gentoo auto-resync : 27:12:2022 - 02:09:02

5 files changed, 93 insertions, 0 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 7a1132df2b16..64cc48575488 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 71dc6fb7d0a0..dcedae35eab8 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -1,3 +1,5 @@
 DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731 SHA512 60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b
+DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06 SHA512 998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3
 EBUILD bcftools-1.15.1.ebuild 891 BLAKE2B 532c584a7620b40136572ac4d8e73b09d9c80bd96cb39992dddc0366323cf96dd30d86bf968129f4bdd49f9f25cc6ad631327a3d4bc325e8f22242461af13806 SHA512 d585cbda0b571576139f1e4edf8c51e64665b06fd73e2ea81f5e9a94d765ff4c4438dfdc3e11ced9e6e05ccefce13997b5faa70905f43b8f27ca07f2db976af7
+EBUILD bcftools-1.16.ebuild 900 BLAKE2B e61d47ca6a9e619e560aa5789c60299eca173ff7a996882af4e99c76fb4566542a67e8b3ae5284fde187cf77d5c477aab2a96ce0db27ba778a0e4e55414afb6b SHA512 54c8f9cde0a5cd1789404563e907eeaf583088ce6ea1f70eb25101b49aad60a3a625b9ee2cb6a65f56f3b423059cfe69193ceed3887d107bed389f0df8460a18
 MISC metadata.xml 344 BLAKE2B 37f8e82e8a5a9ad572580a7e5ae6daa6911d672f17b8526f81b236cbc2e50a32c4cd2566aaed9f5feee016d7e2de7db2a40b60616e86c3e8cae307d60cebc70e SHA512 0160c9606089d610613d71dc0aa9c9c5e5266483fdc9c407b6e0ed911eac8f8b32ffaf5a49bbb427393c8240e9868df51f0fc68b2f45467f65d9b3d54b0ddde1
diff --git a/sci-biology/bcftools/bcftools-1.16.ebuild b/sci-biology/bcftools/bcftools-1.16.ebuild
new file mode 100644
index 000000000000..eeb9a7c890b7
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.16.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} )
+
+inherit python-single-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}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	dev-lang/perl
+	$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
+	=sci-libs/htslib-$(ver_cut 1-2)*:=
+	sys-libs/zlib
+	${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+BDEPEND="${PYTHON_DEPS}"
+
+src_prepare() {
+	default
+
+	python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
+
+	# remove bundled htslib
+	rm -r htslib-* || die
+}
+
+src_configure() {
+	econf \
+		--disable-bcftools-plugins \
+		--disable-libgsl \
+		--with-htslib=system
+}
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 1c8c07cfbbda..faa3a4d5981b 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,6 +1,8 @@
 AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b27093f670e383d2d194b5692b1ba536e3df44204711cf4574b3933e5ce00605b661b1a36d79ca7f193ce36816271a3f8214 SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d
 DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6 SHA512 54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46
+DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1 SHA512 f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
 EBUILD samtools-0.1.20-r4.ebuild 2049 BLAKE2B d377712eaca931258b37645e6a6b3cc379fdb550ef83a0c272a3eb564d7753185fea53416973e4fdf2c25b79475a81ae72b646ce22c570c934e4eabce8a9ded6 SHA512 c0d387f715ebf1f746ea4e4a7eab85a86ef0bff646c9a69639b17ef02e93c39982941d7eb811a6d67b0e635c9c4e05924d2b89a6809c3bd0592db91894dab4aa
 EBUILD samtools-1.15.1.ebuild 917 BLAKE2B ce0e56d9fd4d45f32d53e014648ea154b55363f9b48f1293f1687c2f2c668d7f498bb346bc291bf30c0be23499326cc38eb93065114c932269808825ece939e6 SHA512 dee59486e4942a45450b41aa1df296264dcc6396463a8e2e3ce93f4d7fb14acae252d4798492a19912999ca621c2188ef25ee6063fee7c9bc673ba57169a99c6
+EBUILD samtools-1.16.1.ebuild 926 BLAKE2B 7856fb586ff9b879e353784635eb27d190da7d1dc41a42f103cb1116ebde092b94e086779883bc916d5223632d217ea3f3d5468278d174122845a48be6df2d3d SHA512 b6711d8b955e466cdd79a2a4a92fa9f7f98aaa302901c97f1bab439f7cc407ff65726957627a8182068a7eb5f5556e680b52d9f2514f461e4e2f33ac3dc4dfa3
 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24
diff --git a/sci-biology/samtools/samtools-1.16.1.ebuild b/sci-biology/samtools/samtools-1.16.1.ebuild
new file mode 100644
index 000000000000..8047657df992
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.16.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+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 ~amd64-linux ~x86-linux ~x64-macos"
+
+RDEPEND="
+	dev-lang/perl
+	=sci-libs/htslib-$(ver_cut 1-2)*:=
+	sys-libs/ncurses:=[unicode(+)]
+	sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+	default
+
+	# remove bundled htslib
+	rm -r htslib-* || die
+}
+
+src_configure() {
+	econf \
+		--with-ncurses \
+		--with-htslib=system \
+		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
+}
+
+src_compile() {
+	emake AR="$(tc-getAR)"
+}
+
+src_install() {
+	default
+
+	dodoc -r examples
+	docompress -x /usr/share/doc/${PF}/examples
+}