +0100
committer: V3n3RiX <venerix@redcorelinux.org> 2020-08-25 10:45:55 +0100
commit: 3cf7c3ef441822c889356fd1812ebf2944a59851 (patch)
tree: c513fe68548b40365c1c2ebfe35c58ad431cdd77 /sci-biology
parent: 05b8b0e0af1d72e51a3ee61522941bf7605cd01c (diff)
35 files changed, 361 insertions, 798 deletions
diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild
index 18a07a7b9f9f..1f5693d9a139 100644
--- a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
+++ b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
@@ -12,9 +12,11 @@ HOMEPAGE="https://htseq.readthedocs.io/"
 
 if [[ ${PV} == *9999 ]]; then
 	inherit git-r3
-	EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+	EGIT_REPO_URI="https://github.com/htseq/htseq.git"
 else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+	SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz"
+
+	S="${WORKDIR}"/htseq-release_${PV}
 	KEYWORDS="~amd64"
 fi
 
@@ -25,7 +27,7 @@ RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/matplotlib[${PYTHON_USEDEP}]
 	sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="
-	${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
 	>=dev-lang/swig-3.0.8
 	dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 18a07a7b9f9f..1f5693d9a139 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
@@ -12,9 +12,11 @@ HOMEPAGE="https://htseq.readthedocs.io/"
 
 if [[ ${PV} == *9999 ]]; then
 	inherit git-r3
-	EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+	EGIT_REPO_URI="https://github.com/htseq/htseq.git"
 else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+	SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz"
+
+	S="${WORKDIR}"/htseq-release_${PV}
 	KEYWORDS="~amd64"
 fi
 
@@ -25,7 +27,7 @@ RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/matplotlib[${PYTHON_USEDEP}]
 	sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="
-	${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
 	>=dev-lang/swig-3.0.8
 	dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
index 7112b7eebe07..e8c7f43fc23f 100644
--- a/sci-biology/HTSeq/Manifest
+++ b/sci-biology/HTSeq/Manifest
@@ -1,4 +1,4 @@
-DIST HTSeq-0.9.1.tar.gz 596941 BLAKE2B 6865c36056bff2008ae8bf18d0ac81dbf721fb97cdcc8bbd9150356fc80ae99e0cb872033fac274b40df3d1c95e9bcfd83c4f7d033184725596ffc96081e26d1 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344
-EBUILD HTSeq-0.9.1.ebuild 696 BLAKE2B b24c94dec95e472577986eddaadf778b72e2b4fc1155198bedac99ba4c2bb444220c2f872ea6c48a20afe6b0f5230c63f0265c5b9bff5fd588e6c57ff65a6c07 SHA512 7eca88cfd432bc799ad91fedb0f0b998a948a3e8c3bdfff33c7b3fee3a19276eb5cfe99a09609a179e415833798abb28d27e716f04dd1513b24406b79b9a8be9
-EBUILD HTSeq-9999.ebuild 696 BLAKE2B b24c94dec95e472577986eddaadf778b72e2b4fc1155198bedac99ba4c2bb444220c2f872ea6c48a20afe6b0f5230c63f0265c5b9bff5fd588e6c57ff65a6c07 SHA512 7eca88cfd432bc799ad91fedb0f0b998a948a3e8c3bdfff33c7b3fee3a19276eb5cfe99a09609a179e415833798abb28d27e716f04dd1513b24406b79b9a8be9
+DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64
+EBUILD HTSeq-0.12.4.ebuild 773 BLAKE2B 3e609a2928a83d5ba64900f44de659879950242466bd7df9973e1025b2b313c26c84a7d6457567b3188199c804586349ed61a56fcdd36c1bb99ab0cb459735b4 SHA512 53e6c0d43f1ed04e1b0ecd7a7d0844fdbb9ae8b6ec55c478b5b17ea42dd9067bb7571f36d33d1e4ea1b47560c6c383010679a72ecf8d759351c7651b49b68d04
+EBUILD HTSeq-9999.ebuild 773 BLAKE2B 3e609a2928a83d5ba64900f44de659879950242466bd7df9973e1025b2b313c26c84a7d6457567b3188199c804586349ed61a56fcdd36c1bb99ab0cb459735b4 SHA512 53e6c0d43f1ed04e1b0ecd7a7d0844fdbb9ae8b6ec55c478b5b17ea42dd9067bb7571f36d33d1e4ea1b47560c6c383010679a72ecf8d759351c7651b49b68d04
 MISC metadata.xml 329 BLAKE2B f06dd42c6a1d3bca399cbe48d519346519b9acb0e4176ee79657e058ad1724b542242704e5cc3237873f338b1b23887715f95673957e533c057464ef07e8634f SHA512 04b82836732bf1415d6ce9d3b4c75139aa7d96382da2fd3343a54053172cffcac9ce96dab49b91852dea1a2a38b73cd90279c2c86496577bd6a79040a1fb6026
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index dad4a363d8d0..fb1ebe38a141 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index c247c7af050a..2dc014f78dfe 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,9 +1,3 @@
-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-r2.ebuild 1000 BLAKE2B eb5e7bb5f33f5ef22594eb241f3900ee6a6c125cb83b0e425732fbd6d781dac382b1664281e3256587ea8f344db578c1ec778ac2d5ae4794fa67931468cb580c SHA512 90d56585baae31be060fc8a54de5d86c1bd015da187d86a37ceee1176a685a864214e124770dfb895d568bb57e143f9a35b7f627f36598dbf4cb544119f2185d
+DIST bcftools-1.10.2.tar.bz2 3702679 BLAKE2B 51acce94d463868562199206504dc8afb50c671c11139c5a96f52cedf135bb7a46115c69411b9943b970a2395e3c866275c85e345a4a40a90194d1094698314e SHA512 f07e405efa16b9b1b18521342df3eaf840ed1b3028b736a6b4d139012ea85769ddfb3cd3a2c94958415d984d07805dfcd3d4bbec0db401b3f071b861a56d1300
+EBUILD bcftools-1.10.2.ebuild 870 BLAKE2B 2368cbe0d749a1214a8f1ad659bc3ea9b51b34c7c45b88e13d8c79eb6919ffcdd73a18e0a1119c5e92781cd79aa184360a9b0fd4187beebaed66ac89d934396f SHA512 9888597c6bd9412688c8375962e9f8a1c4722ca905f57b1d7c729e433ee353b3956fddf397fe65f0f8523f8e588062f02267ec9024bf6c8c3858cd9fa183916a
 MISC metadata.xml 343 BLAKE2B e1664c6d67ebde81b9f99b69d442e0b16891ecd392fddd55ed2aaa885dcb2f4ca39cd627cd3f6367f39b13e35eb1141119e53756d6efc4ac62c819ab1d611633 SHA512 cfa167a5733f40d7e36e9e229229acd883ba7bfd812afb9060c742c505354b1c754070e2e897a48d7611a123b9606b6f43a0816c089e71bf64f3d0dbd8b7184d
diff --git a/sci-biology/bcftools/bcftools-1.9-r2.ebuild b/sci-biology/bcftools/bcftools-1.10.2.ebuild
index 0963c692fcd6..179f7dea77e4 100644
--- a/sci-biology/bcftools/bcftools-1.9-r2.ebuild
+++ b/sci-biology/bcftools/bcftools-1.10.2.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit python-single-r1
 
@@ -26,11 +26,6 @@ RDEPEND="
 	${PYTHON_DEPS}"
 DEPEND="${RDEPEND}"
 
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.9-buildsystem.patch
-	"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
-)
-
 src_prepare() {
 	default
 
@@ -44,6 +39,5 @@ src_configure() {
 	econf \
 		--disable-bcftools-plugins \
 		--disable-libgsl \
-		--disable-configure-htslib \
 		--with-htslib=system
 }
diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild
deleted file mode 100644
index 9b5df1130999..000000000000
--- a/sci-biology/bcftools/bcftools-1.5.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-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
-	=sci-libs/htslib-${PV}*:=
-	sys-libs/zlib
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.5-buildsystem.patch
-	"${FILESDIR}"/${PN}-1.5-fix-shebangs.patch
-)
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--disable-configure-htslib \
-		--with-htslib=system
-}
diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch
deleted file mode 100644
index 304fc03e7441..000000000000
--- a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -275,7 +275,6 @@
- 	$(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 *~ $(PROG) version.h plugins/*.so plugins/*.P
diff --git a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch
deleted file mode 100644
index c6cfc8b991d3..000000000000
--- a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/misc/guess-ploidy.py
-+++ b/misc/guess-ploidy.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2.7
- #
- # Plot the output of "bcftools +guess-ploidy -v"
- #
---- a/misc/plot-roh.py
-+++ b/misc/plot-roh.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/env python2.7
- 
- import glob, gzip, csv, sys, os, copy, re
- csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)
---- a/misc/vcfutils.pl
-+++ b/misc/vcfutils.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl -w
-+#!/usr/bin/env perl
- #
- #   Copyright (C) 2010 Broad Institute.
- #   Copyright (C) 2011, 2014 Genome Research Ltd.
diff --git a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
deleted file mode 100644
index a0df4b917bcb..000000000000
--- a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- 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/bcftools/files/bcftools-1.9-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch
deleted file mode 100644
index 76610187c493..000000000000
--- a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch
+++ /dev/null
@@ -1,8 +0,0 @@
---- a/misc/vcfutils.pl
-+++ b/misc/vcfutils.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl -w
-+#!/usr/bin/env perl
- #
- #   Copyright (C) 2010 Broad Institute.
- #   Copyright (C) 2011, 2014 Genome Research Ltd.
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 8d91db427f4f..5258bcd3f805 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,4 +1,6 @@
-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 959 BLAKE2B c3d42f033913e18a9bd1f0b6f669a4000bc6b6892bbd5986a33a99ed496ae4af11b690f1c7c350644b62e77baef80a9eb52f15e87818a74b684d4fac816a2512 SHA512 a3914d04806fa4b3f14f83d91717d00fd183e1f6d4a39690ae04e7767791605a8e90d86cefc4deaa50327651c64125808658de4471f05df936c19e46768bf988
+AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece3823680e99053790aeb30b2dcab06a52f6827c3cca85543c899fbabcc75ac5872cdfe632c9c5bf8b5dc24146c50a00dbd4ea56a1d SHA512 a76ec350aedfce4926f8fbaed742a992f81b2280727383f7aefd7f3629f7e04f300f9d3d9cce2a98c6fe2767cb6d2261074bd6242d6d5ae26a5095730c054a85
+AUX bedtools-2.29.2-python.patch 1235 BLAKE2B 34381a33be915f983b2c93f04954486e7611f56b1bc3259887e5ac3aa54107e3392a784980779948136f97424485a31a53959f2f76b573cb44b7d83023c69005 SHA512 8c22230e3bc1eaeb7d85379eab402eb1e95443f88f60a9c04f628cd38a96b91d138149a1a46d941189a8cd6097e075a8bde8d4ad883757ec7b2c129268cdb37f
+AUX bedtools-2.29.2-samtools-1.10.patch 659 BLAKE2B 5ec159e0a9bc9f4b5d661bcf93ba8a0cd08f62e8e6d3f92229b71d5dfb122d89eb6a68637e12394e6082cf9be99014787f9a780f7fb547ec61f5f8b8d405713d SHA512 0160c54ad3781e17df53b2525cbf0e6b5d1ebf5ce07257b16c35eed525623aa46b5ee32f158ab64b2e18a283eba0f8331a521ac8382cc31ca03cd88d1376c057
+DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5
+EBUILD bedtools-2.29.2.ebuild 1232 BLAKE2B 6e5204cbdae38787b2667fd383ee2c5f8dcd2f08569b2454280bfc1e8821dafe46dce4eb4ed4b3f55b22c19dea5705fea25816f93b449feea3163dac6667dbc5 SHA512 ba09db688e841fa10d65e19534b6c0d903352f5a04996bd451df5ada09f8379b6a0b8bdbbdedd7b5ecda51036bc6c37bc512dd9a4c321ade4fdca10f30407474
 MISC metadata.xml 406 BLAKE2B 5a16830031644c5087241b9e20afcb6315095c877e2b019eace76ee0602929c168c2273e27e99f03ca3c1a57db0bf728c2d8ccc39b7f80588bb215d1fd6a3ea6 SHA512 35a9b50a772503e6691faf1e2f1093bd6ffd5f6f5be08b1ad8581948f4f3e8fb7e54faa101cff757fc561ed71696253114c32fb6293df59cda3e8fd7c24d2bb0
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
deleted file mode 100644
index b062a6fef84d..000000000000
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_6 )
-
-inherit flag-o-matic python-any-r1 toolchain-funcs
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz
-	https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${PYTHON_DEPS}
-	test? (
-		sci-libs/htslib
-		sci-biology/samtools:0
-	)"
-RDEPEND="sys-libs/zlib"
-
-S="${WORKDIR}/${PN}2"
-
-DOCS=( README.md RELEASE_HISTORY )
-PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
-
-src_configure() {
-	append-lfs-flags
-	export prefix="${EPREFIX}/usr"
-	tc-export AR CXX
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/${PN}
-	doins -r genomes
-}
diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild
new file mode 100644
index 000000000000..fbc1f3a9b4f9
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.29.2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit python-any-r1 toolchain-funcs
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
+HOMEPAGE="https://bedtools.readthedocs.io/"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	app-arch/bzip2
+	app-arch/xz-utils
+	sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	${PYTHON_DEPS}
+	test? ( >=sci-biology/samtools-1.10:0 )"
+
+S="${WORKDIR}"/${PN}2
+
+# bedtools2 has a *terrible* build system and development practices.
+# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
+# that make unbundling it nigh impossible. There are no signs of upstream porting
+# their fork to 1.10, which means we're stuck with the bundled version.
+PATCHES=(
+	"${FILESDIR}"/${PN}-2.29.2-buildsystem.patch
+	"${FILESDIR}"/${PN}-2.29.2-python.patch
+	"${FILESDIR}"/${PN}-2.29.2-samtools-1.10.patch
+)
+
+src_configure() {
+	tc-export AR CC CXX RANLIB
+}
+
+src_install() {
+	default
+
+	insinto /usr/share/${PN}
+	doins -r genomes
+}
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
new file mode 100644
index 000000000000..573e88993bc9
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
@@ -0,0 +1,82 @@
+--- a/Makefile
++++ b/Makefile
+@@ -4,44 +4,29 @@
+ # (c) 2009 Aaron Quinlan
+ # ==========================
+ 
+-SHELL := /bin/bash -e
++SHELL := bash -e
+ 
+ VERSION_FILE=./src/utils/version/version_git.h
+ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
+ 
+ 
+ # define our object and binary directories
+-ifeq ($(VERBOSE),1)
+ CCPREFIX =
+-else
+-CCPREFIX = @
+-endif
+ 
+ OBJ_DIR	= obj
+ BIN_DIR	= bin
+ SRC_DIR	= src
+ 
+-CXX     = g++
+-
+-ifeq ($(DEBUG),1)
+-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
+-else
+ BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -g -Wall -O2
+-endif
++BT_CXXFLAGS = -Wall
+ 
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+-ifeq ($(USE_RAND),1)
+-BT_CXXFLAGS += -DUSE_RAND
+-else
+ BT_CXXFLAGS += -std=c++11
+-endif
+ 
+ BT_LDFLAGS =
+ BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
+ 
+-prefix ?= /usr/local
++prefix = $(EPREFIX)/usr
+ 
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ 		  $(SRC_DIR)/bamToBed \
+@@ -204,7 +189,7 @@
+ 
+ # make the "obj/" and "bin/" directories, if they don't exist
+ $(OBJ_DIR) $(BIN_DIR):
+-	@mkdir -p $@
++	mkdir -p $@
+ 
+ 
+ # Usually HTSlib's configure script has not been used (detected via config.mk
+--- a/src/utils/htslib/Makefile
++++ b/src/utils/htslib/Makefile
+@@ -22,20 +22,13 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
+-AR     = ar
+-RANLIB = ranlib
+-
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+ 
+-CPPFLAGS =
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+ # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+ #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
+-CFLAGS   = -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS  =
+ LIBS     = $(htslib_default_libs)
+ 
+ prefix      = /usr/local
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-python.patch b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
new file mode 100644
index 000000000000..9576a78bd1dd
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
@@ -0,0 +1,41 @@
+--- a/Makefile
++++ b/Makefile
+@@ -183,7 +168,7 @@
+ 
+ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+ 	@echo "- Creating executables for old CLI."
+-	@python scripts/makeBashScripts.py
++	$(EPYTHON) scripts/makeBashScripts.py
+ 	@chmod +x bin/*
+ 	@echo "done."
+ 
+--- a/src/utils/BamTools/Makefile.frag
++++ b/src/utils/BamTools/Makefile.frag
+@@ -1,4 +1,4 @@
+ src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map
+ 
+ src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map
+-	python $^ > $@
++	$(EPYTHON) $^ > $@
+--- a/test/bigchroms/test-bigchroms.sh
++++ b/test/bigchroms/test-bigchroms.sh
+@@ -28,7 +28,7 @@
+ rm obs
+ 
+ if [[ "$BT_NO_BIG_FILES" != "" ]]; then
+-python make-big-chrom.py
++${EPYTHON} make-big-chrom.py
+ 
+ echo -e "    bigchroms.t03...big get fasta \c"
+ $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
+--- a/test/fisher/cmp.sh
++++ b/test/fisher/cmp.sh
+@@ -3,7 +3,7 @@
+ echo "fisher,shuffled"
+ 
+ for i in $(seq 1000); do
+-    fisher=$(python ./sim.py | tail -1 | cut -f 2)
++    fisher=$(${EPYTHON} ./sim.py | tail -1 | cut -f 2)
+     shuffle=$(bash shuf.sh)
+     echo "$fisher,$shuffle"
+ done
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
new file mode 100644
index 000000000000..7cc0e23de2d4
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
@@ -0,0 +1,13 @@
+--- a/test/intersect/new_test-intersect.sh
++++ b/test/intersect/new_test-intersect.sh
+@@ -975,8 +975,8 @@
+ #  Test intersect preserve the text header in bam
+ ############################################################
+ echo -e "    intersect.new.t78...\c"
+-echo -e "@HD     VN:1.5  SO:coordinate" > exp
+-echo "@HD     VN:1.5  SO:coordinate" | samtools view -b  | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
++echo -e "@HD	VN:1.5	SO:coordinate" > exp
++echo "@HD	VN:1.5	SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;
diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest
index bc34d9deef95..9504afbb1e06 100644
--- a/sci-biology/biopandas/Manifest
+++ b/sci-biology/biopandas/Manifest
@@ -1,3 +1,3 @@
-DIST biopandas-0.2.1.tar.gz 209379 BLAKE2B 839a6f569f12b95c9b1c75dc755d009c77d7ef8224e517aed5026ffa6c33bd3826fe3862fec03469e967005a500600782fc372951d61358e2fe3bb56af734228 SHA512 0ea7aec84251d8d6ec4736c4968228133bd8622afb17d6916287168cb9f9757c5a97a4d5a52ac0e2f30027bf0edf9d76413db142f70d606f1359b8a4e06de7c8
-EBUILD biopandas-0.2.1.ebuild 1074 BLAKE2B df4d27cdd692e603cb70889c9ce17768a76de67b1c92d5fa9b9c6df4e2ac1973f5e35f8bdee85b4eeac9b706fe0729cba28e868c460cf3f6ca43363c51131aee SHA512 af744459bcf4460c2303b78064f3855041efd3a03b26f8a60cca844e6fdc7eb2bb39c22d981e464a4357c15787aed2f0cda58afe3604bcc96e0d11303e0e4306
+DIST biopandas-0.2.7.tar.gz 255846 BLAKE2B b8c6a66f51a00266bc1a271ecfe00b4cfddd24b9766e63e2ad4187048ddd8f985d70eb8083b1be3887a0fd9b666c97553029ecd90c7b73ae882e5347bbc54d2e SHA512 cf4f12601b7f63ca3d5e9a17c6628e4975968f722c9db72e32c00e80ec335c5bf6a928a5f887b16ecd316c49b298d77634cbe1c4ef1ca505379b1de5335e2569
+EBUILD biopandas-0.2.7.ebuild 1027 BLAKE2B ffea926f1e452998df12ecef094f69e7100bb4c1a8e32dd444e9ae605023d651dba05f148e004d7ffa367e7434c5dec5fb35dec5c379ead9cb9cac6d10948f1c SHA512 d77e77c37353e71fbd8094984ac75d5c21b6bd6ca09fa8146648f388eb352240f78f80b7f23c82b9ff4295c2a84452f902dc5cfc1ddcaaba8a1d3ad6a4fd8de8
 MISC metadata.xml 536 BLAKE2B e3cb776d0332fff486a7e1ea1353c54694ff687d4685bbb51728db0ed2025bb3d09d39cf7c9ea9f11546cbf9c4727661348e2f5fdfc13ffac2329ef6dfbe7450 SHA512 502803e30ecfac53516b56501a7bffeb49c3c0bc44ce5b3dd87aac5c745de614c235523ba3be374fcbede1a9a7bcf11c328abb27d82e087b275303f38b80b166
diff --git a/sci-biology/biopandas/biopandas-0.2.1.ebuild b/sci-biology/biopandas/biopandas-0.2.7.ebuild
index 8c892419b29c..9be9a8ac4a3c 100644
--- a/sci-biology/biopandas/biopandas-0.2.1.ebuild
+++ b/sci-biology/biopandas/biopandas-0.2.7.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
@@ -26,18 +26,15 @@ RESTRICT="!test? ( test )"
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/pandas[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-	)"
+	sci-libs/scipy[${PYTHON_USEDEP}]"
+
+distutils_enable_tests nose
 
 python_test() {
-	"${EPYTHON}" --version
-	"${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)"
-	"${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)"
-	"${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)"
+	"${EPYTHON}" --version || die
+	"${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)" || die
+	"${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)" || die
+	"${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)" || die
+
 	nosetests -s --verbose ${PN} || die
 }
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index f252db4b4e14..0141c7450dbb 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,3 +1,3 @@
-DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f
-EBUILD biopython-1.73.ebuild 1671 BLAKE2B d899d54d6983bbbcc43e34a051cd5cfdbed4ff92d50dcc95fd38df84f60882bfdda7d95cf4a5fa84ece32e36e10e53010340cdceb2f50b37351b917afd0dc062 SHA512 3d648fe4b0a62f984fe4541c8b4298759dcf772ef0119ca7de42b207fc09994ed2c5d0b3a561fc647382c2e41f2ec1832fe388c7fdf1f8b8d83ee4565d0e20b1
+DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5
+EBUILD biopython-1.77.ebuild 1855 BLAKE2B 739e5cc4a954ac9cc5fe0640ac5f418ad1ee1aadb66570a41996e8e260dc75c8c4373c94b53b0d147d1b661169c1aa3352b9367ab0e37cfd8bd05c220186ac92 SHA512 e2dd1ef79804c779645162410e6890d0618d080ac20195cae0097fe3a42c204d270321949e8d5056b85f9e9a5ed598e05c20f2869178dd16ea86ea105167271a
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/biopython/biopython-1.73.ebuild b/sci-biology/biopython/biopython-1.77.ebuild
index 94acdfc2a2cb..486e9fe694d1 100644
--- a/sci-biology/biopython/biopython-1.73.ebuild
+++ b/sci-biology/biopython/biopython-1.77.ebuild
@@ -3,7 +3,8 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6..9} )
+
 inherit distutils-r1 eutils
 
 DESCRIPTION="Python modules for computational molecular biology"
@@ -13,7 +14,6 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 LICENSE="HPND"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 RDEPEND="
 	dev-python/matplotlib[${PYTHON_USEDEP}]
@@ -23,15 +23,20 @@ RDEPEND="
 	dev-python/pygraphviz[${PYTHON_USEDEP}]
 	>=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}]
 	dev-python/pydot[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	sys-devel/flex"
+DEPEND="${RDEPEND}"
+BDEPEND="sys-devel/flex"
 
 DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
 
 python_test() {
 	distutils_install_for_testing
-	cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die
+	cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die
+
+	# need to create symlinks for doctests
+	mkdir -p "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
+	ln -r -s "${S}"/Bio/Align/substitution_matrices/data \
+		"${TEST_DIR}"/lib/Bio/Align/substitution_matrices/data || die
+
 	cd "${TEST_DIR}"/lib/Tests || die
 	rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die
 	"${EPYTHON}" run_tests.py --offline --verbose || die
diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
index 7a4e2f33be3e..b4ae775226b6 100644
--- a/sci-biology/blat/Manifest
+++ b/sci-biology/blat/Manifest
@@ -1,4 +1,5 @@
 AUX blat-34-fix-build-system.patch 5249 BLAKE2B d32fcb326cd204c847a678cabd3fc666ed9285876ec4a3f3dc1873b9b8c83042eb705cf62e63d00b6f388540571d4ebadc497eef51827a30443d3a2aebed9420 SHA512 1c4b592ef1b45ea19d84a798f4d526c43851bf8545d4a9aaaa8842c76eff1e0e31a179d1cd914e44f67c1d5ac709b97a73a5b7e66fa680f6531efe50b6dc6246
+AUX blat-34-fno-common.patch 466 BLAKE2B 51dd1778f09e51ce1e345ae9474d3aaeb8535b739bc6d46e5d9271204b7043e1c5da0865ed3392b62d85b75c4d6c6611015042d359a113a9b0540c9ae1f6e448 SHA512 fa0b327f212137afa41d8d21717b02c77cf7e8228fe6b104af4a9a430fb0ed11a49be1ae38e8b51016ed5b6c43073c6cbbf27cd8b6f8396d39e623039d700abf
 DIST blatSrc34.zip 2142975 BLAKE2B 88a2da3b1551d5d50aaa507978c17cbe34de5a27efee9405829aea51b0950b748775f21e8d806470ba5ee7831fe71d6d87cd126c38727f25306a0f793543912e SHA512 67a1dc9a93d8ddee0fca7ce94096ecfffc71d4e0697afb285f4b64205e9eb62150a145375c29dd1ccb3cea8e8a7a71a817c8e73d7aba3e97616f1606b751afe8
-EBUILD blat-34-r2.ebuild 807 BLAKE2B 03979dd5b1b320c8560a8d9a50c6484fc052fadfd5e7d4cb80f3ac7a769f99b3da20fb42192087cd5652d947385de32ec9649c4d33b6f2c0430bfb5b14e9ce63 SHA512 451b189b505331cd7c045fc19982d55d11673afdfa8f0f9bd2b57cd23097c5a066afe477d973a0f30e1a47a8d1893abc552ef8ccc5f59ce9f3a66e0ceedc94b2
+EBUILD blat-34-r2.ebuild 841 BLAKE2B b85ced6d272519445d60bb5846a6fa135a214aaa4b5ffed12f77b5beef8be5f3f48ffe0e4835ecc8cbf937f233c0d18a15a7168149d31fb5d2eea508ac915431 SHA512 3b34227db3d38640ba5affe00c43c0512091e007dc21625310c169e9f44a412d47039160d952c873c0afb6f5b062e1186ea5eaacf71086093807b3169ba7b956
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r2.ebuild
index e10bc367a311..b07246356381 100644
--- a/sci-biology/blat/blat-34-r2.ebuild
+++ b/sci-biology/blat/blat-34-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -21,7 +21,10 @@ DEPEND="app-arch/unzip"
 
 S=${WORKDIR}/${MY_PN}
 
-PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch )
+PATCHES=(
+	"${FILESDIR}"/${PN}-34-fix-build-system.patch
+	"${FILESDIR}"/${PN}-34-fno-common.patch
+)
 
 src_compile() {
 	tc-export AR CC
diff --git a/sci-biology/blat/files/blat-34-fno-common.patch b/sci-biology/blat/files/blat-34-fno-common.patch
new file mode 100644
index 000000000000..63a49cf81299
--- /dev/null
+++ b/sci-biology/blat/files/blat-34-fno-common.patch
@@ -0,0 +1,11 @@
+--- a/inc/htmshell.h
++++ b/inc/htmshell.h
+@@ -85,7 +85,7 @@ void htmlBadVar(char *varName);
+ void htmlImage(char *fileName, int width, int height); 
+ /* Display centered image file. */
+ 
+-jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */
++extern jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */
+ 
+ void htmlVaWarn(char *format, va_list args);
+ /* Write an error message.  (Generally you just call warn() or errAbort().
diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
index 30219f3ec6ee..70b96c98971e 100644
--- a/sci-biology/clustalw/Manifest
+++ b/sci-biology/clustalw/Manifest
@@ -2,5 +2,5 @@ AUX 1.83-as-needed.patch 388 BLAKE2B 8da98e05dcdc74ee41ff7a3d75b11590507bc769df0
 DIST clustalw-2.1.tar.gz 350761 BLAKE2B 479acb42ec0b0adee8e04e99132a782c947a1261f48e674c6a11e4f38e44e5709d03f0c864f0cd3cf7eb4faf76a36b6121c3e3d3573c86ee3895971df07f1a58 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921
 DIST clustalw1.83.UNIX.tar.gz 166863 BLAKE2B a3b1eabad8bc736cde4655f13fa8544759b7b5c50ea97fd45ee0be45ac6c361db5ced8ad21622ac2530b57c37c77dfd67657afd2c411acbfb7ff2a3ba014637e SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a
 EBUILD clustalw-1.83-r4.ebuild 815 BLAKE2B 9a887de5a2a1e96652d260963e13c9aca786b684ee2a9b0c02adba0b2fbfcf0f500f5edabaf4469b2e5ff13b3cf445245d59010b5f8a50e9d830d636f0f76699 SHA512 c884a8fb3029e7834299217c6db91da4f3430c738ba346dc7c3431695c235852c830151452ec534f1c1e59aaff5fbd4bb2d1030ed7779f30a675cbb30d76c218
-EBUILD clustalw-2.1-r1.ebuild 473 BLAKE2B 76c7432b4cd6d68b5dd51bdc9b4e1629d8e958f432bb9c35738373bc7ea34180e74c9d0ba498d02e5d4db3243ccd711255157490d4b42d84bc7b0b493f526234 SHA512 6cd64a7ffa784daeef1146a695e588a78e74b5b453e3cc1751907fbe09aa394eb9c962e681ecdef9eb2627d5c490a49ff58484c2c77599f169d48482521749e0
+EBUILD clustalw-2.1-r1.ebuild 489 BLAKE2B af8ab15dcb6e2fb20199c7054940eaf53bbbcc72ec1fd7c37fc0aa3f3c28e7a23c640e70eb33956367a12ecc04990a3d6b63ad2b3d8bdf35396debff35dc6da6 SHA512 ad9b200b16d55df114440a44f8d771a406e518a49ca140de106ee38b4e8afc7f0acc7ccb18d81ea90f541637013915c6e793832d26a8b4465925fa101747498c
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r1.ebuild
index 0b46aeb5bfd4..f42f1ed031b0 100644
--- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild
+++ b/sci-biology/clustalw/clustalw-2.1-r1.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
@@ -9,7 +9,7 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"
 
 LICENSE="GPL-3 LGPL-3"
 SLOT="2"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 IUSE=""
 
 src_install() {
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 7f96ff719811..b61c521c5275 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,4 +1,4 @@
-AUX pysam-0.12-fix-buildsystem.patch 2356 BLAKE2B 95542f99b411a00eeaa24836cb7489bf2bbf690d804669f69f6f1a8c07f66d9c6ef34624eb511036cd36b1268b49959d38db497cb557e9cc40f3a35b2d349f4d SHA512 24c5c521ddd2e8a88a713c2cab2aedb0cd9a589e2ae87696a60815f9714e2b222a5e0824c5ac293f9023f6f772a599256a5c07228b5a2df40b62a1bf7616c84a
-DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d
-EBUILD pysam-0.12.0.1.ebuild 1182 BLAKE2B 11c3a036ca7c6560a6316963ea6133708d36cce2d0f21a1e327180d303406ae23ad021ba04024191eda1687ef538f41c0bfe34bbed742bc85f9aeb12b38dc6da SHA512 fd71cf196e68f640343e2b43e3bb8b5355462f6816a1eb0e7755d188435c567ce53209f6f2599a84e5052d26b4747038c7a4b5a2e9b916c117f388ca369a3919
+AUX pysam-0.16.0.1-fix-tests.patch 1128 BLAKE2B 8e395496c23186b29622b8e87369f910326724b70b63f3eccfd6d4b6cea86abf8b34a712a931f205711e2c5a6e76c9572a93aa9bd994f915312c55dcc888da52 SHA512 e725143c72d04fc0e2e37e607e6d9b85b4c883bcc5a530ff3c92e3bbd45d7d7fb09c315766a19254bea2a19a2d00a5f64220094a4e9b1090e412b26ea489b530
+DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28
+EBUILD pysam-0.16.0.1.ebuild 1393 BLAKE2B a124ddf7b18e31a89d3fe0d47c7f938d5edfe65938bf0360de209cfa7545474f4be780b7a9e8b4c73fa4cd9282ac9176d8289a34805e062176dbacf3405f33d7 SHA512 b24b2c7d9d764a2e451f4f1c00a20ccc203079e17c238f909b5afb5c6d0a26303822ef54920209f22bf9ba08b3a8a27ff7c052d8bf571a14baca511524a28cdc
 MISC metadata.xml 410 BLAKE2B ed86e3ffe38a306e581762625b37cf6596dc2a2ba404406ab12f681d5b48529764e281d40411bedbdf6016bc57d02adb705e8c8703b8120cf89b4961f75bed67 SHA512 38bcd511561b2466ef5d39473a6d1a838af0aff6eeb520307331fe0fc3177be3062fa0be39f48a333bb8e31841115cafd9dfb80a5985c316c9b8df1609f00810
diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
deleted file mode 100644
index 8b323a63fba5..000000000000
--- a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-The build system is not designed with partial out-of-source
-builds in mind. This is evident by using relative includes
-such as '-Isamtools' instead of proper relative or absolute
-paths.
-
-Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
-
---- a/setup.py
-+++ b/setup.py
-@@ -359,6 +359,8 @@
- 
- define_macros = []
- 
-+samtools_include_dirs = [os.path.abspath("samtools")]
-+
- chtslib = Extension(
-     "pysam.libchtslib",
-     [source_pattern % "htslib",
-@@ -385,7 +387,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=htslib_library_dirs,
--    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
-+    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-     extra_compile_args=extra_compile_args,
-@@ -404,7 +406,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=htslib_library_dirs,
--    include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs,
-+    include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-     extra_compile_args=extra_compile_args,
-@@ -423,7 +425,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=htslib_library_dirs,
--    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
-+    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-     extra_compile_args=extra_compile_args,
-@@ -467,7 +469,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=["pysam"] + htslib_library_dirs,
--    include_dirs=["samtools", "pysam", "."] +
-+    include_dirs=["pysam", "."] + samtools_include_dirs +
-     include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
-@@ -482,7 +484,7 @@
-     htslib_sources +
-     os_c_files,
-     library_dirs=["pysam"] + htslib_library_dirs,
--    include_dirs=["bcftools", "pysam", "."] +
-+    include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs +
-     include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries + internal_htslib_libraries,
-     language="c",
diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
new file mode 100644
index 000000000000..9d269878e651
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
@@ -0,0 +1,37 @@
+--- a/tests/pysam_data/Makefile
++++ b/tests/pysam_data/Makefile
+@@ -3,7 +3,7 @@
+ BAI=$(BAM:%.bam=%.bam.bai)
+ CRAM=ex1.cram ex2.cram ex3.cram
+ CRAI=$(CRAM:%.cram=%.cram.crai)
+-NO_PG:=$(findstring --no-PG,$(shell samtools view))
++NO_PG:=--no-PG
+ 
+ # ex2.bam - bam file without index
+ 
+--- a/tests/tabix_test.py
++++ b/tests/tabix_test.py
+@@ -14,6 +14,7 @@
+ import subprocess
+ import glob
+ import re
++import pytest
+ from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
+     load_and_convert, TABIX_DATADIR, get_temp_filename
+ 
+@@ -1014,6 +1015,7 @@
+     globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
+ 
+ 
++@pytest.mark.skip(reason="requires internet connectivity")
+ class TestRemoteFileHTTP(unittest.TestCase):
+ 
+     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
+@@ -1053,6 +1055,7 @@
+         self.assertEqual(list(self.local_file.header), [])
+ 
+ 
++@pytest.mark.skip(reason="requires internet connectivity")
+ class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
+ 
+     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.16.0.1.ebuild
index e7567f3501bf..acc0cb99892f 100644
--- a/sci-biology/pysam/pysam-0.12.0.1.ebuild
+++ b/sci-biology/pysam/pysam-0.16.0.1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
@@ -11,18 +11,25 @@ DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping for
 HOMEPAGE="
 	https://github.com/pysam-developers/pysam
 	https://pypi.org/project/pysam/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-RDEPEND="=sci-libs/htslib-1.5*:="
+RDEPEND="=sci-libs/htslib-1.10*:="
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		=sci-biology/bcftools-1.10*
+		=sci-biology/samtools-1.10*
+	)"
 
-PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
 
 python_prepare_all() {
 	# unbundle htslib
@@ -31,17 +38,23 @@ python_prepare_all() {
 	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
 	rm -r htslib || die
 
-	# prevent setup.py from adding RPATHs
-	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
-		-i cy_build.py || die
+	# prevent setup.py from adding RPATHs (except $ORIGIN)
 	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
 		-i setup.py || die
 
+	eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
 	distutils-r1_python_prepare_all
 }
 
-src_compile() {
-	# TODO
-	# empty compile, as the build system runs the whole build again in install
-	:
+python_compile() {
+	# breaks with parallel build
+	local MAKEOPTS=-j1
+	distutils-r1_python_compile
 }
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 45ef440561f3..0c9eb58c3dc7 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,9 +1,6 @@
 AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b27093f670e383d2d194b5692b1ba536e3df44204711cf4574b3933e5ce00605b661b1a36d79ca7f193ce36816271a3f8214 SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d
-AUX samtools-1.5-buildsystem.patch 18442 BLAKE2B df389fd2eb6cfa4fafc987eb8e2e1e5d050a9373305f752516c77f415619f5c5b7ff8e2f8c8fd04769c269f9d385f0130443311d9468a591a4531a9e3127725f SHA512 2405c9c5bd2892756dd70147d0bc57f11f869ac2b6bb12d4350e3f7145727a4c8a602489bca5dbcbe8131d52572d4573e8507a2b989ac0ac86aa8dfef92e58d4
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
-DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf580244f5ba5bc1ddd14d1b13c723c6fddc24cdadf0a23ca5dcd7007a9985f54e7532cb15d5d9433b1164f5a22023 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059
-DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
-EBUILD samtools-0.1.20-r3.ebuild 2363 BLAKE2B 6050d698f26b9962192cdbc6c3729bb812041fc92f4ba4490dc6f50e71c08853d6e2e4c6592c324c3efc3ac0da058e8b254475d6fc788f314798cdcaf85a4fc0 SHA512 f79e0f723d86e7c2060163a3b79e6624ea58d21e7c8ddeb87be40a7972cd97e60df82dacaae23b8a89cec2a0517ffdae8804ac71044685b40d5c5769f8964557
-EBUILD samtools-1.5.ebuild 1107 BLAKE2B 2088a3fcc483de227bd92c80cd9ae2bf0257af773298bebcd077d7b2385eb43a6bfde82c7fadb0e2af3400b825e5b1b3c3c4f633cc7631beb4d0dcbb39cdd2cf SHA512 2f1701695fe3aa270bd75bedc3f847b3057ea1a6d9dca386a8f420df22ab78f51b12c8e1ca80d7d2fb1221d246047a78e914022c8e4c8bae5b0b053f3b130cfd
-EBUILD samtools-1.9-r1.ebuild 926 BLAKE2B a71ab1165f9fad65f0ff932880a661fb43435ebc1c72839ed8f57d3a1ee8b11d5441d53404ed650d634334a8f197d4275f82831d7332bdbbe6f110506f0d0230 SHA512 f75851ece84f8863c7352fad6133fe66299cfe94561a62f7dd4a2bf9a82d2a2400be483874d109b67b643807a25d6907d47c8310732d4b13577e27af685857bd
+DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a
+EBUILD samtools-0.1.20-r4.ebuild 2040 BLAKE2B d90fc78a99b4134ba1a277ceb904c65592f1d29222822f5c97e31a46cbc4138af6adc763c7b05cf26bc0de06ac23ca0b8d8891841ecfd6c1b3fafd270e24216d SHA512 855e19ca8d0dcb9d472398895c666324d00355a7b04c075744e7ac58be1d183f7739f9a254c5bbdaf4171ab6324159860be40171693d0f2f5074884b9eba5e87
+EBUILD samtools-1.10.ebuild 991 BLAKE2B 206a77657bc9a82d6a7536d030b726a0450bbba406e4e7ec9cc670ee530b87d871111952c850d4008c436f81d3daeba802eb4a3442b59ff9ab0f5864bc4fcf21 SHA512 efb1f235e3e3996599df79317e9c7c2ca5434b666a93f91c495550ac4846905e99d96dd1a6876d22a489b684bf24a90c6f6afb4cec5677c5c45f28f0c4f35b35
 MISC metadata.xml 408 BLAKE2B 28b519bf32b116c92c1a695553637a44815ff1aaf18468a5d2d5ef448d8dd53728aadf7606c6ab53ae6bb21e88fa4a48c7b443e3d0a13a5658592dc0e768ed3c SHA512 8c8d240fd37400e43637e12f008f8f2b03fcca062883dd63ccc6956bbfc46d05709f032d146a95452db35b546ff828239b108b3a331f5295ec97872d6c9478fb
diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
deleted file mode 100644
index c466e66a9d17..000000000000
--- a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch
+++ /dev/null
@@ -1,413 +0,0 @@
---- a/config.mk.in
-+++ b/config.mk.in
-@@ -28,27 +28,26 @@
- # in the Makefile to reflect your configuration choices.  If you don't run
- # configure, the main Makefile contains suitable conservative defaults.
- 
--prefix       = @prefix@
--exec_prefix  = @exec_prefix@
--bindir       = @bindir@
--datarootdir  = @datarootdir@
--mandir       = @mandir@
-+prefix      = @prefix@
-+exec_prefix = @exec_prefix@
-+bindir      = @bindir@
-+libdir      = @libdir@
-+datarootdir = @datarootdir@
-+mandir      = @mandir@
-+man1dir     = $(mandir)/man1
- 
- CC       = @CC@
-+AR       = @AR@
- CPPFLAGS = @CPPFLAGS@
- CFLAGS   = @CFLAGS@
- LDFLAGS  = @LDFLAGS@
- LIBS     = @LIBS@
- 
--@Hsource@HTSDIR = @HTSDIR@
--@Hsource@include $(HTSDIR)/htslib.mk
--@Hsource@include $(HTSDIR)/htslib_static.mk
--@Hsource@HTSLIB = $(HTSDIR)/libhts.a
--@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
--@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
--@Hsource@BGZIP = $(HTSDIR)/bgzip
--HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
--@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
--@Hinstall@HTSLIB_LIB = -lhts
-+HTSLIB_CFLAGS = @HTSLIB_CFLAGS@
-+HTSLIB_LIBS = @HTSLIB_LIBS@
- 
--CURSES_LIB = @CURSES_LIB@
-+NCURSES_CFLAGS = @NCURSES_CFLAGS@
-+NCURSES_LIBS = @NCURSES_LIBS@
-+
-+ZLIB_CFLAGS = @ZLIB_CFLAGS@
-+ZLIB_LIBS = @ZLIB_LIBS@
---- a/configure.ac
-+++ b/configure.ac
-@@ -29,9 +29,6 @@
- AC_CONFIG_SRCDIR([bamtk.c])
- AC_CONFIG_HEADERS([config.h])
- 
--m4_include([m4/ax_with_curses.m4])
--m4_include([m4/ax_with_htslib.m4])
--
- dnl Copyright notice to be copied into the generated configure script
- AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
- 
-@@ -39,73 +36,27 @@
- redistribute it.  There is NO WARRANTY, to the extent permitted by law.])
- 
- AC_PROG_CC
-+AM_PROG_AR
- 
- AC_SYS_LARGEFILE
- 
--AX_WITH_HTSLIB
--if test "$ax_cv_htslib" != yes; then
--  AC_MSG_ERROR([HTSlib development files not found
--
--Samtools uses HTSlib to parse bioinformatics file formats etc.  Building it
--requires an unpacked HTSlib source tree (which will be built in conjunction
--with samtools) or a previously-installed HTSlib.  In either case you may
--need to configure --with-htslib=DIR to locate the appropriate HTSlib.
--
--FAILED.  You must supply an HTSlib in order to build samtools successfully.])
--fi
--
--if test "$ax_cv_htslib_which" = source; then
--  Hsource=
--  Hinstall='#'
--else
--  Hsource='#'
--  Hinstall=
--fi
--AC_SUBST([Hsource])
--AC_SUBST([Hinstall])
-+dnl htslib
-+PKG_CHECK_MODULES([HTSLIB], [htslib])
- 
-+dnl ncurses
- AC_ARG_WITH([curses],
-   [AS_HELP_STRING([--without-curses],
-                   [omit curses support, so no curses library needed])])
- 
--if test "$with_curses" != no; then
--  AX_WITH_CURSES
--  if test "$ax_cv_curses" != yes; then
--    AC_MSG_ERROR([curses development files not found
--
--The 'samtools tview' command uses the curses text user interface library.
--Building samtools with tview requires curses/ncurses/etc development files
--to be installed on the build machine; you may need to ensure a package such
--as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based
--Linux distributions) is installed.
--
--FAILED.  Either configure --without-curses or resolve this error to build
--samtools successfully.])
--  fi
--else
--  CURSES_LIB=
--  CURSES_CPPFLAGS=
--  AC_SUBST([CURSES_LIB])
--  AC_SUBST([CURSES_CPPFLAGS])
--fi
--
--save_LIBS=$LIBS
--zlib_devel=ok
--dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests
--AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;])
--AC_CHECK_LIB(z, inflate,  [], [zlib_devel=missing])
--LIBS=$save_LIBS
--
--if test $zlib_devel != ok; then
--  AC_MSG_ERROR([zlib development files not found
--
--Samtools uses compression routines from the zlib library <http://zlib.net>.
--Building samtools requires zlib development files to be installed on the build
--machine; you may need to ensure a package such as zlib1g-dev (on Debian or
--Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.
-+AS_IF([test "x$with_curses" != "xno"], [
-+  PKG_CHECK_MODULES([NCURSES], [ncurses])
-+
-+  AC_DEFINE([HAVE_CURSES], [1])
-+  AC_DEFINE([HAVE_NCURSES_H], [1])
-+])
- 
--FAILED.  This error must be resolved in order to build samtools successfully.])
--fi
-+dnl zlib
-+PKG_CHECK_MODULES([ZLIB], [zlib])
- 
- AC_CONFIG_FILES([config.mk])
- AC_OUTPUT
---- a/Makefile
-+++ b/Makefile
-@@ -21,14 +21,6 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC       = gcc
--AR       = ar
--CPPFLAGS =
--#CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
--CFLAGS   = -g -Wall -O2
--LDFLAGS  =
--LIBS     =
--
- LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
-             sam_header.o bam_plbuf.o
- AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
-@@ -40,13 +32,6 @@
-             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
-             bam_quickcheck.o bam_addrprg.o
- 
--prefix      = /usr/local
--exec_prefix = $(prefix)
--bindir      = $(exec_prefix)/bin
--datarootdir = $(prefix)/share
--mandir      = $(datarootdir)/man
--man1dir     = $(mandir)/man1
--
- # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
- misc_bindir = $(bindir)
- 
-@@ -85,15 +70,14 @@
- 
- all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS)
- 
--ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
--ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
--ALL_LIBS     = -lz $(LIBS)
-+ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS)
-+ALL_LIBS     = $(ZLIB_LIBS) $(LIBS)
- 
- # Usually config.mk and config.h are generated by running configure
- # or config.status, but if those aren't used create defaults here.
- 
- config.mk:
--	@sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@
-+	@sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@
- 
- config.h:
- 	echo '/* Basic config.h generated by Makefile */' > $@
-@@ -133,17 +117,22 @@
- .c.o:
- 	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
- 
-+$(LOBJS):
-+	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $<
-+
- 
- LIBST_OBJS = sam_opts.o sam_utils.o
- 
- 
--lib:libbam.a
-+lib: libbam.so.1.0
- 
--libbam.a:$(LOBJS)
--	$(AR) -csru $@ $(LOBJS)
-+libbam.so.1.0:$(LOBJS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB)
-+	ln -sf $@ libbam.so.1
-+	ln -sf $@ libbam.so
- 
--samtools: $(AOBJS) libbam.a libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread
-+samtools: $(AOBJS) libbam.so.1.0 libst.a
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread
- 
- # For building samtools and its test suite only: NOT to be installed.
- libst.a: $(LIBST_OBJS)
-@@ -151,58 +140,58 @@
- 	$(AR) -rcs $@ $(LIBST_OBJS)
- 
- 
--bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
--bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
--bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
--bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
--bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h)
--sam_h = sam.h $(htslib_sam_h) $(bam_h)
--sam_opts_h = sam_opts.h $(htslib_hts_h)
--sample_h = sample.h $(htslib_kstring_h)
--
--bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h
--bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h)
--bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h)
--bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h)
--bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)
-+bam_h = bam.h
-+bam2bcf_h = bam2bcf.h
-+bam_lpileup_h = bam_lpileup.h
-+bam_plbuf_h = bam_plbuf.h
-+bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h)
-+sam_h = sam.h $(bam_h)
-+sam_opts_h = sam_opts.h
-+sample_h = sample.h
-+
-+bam.o: bam.c config.h $(bam_h) sam_header.h
-+bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h)
-+bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h)
-+bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h)
-+bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h)
- bam_aux.o: bam_aux.c config.h $(bam_h)
--bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h
-+bam_cat.o: bam_cat.c config.h samtools.h
- bam_color.o: bam_color.c config.h $(bam_h)
--bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)
--bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h
--bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)
--bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h
--bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h
--bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
--bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
--bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h)
--bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h
--bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h)
--bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h
--bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h
--bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h
--bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h
--bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h)
-+bam_import.o: bam_import.c config.h $(bam_h)
-+bam_index.o: bam_index.c config.h samtools.h
-+bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h)
-+bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h
-+bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h
-+bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h)
-+bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
-+bam_quickcheck.o: bam_quickcheck.c config.h
-+bam_reheader.o: bam_reheader.c config.h samtools.h
-+bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h)
-+bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h
-+bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h
-+bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h
-+bam_stat.o: bam_stat.c config.h samtools.h
-+bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h)
- bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h)
- bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h)
--bam_flags.o: bam_flags.c config.h $(htslib_sam_h)
--bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)
--bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h
--bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)
--bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)
--cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h)
--dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h)
--faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h
--padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h
--phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)
--sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h)
--sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h)
-+bam_flags.o: bam_flags.c config.h
-+bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h)
-+bamtk.o: bamtk.c config.h samtools.h version.h
-+bedcov.o: bedcov.c config.h $(sam_opts_h)
-+bedidx.o: bedidx.c config.h
-+cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h)
-+dict.o: dict.c config.h
-+faidx.o: faidx.c config.h samtools.h
-+padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h
-+phase.o: phase.c config.h $(sam_opts_h) samtools.h
-+sam.o: sam.c config.h $(sam_h)
-+sam_header.o: sam_header.c config.h sam_header.h
- sam_opts.o: sam_opts.c config.h $(sam_opts_h)
- sam_utils.o: sam_utils.c config.h samtools.h
--sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)
--sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)
--stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h)
--stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h)
-+sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h)
-+sample.o: sample.c config.h $(sample_h)
-+stats_isize.o: stats_isize.c config.h stats_isize.h
-+stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h)
- 
- 
- # test programs
-@@ -224,30 +213,30 @@
- 
- 
- test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
- test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
- test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
- test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
- test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
- test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
- test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
- test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
- 
--test_test_h = test/test.h $(htslib_sam_h)
-+test_test_h = test/test.h
- 
- test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h)
- test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o
-@@ -256,34 +245,34 @@
- test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h)
- test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h)
- test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h)
--test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h)
--test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h)
-+test/test.o: test/test.c config.h $(test_test_h)
-+test/vcf-miniview.o: test/vcf-miniview.c config.h
- 
- 
- # misc programs
- 
- misc/ace2sam: misc/ace2sam.o
--	$(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)
- 
- misc/maq2sam-short: misc/maq2sam-short.o
--	$(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)
- 
- misc/maq2sam-long: misc/maq2sam-long.o
--	$(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
- 
- misc/md5fa: misc/md5fa.o $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS)
- 
- misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)
--	$(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS)
- 
- misc/wgsim: misc/wgsim.o
--	$(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)
- 
--misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h)
--misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h)
--misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h)
--misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h)
-+misc/ace2sam.o: misc/ace2sam.c config.h
-+misc/md5fa.o: misc/md5fa.c config.h
-+misc/md5sum-lite.o: misc/md5sum-lite.c config.h
-+misc/wgsim.o: misc/wgsim.c config.h
- 
- misc/maq2sam-short.o: misc/maq2sam.c config.h
- 	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c
diff --git a/sci-biology/samtools/samtools-0.1.20-r3.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
index 5cfcfd7f6a79..d598a3292728 100644
--- a/sci-biology/samtools/samtools-0.1.20-r3.ebuild
+++ b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1 toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
 HOMEPAGE="http://samtools.sourceforge.net/"
@@ -14,23 +12,17 @@ SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.g
 LICENSE="MIT"
 SLOT="0.1-legacy"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
-RDEPEND="${PYTHON_DEPS}
+RDEPEND="
 	sys-libs/ncurses:0=
 	dev-lang/perl"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
-PATCHES=(
-	"${FILESDIR}/${P}-buildsystem.patch"
-)
+PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
 
 src_prepare() {
 	default
-	# required, otherwise python_fix_shebang errors out
-	sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die
 	tc-export CC AR
 }
 
@@ -44,16 +36,16 @@ src_install() {
 	# install executables and hide them away from sight
 	dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \
 		misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck}
-	mv "${ED%/}"/usr/{bin,${PN}-${SLOT}} || die
-	mkdir "${ED%/}"/usr/bin || die
-	mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die
+	mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die
+	mkdir "${ED}"/usr/bin || die
+	mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die
 
-	# ... do the same with the python script, but also fix the shebang
-	mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die
-	python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py
+	# remove py2 script, has been removed upstream anyways
+	# https://github.com/samtools/samtools/issues/1125
+	rm "${ED}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
 
 	# fix perl shebangs
-	pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die
+	pushd "${ED}"/usr/bin/${PN}-${SLOT} >/dev/null || die
 		local i
 		for i in plot-bamcheck *.pl; do
 			sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
@@ -70,14 +62,12 @@ src_install() {
 	doman ${PN}-${SLOT}.1
 	einstalldocs
 
-	if use examples; then
-		dodoc -r examples
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
+	dodoc -r examples
+	docompress -x /usr/share/doc/${PF}/examples
 }
 
 pkg_postinst() {
 	elog "This version of samtools should *not* be your first choice for working"
 	elog "with NGS data. It is installed solely for programs requiring it."
-	elog "It is recommended that you use >=sci-biology/samtools-1.2."
+	elog "It is recommended that you use >=sci-biology/samtools-1.10."
 }
diff --git a/sci-biology/samtools/samtools-1.9-r1.ebuild b/sci-biology/samtools/samtools-1.10.ebuild
index 0d0f993895fc..0ef5e6c19e8e 100644
--- a/sci-biology/samtools/samtools-1.9-r1.ebuild
+++ b/sci-biology/samtools/samtools-1.10.ebuild
@@ -12,12 +12,11 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="examples"
 
 RDEPEND="
 	dev-lang/perl
 	=sci-libs/htslib-${PV}*
-	sys-libs/ncurses:0=
+	sys-libs/ncurses:0=[unicode]
 	sys-libs/zlib:="
 DEPEND="${RDEPEND}"
 BDEPEND="virtual/pkgconfig"
@@ -31,19 +30,27 @@ src_prepare() {
 	eautoreconf
 }
 
+src_configure() {
+	econf \
+		--with-ncurses \
+		--with-htslib=system \
+		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw)"
+}
+
+src_compile() {
+	emake AR="$(tc-getAR)"
+}
+
 src_test() {
-	local -x LD_LIBRARY_PATH="${S}"
+	# the tview test diffs expect 80-columns output
+	unset COLUMNS
+
 	default
 }
 
 src_install() {
 	default
 
-	# varfilter.py has been retired upstream for being py2 only
-	rm "${ED}"/usr/bin/varfilter.py || die
-
-	if use examples; then
-		dodoc -r examples
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
+	dodoc -r examples
+	docompress -x /usr/share/doc/${PF}/examples
 }
diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild
deleted file mode 100644
index c2bc7ce89cf6..000000000000
--- a/sci-biology/samtools/samtools-1.5.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools python-r1 toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-${PV}*
-	sys-libs/ncurses:0=
-	sys-libs/zlib
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}/${PN}-1.5-buildsystem.patch" )
-
-src_prepare() {
-	default
-
-	python_setup
-	python_fix_shebang misc/varfilter.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-
-	eautoreconf
-}
-
-src_test() {
-	local -x LD_LIBRARY_PATH="${S}"
-	default
-}
-
-src_install() {
-	default
-
-	# install libbam and headers
-	dolib.so libbam.so*
-
-	insinto /usr/include/bam
-	doins *.h
-
-	if use examples; then
-		dodoc -r examples
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
-}
author	V3n3RiX <venerix@redcorelinux.org>	2020-08-25 10:45:55 +0100
committer	V3n3RiX <venerix@redcorelinux.org>	2020-08-25 10:45:55 +0100
commit	3cf7c3ef441822c889356fd1812ebf2944a59851 (patch)
tree	c513fe68548b40365c1c2ebfe35c58ad431cdd77 /sci-biology
parent	05b8b0e0af1d72e51a3ee61522941bf7605cd01c (diff)