gentoo auto-resync : 25:05:2024 - 00:07:14

6 files changed, 32 insertions, 33 deletions

diff --git a/metadata/md5-cache/sci-biology/Manifest.gz b/metadata/md5-cache/sci-biology/Manifest.gz
index 4c65c258b812..016461d56d5c 100644
--- a/metadata/md5-cache/sci-biology/Manifest.gz
+++ b/metadata/md5-cache/sci-biology/Manifest.gz
diff --git a/metadata/md5-cache/sci-biology/bcftools-1.17 b/metadata/md5-cache/sci-biology/bcftools-1.20
index 97bb25ddd980..dc122534cec9 100644
--- a/metadata/md5-cache/sci-biology/bcftools-1.17
+++ b/metadata/md5-cache/sci-biology/bcftools-1.20
@@ -1,16 +1,16 @@
-BDEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 )
+BDEPEND=python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 )
 DEFINED_PHASES=configure prepare setup
-DEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) =sci-libs/htslib-1.17*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 )
+DEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) python_single_target_python3_12? ( dev-python/matplotlib[python_targets_python3_12(-)] ) =sci-libs/htslib-1.20*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 )
 DESCRIPTION=Utilities for variant calling and manipulating VCF and BCF files
 EAPI=8
 HOMEPAGE=http://www.htslib.org
 INHERIT=python-single-r1
-IUSE=python_single_target_python3_10 python_single_target_python3_11
+IUSE=python_single_target_python3_10 python_single_target_python3_11 python_single_target_python3_12
 KEYWORDS=~amd64 ~x86
 LICENSE=MIT
-RDEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) =sci-libs/htslib-1.17*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 )
-REQUIRED_USE=^^ ( python_single_target_python3_10 python_single_target_python3_11 )
+RDEPEND=dev-lang/perl python_single_target_python3_10? ( dev-python/matplotlib[python_targets_python3_10(-)] ) python_single_target_python3_11? ( dev-python/matplotlib[python_targets_python3_11(-)] ) python_single_target_python3_12? ( dev-python/matplotlib[python_targets_python3_12(-)] ) =sci-libs/htslib-1.20*:= sys-libs/zlib python_single_target_python3_10? ( dev-lang/python:3.10 ) python_single_target_python3_11? ( dev-lang/python:3.11 ) python_single_target_python3_12? ( dev-lang/python:3.12 )
+REQUIRED_USE=^^ ( python_single_target_python3_10 python_single_target_python3_11 python_single_target_python3_12 )
 SLOT=0
-SRC_URI=https://github.com/samtools/bcftools/releases/download/1.17/bcftools-1.17.tar.bz2
+SRC_URI=https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
 _eclasses_=multilib	c19072c3cd7ac5cb21de013f7e9832e0	multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	python-single-r1	75118e916668a74c660a13b0ecb22562	python-utils-r1	8b220bbce5c119fb1d4d5c2f5588f3ea	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084
-_md5_=5271780ace94107aae357a985f191e14
+_md5_=88036066dfeb432f0a530195f08f59f7
diff --git a/metadata/md5-cache/sci-biology/pysam-0.21.0 b/metadata/md5-cache/sci-biology/pysam-0.21.0
deleted file mode 100644
index 9c15d61f31a6..000000000000
--- a/metadata/md5-cache/sci-biology/pysam-0.21.0
+++ /dev/null
@@ -1,17 +0,0 @@
-BDEPEND=test? ( =sci-biology/bcftools-1.17* =sci-biology/samtools-1.17* ) test? ( =sci-libs/htslib-1.17*:= >=dev-python/pytest-7.4.4[python_targets_python3_10(-)?,python_targets_python3_11(-)?] ) python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) >=dev-python/setuptools-69.0.3[python_targets_python3_10(-)?,python_targets_python3_11(-)?]
-DEFINED_PHASES=compile configure install prepare test
-DEPEND==sci-libs/htslib-1.17*:= dev-python/cython[python_targets_python3_10(-)?,python_targets_python3_11(-)?] dev-python/setuptools[python_targets_python3_10(-)?,python_targets_python3_11(-)?]
-DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format
-EAPI=8
-HOMEPAGE=https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/
-INHERIT=distutils-r1
-IUSE=test python_targets_python3_10 python_targets_python3_11
-KEYWORDS=~amd64 ~x86
-LICENSE=MIT
-RDEPEND==sci-libs/htslib-1.17*:= python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 )
-REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 )
-RESTRICT=!test? ( test )
-SLOT=0
-SRC_URI=https://github.com/pysam-developers/pysam/archive/v0.21.0.tar.gz -> pysam-0.21.0.gh.tar.gz
-_eclasses_=distutils-r1	5400d21736d8621562bf93be4fa98eec	flag-o-matic	d309b9713dfc18e754cba88d3ba69653	multibuild	d67e78a235f541871c7dfe4cf7931489	multilib	c19072c3cd7ac5cb21de013f7e9832e0	multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	ninja-utils	2df4e452cea39a9ec8fb543ce059f8d6	out-of-source-utils	1a9007554652a6e627edbccb3c25a439	python-r1	8a28fa6d3e3bc96ff8a7eff2badbe71f	python-utils-r1	8b220bbce5c119fb1d4d5c2f5588f3ea	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084
-_md5_=d2f337ee806641d85739cd55c8698806
diff --git a/metadata/md5-cache/sci-biology/pysam-0.22.1 b/metadata/md5-cache/sci-biology/pysam-0.22.1
new file mode 100644
index 000000000000..1e11f68d7d5b
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/pysam-0.22.1
@@ -0,0 +1,17 @@
+BDEPEND=dev-python/cython[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] test? ( =sci-biology/bcftools-1.20* =sci-biology/samtools-1.20* ) test? ( =sci-libs/htslib-1.20*:= >=dev-python/pytest-7.4.4[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?] ) python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 ) >=dev-python/setuptools-69.0.3[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?]
+DEFINED_PHASES=compile configure install prepare test
+DEPEND==sci-libs/htslib-1.20*:= dev-python/setuptools[python_targets_python3_10(-)?,python_targets_python3_11(-)?,python_targets_python3_12(-)?]
+DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping format
+EAPI=8
+HOMEPAGE=https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/
+INHERIT=distutils-r1
+IUSE=test python_targets_python3_10 python_targets_python3_11 python_targets_python3_12
+KEYWORDS=~amd64 ~x86
+LICENSE=MIT
+RDEPEND==sci-libs/htslib-1.20*:= python_targets_python3_10? ( dev-lang/python:3.10 ) python_targets_python3_11? ( dev-lang/python:3.11 ) python_targets_python3_12? ( dev-lang/python:3.12 )
+REQUIRED_USE=|| ( python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 )
+RESTRICT=!test? ( test )
+SLOT=0
+SRC_URI=https://github.com/pysam-developers/pysam/archive/v0.22.1.tar.gz -> pysam-0.22.1.gh.tar.gz
+_eclasses_=distutils-r1	5400d21736d8621562bf93be4fa98eec	flag-o-matic	d309b9713dfc18e754cba88d3ba69653	multibuild	d67e78a235f541871c7dfe4cf7931489	multilib	c19072c3cd7ac5cb21de013f7e9832e0	multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	ninja-utils	2df4e452cea39a9ec8fb543ce059f8d6	out-of-source-utils	1a9007554652a6e627edbccb3c25a439	python-r1	8a28fa6d3e3bc96ff8a7eff2badbe71f	python-utils-r1	8b220bbce5c119fb1d4d5c2f5588f3ea	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084
+_md5_=a742eeecf26e6de57df273759b8491aa
diff --git a/metadata/md5-cache/sci-biology/raxml-7.2.6 b/metadata/md5-cache/sci-biology/raxml-8.2.13
index 3439f6b6df23..560edd6c6a8a 100644
--- a/metadata/md5-cache/sci-biology/raxml-7.2.6
+++ b/metadata/md5-cache/sci-biology/raxml-8.2.13
@@ -1,13 +1,12 @@
 DEFINED_PHASES=compile configure install
 DESCRIPTION=Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
-EAPI=7
-HOMEPAGE=http://wwwkramer.in.tum.de/exelixis/software.html
+EAPI=8
+HOMEPAGE=https://github.com/stamatak/standard-RAxML
 INHERIT=flag-o-matic toolchain-funcs
 IUSE=cpu_flags_x86_sse3 +threads
 KEYWORDS=~amd64 ~x86
 LICENSE=GPL-2
-REQUIRED_USE=cpu_flags_x86_sse3
 SLOT=0
-SRC_URI=http://wwwkramer.in.tum.de/exelixis/software/RAxML-7.2.6.tar.bz2
+SRC_URI=https://github.com/stamatak/standard-RAxML/archive/refs/tags/v8.2.13.tar.gz -> raxml-8.2.13.tar.gz
 _eclasses_=flag-o-matic	d309b9713dfc18e754cba88d3ba69653	multilib	c19072c3cd7ac5cb21de013f7e9832e0	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084
-_md5_=14b77d8b019468c10a65f1358be0d8ae
+_md5_=b1b4de0bedc435411038a43f078ba175
diff --git a/metadata/md5-cache/sci-biology/samtools-1.17 b/metadata/md5-cache/sci-biology/samtools-1.20
index bcb720f8e8e9..7938609b9903 100644
--- a/metadata/md5-cache/sci-biology/samtools-1.17
+++ b/metadata/md5-cache/sci-biology/samtools-1.20
@@ -1,14 +1,14 @@
 BDEPEND=virtual/pkgconfig
 DEFINED_PHASES=compile configure install prepare
-DEPEND=dev-lang/perl =sci-libs/htslib-1.17*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib
+DEPEND=dev-lang/perl =sci-libs/htslib-1.20*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib
 DESCRIPTION=Utilities for analysing and manipulating the SAM/BAM alignment formats
 EAPI=8
 HOMEPAGE=http://www.htslib.org/
 INHERIT=toolchain-funcs
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos
 LICENSE=MIT
-RDEPEND=dev-lang/perl =sci-libs/htslib-1.17*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib
+RDEPEND=dev-lang/perl =sci-libs/htslib-1.20*:= sys-libs/ncurses:=[unicode(+)] sys-libs/zlib
 SLOT=0
-SRC_URI=https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
+SRC_URI=https://github.com/samtools/samtools/releases/download/1.20/samtools-1.20.tar.bz2
 _eclasses_=multilib	c19072c3cd7ac5cb21de013f7e9832e0	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084
-_md5_=d899fa7ac2ab4404dcca131cb83b93ab
+_md5_=582b7ec64e75c223a70f748cfa2d9bca