6 files changed, 22 insertions, 23 deletions
diff --git a/metadata/md5-cache/sci-biology/bcftools-1.17 b/metadata/md5-cache/sci-biology/bcftools-1.20
index 84ca16280ad1..1c83b96f75e8 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_=multiprocessing	30ead54fa2e2b5f9cd4e612ffc34d0fe	toolchain-funcs	e56c7649b804f051623c8bc1a1c44084	multilib	c19072c3cd7ac5cb21de013f7e9832e0	python-utils-r1	8b220bbce5c119fb1d4d5c2f5588f3ea	python-single-r1	75118e916668a74c660a13b0ecb22562
-_md5_=5271780ace94107aae357a985f191e14
+_md5_=88036066dfeb432f0a530195f08f59f7
diff --git a/metadata/md5-cache/sci-biology/raxml-7.2.6 b/metadata/md5-cache/sci-biology/raxml-8.2.13
index 3475c9aa4262..a81b3d61e0c5 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_=toolchain-funcs	e56c7649b804f051623c8bc1a1c44084	multilib	c19072c3cd7ac5cb21de013f7e9832e0	flag-o-matic	d309b9713dfc18e754cba88d3ba69653
-_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 dc1480f4fb1d..b3e1f2a4db84 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_=toolchain-funcs	e56c7649b804f051623c8bc1a1c44084	multilib	c19072c3cd7ac5cb21de013f7e9832e0
-_md5_=d899fa7ac2ab4404dcca131cb83b93ab
+_md5_=582b7ec64e75c223a70f748cfa2d9bca
diff --git a/metadata/md5-cache/sci-libs/htslib-1.17 b/metadata/md5-cache/sci-libs/htslib-1.20
index 8e372f8318ee..5c27d2cd59fc 100644
--- a/metadata/md5-cache/sci-libs/htslib-1.17
+++ b/metadata/md5-cache/sci-libs/htslib-1.20
@@ -9,6 +9,6 @@ KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
 LICENSE=MIT
 RDEPEND=sys-libs/zlib bzip2? ( app-arch/bzip2 ) curl? ( net-misc/curl ) lzma? ( app-arch/xz-utils )
 SLOT=0/3
-SRC_URI=https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2
+SRC_URI=https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
 _eclasses_=toolchain-funcs	e56c7649b804f051623c8bc1a1c44084	multilib	c19072c3cd7ac5cb21de013f7e9832e0
-_md5_=33dc238498dee368c716d086b46cb58f
+_md5_=c490e0280088776fd28ff233d642a300
diff --git a/metadata/pkg_desc_index b/metadata/pkg_desc_index
index f4dad9310d1e..d31a8b796559 100644
--- a/metadata/pkg_desc_index
+++ b/metadata/pkg_desc_index
@@ -15749,7 +15749,7 @@ sci-biology/abyss 2.3.4: Assembly By Short Sequences - a de novo, parallel, pair
 sci-biology/amap 2.2-r5: Protein multiple-alignment-based sequence annealing
 sci-biology/augustus 2.5.5 3.4.0-r3: Eukaryotic gene predictor
 sci-biology/bamtools 2.5.2 9999: A programmer's API and an end-user's toolkit for handling BAM files
-sci-biology/bcftools 1.17 1.19: Utilities for variant calling and manipulating VCF and BCF files
+sci-biology/bcftools 1.19 1.20: Utilities for variant calling and manipulating VCF and BCF files
 sci-biology/bedtools 2.30.0 2.31.1: Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats
 sci-biology/bfast 0.7.0a: Blat-like Fast Accurate Search Tool
 sci-biology/biogrep 1.0-r3: Multithreaded tool for matching large sets of patterns against biosequence DBs
@@ -15833,11 +15833,11 @@ sci-biology/profphd 1.0.40: Secondary structure and solvent accessibility predic
 sci-biology/prosite 2017.02-r1: A protein families and domains database
 sci-biology/pysam 0.21.0 9999: Python interface for the SAM/BAM sequence alignment and mapping format
 sci-biology/qrna 2.0.3c-r3 2.0.4: Prototype ncRNA genefinder
-sci-biology/raxml 7.2.6: Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
+sci-biology/raxml 8.2.13: Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
 sci-biology/rebase 1901-r2: A restriction enzyme database
 sci-biology/recon 1.08-r1: Automated de novo identification of repeat families from genomic sequences
 sci-biology/rnaview 20040713-r5: Generates 2D displays of RNA/DNA secondary structures with tertiary interactions
-sci-biology/samtools 1.17 1.19.2: Utilities for analysing and manipulating the SAM/BAM alignment formats
+sci-biology/samtools 1.19.2 1.20: Utilities for analysing and manipulating the SAM/BAM alignment formats
 sci-biology/seaview 4.6-r1: A graphical multiple sequence alignment editor
 sci-biology/seqan 3.1.0: C++ Sequence Analysis Library
 sci-biology/sibsim4 0.20: A rewrite and improvement upon sim4, a DNA-mRNA aligner
@@ -16161,7 +16161,7 @@ sci-libs/hipFFT 5.1.3-r1 5.7.1-r1: CU / ROCM agnostic hip FFT implementation
 sci-libs/hipRAND 5.6.0-r1 5.7.1: CU / ROCM agnostic hip RAND implementation
 sci-libs/hipSOLVER 5.7.1: CU / ROCM agnostic marshalling library for LAPACK routines on the GPU
 sci-libs/hipSPARSE 5.1.3-r1 5.7.1: ROCm SPARSE marshalling library
-sci-libs/htslib 1.17 1.19.1: C library for high-throughput sequencing data formats
+sci-libs/htslib 1.19.1 1.20: C library for high-throughput sequencing data formats
 sci-libs/huggingface_hub 0.20.3 0.21.4: a client library to interact with the Hugging Face Hub
 sci-libs/hypre 2.20.0 2.21.0 2.24.0: Parallel matrix preconditioners library
 sci-libs/ideep 3.1.1 3.3.2: Intel® Optimization for Chainer
diff --git a/metadata/timestamp.chk b/metadata/timestamp.chk
index aefe626aed67..5ea330201089 100644
--- a/metadata/timestamp.chk
+++ b/metadata/timestamp.chk
@@ -1 +1 @@
-Fri, 24 May 2024 08:33:48 +0000
+Fri, 24 May 2024 09:03:53 +0000