From f6f7da33daafe2e5f4a646b81172b8631bd34152 Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Thu, 2 May 2024 11:24:44 -0700 Subject: [PATCH 1/4] LANG: python 3.9 update (metagenome) --- .../passed/seed-environment-conda.yml | 28 ++++++++++--------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/2024.5/metagenome/passed/seed-environment-conda.yml b/2024.5/metagenome/passed/seed-environment-conda.yml index e82e6cc0..54cc53ab 100644 --- a/2024.5/metagenome/passed/seed-environment-conda.yml +++ b/2024.5/metagenome/passed/seed-environment-conda.yml @@ -4,17 +4,18 @@ channels: - bioconda - defaults dependencies: -- biom-format=2.1.14 +- biom-format=2.1.15 - bowtie2=2.5.1 -- h5py=3.8.0 +- h5py=3.11.0 - hdf5=1.14.0 -- matplotlib=3.6.0 +- matplotlib=3.8.4 - notebook=6.5.5 -- numpy=1.24.4 -- pandas=1.5.3 -- parsl=2023.12.04 -- patsy=0.5.3 -- python=3.8 +- numpy=1.26.4 +- pandas=2.2.2 +- parsl=2024.4.15 +- patsy=0.5.6 +- python=3.9.19 +- python_abi=3.9 - q2-assembly=2024.5.0.dev0+2.gea8f24f - q2-composition=2024.5.0.dev0 - q2-cutadapt=2024.5.0.dev0 @@ -39,14 +40,15 @@ dependencies: - q2cli=2024.5.0.dev0 - q2templates=2024.5.0.dev0 - qiime2=2024.5.0.dev0+2.g27f5ec0 -- r-base=4.2.2 +- r-base=4.3.3 +- r-reticulate=1.36.0 - rescript=2024.5.0.dev0+3.g6e87cfe -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 - seaborn=0.12.2 - umap-learn=0.5.4 -- unifrac-binaries=1.3.2 +- unifrac-binaries=1.4 - unifrac=1.3 extras: variant_override: From b78a6de7ebff453bec8e7b8e3ba72bbd4f609692 Mon Sep 17 00:00:00 2001 From: Evan Bolyen Date: Fri, 3 May 2024 09:27:46 -0700 Subject: [PATCH 2/4] Update 2024.5/metagenome/passed/seed-environment-conda.yml --- 2024.5/metagenome/passed/seed-environment-conda.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/2024.5/metagenome/passed/seed-environment-conda.yml b/2024.5/metagenome/passed/seed-environment-conda.yml index 54cc53ab..197e85e5 100644 --- a/2024.5/metagenome/passed/seed-environment-conda.yml +++ b/2024.5/metagenome/passed/seed-environment-conda.yml @@ -7,7 +7,7 @@ dependencies: - biom-format=2.1.15 - bowtie2=2.5.1 - h5py=3.11.0 -- hdf5=1.14.0 +- hdf5=1.14.3 - matplotlib=3.8.4 - notebook=6.5.5 - numpy=1.26.4 From 74f25e5dc8320a4706e50530f99378f038f8cdbc Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Mon, 6 May 2024 15:22:48 -0700 Subject: [PATCH 3/4] adds some external deps from metagenome plugins --- 2024.5/metagenome/passed/seed-environment-conda.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/2024.5/metagenome/passed/seed-environment-conda.yml b/2024.5/metagenome/passed/seed-environment-conda.yml index 197e85e5..482c3187 100644 --- a/2024.5/metagenome/passed/seed-environment-conda.yml +++ b/2024.5/metagenome/passed/seed-environment-conda.yml @@ -5,7 +5,10 @@ channels: - defaults dependencies: - biom-format=2.1.15 +- biopython=1.83 +- busco=5.5.0 - bowtie2=2.5.1 +- entrezpy=2.1.2 - h5py=3.11.0 - hdf5=1.14.3 - matplotlib=3.8.4 @@ -47,6 +50,8 @@ dependencies: - scikit-learn=1.4.2 - scipy=1.13.0 - seaborn=0.12.2 +- sepp=4.4.0 +- tqdm=4.62.3 - umap-learn=0.5.4 - unifrac-binaries=1.4 - unifrac=1.3 From 3315463ecdbd5e74192f8644bbf7d03087445774 Mon Sep 17 00:00:00 2001 From: q2d2 Date: Tue, 7 May 2024 01:10:59 +0000 Subject: [PATCH 4/4] Update conda environments (Language-python39-update/metagenome) --- .../qiime2-metagenome-macos-latest-conda.yml | 420 ++++++++--------- .../qiime2-metagenome-ubuntu-latest-conda.yml | 432 +++++++++--------- .../passed/seed-environment-conda.yml | 34 +- .../staged/seed-environment-conda.yml | 67 +-- 4 files changed, 488 insertions(+), 465 deletions(-) diff --git a/2024.5/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml b/2024.5/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml index 4b5c5dd0..7b683479 100644 --- a/2024.5/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml +++ b/2024.5/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml @@ -13,79 +13,81 @@ dependencies: - argh=0.31.2 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 -- aria2=1.36.0 +- aria2=1.37.0 - arrow=1.3.0 - astor=0.8.1 - asttokens=2.4.1 - atpublic=3.0.1 - attrs=23.2.0 - augustus=3.5.0 -- backcall=0.2.0 - bamtools=2.5.1 -- bbmap=39.01 +- bbmap=39.06 - bcrypt=4.1.2 - beautifulsoup4=4.12.3 - bedtools=2.31.1 - bibtexparser=1.4.1 -- bioconductor-ancombc=2.0.1 -- bioconductor-annotationdbi=1.60.0 -- bioconductor-beachmat=2.14.0 -- bioconductor-biobase=2.58.0 -- bioconductor-biocbaseutils=1.0.0 -- bioconductor-biocfilecache=2.6.0 -- bioconductor-biocgenerics=0.44.0 -- bioconductor-biocio=1.8.0 -- bioconductor-biocneighbors=1.16.0 -- bioconductor-biocparallel=1.32.5 -- bioconductor-biocsingular=1.14.0 -- bioconductor-biomart=2.54.0 -- bioconductor-biomformat=1.26.0 -- bioconductor-biostrings=2.66.0 -- bioconductor-bsgenome=1.66.3 +- bioconductor-ancombc=2.4.0 +- bioconductor-annotationdbi=1.64.1 +- bioconductor-beachmat=2.18.0 +- bioconductor-biobase=2.62.0 +- bioconductor-biocbaseutils=1.4.0 +- bioconductor-biocfilecache=2.10.1 +- bioconductor-biocgenerics=0.48.1 +- bioconductor-biocio=1.12.0 +- bioconductor-biocneighbors=1.20.0 +- bioconductor-biocparallel=1.36.0 +- bioconductor-biocsingular=1.18.0 +- bioconductor-biomart=2.58.0 +- bioconductor-biomformat=1.30.0 +- bioconductor-biostrings=2.70.1 +- bioconductor-bluster=1.12.0 +- bioconductor-bsgenome=1.70.1 - bioconductor-data-packages=20231203 -- bioconductor-decipher=2.26.0 -- bioconductor-decontam=1.18.0 -- bioconductor-delayedarray=0.24.0 -- bioconductor-delayedmatrixstats=1.20.0 -- bioconductor-dirichletmultinomial=1.40.0 -- bioconductor-genomeinfodb=1.34.9 -- bioconductor-genomeinfodbdata=1.2.9 -- bioconductor-genomicalignments=1.34.0 -- bioconductor-genomicfeatures=1.50.2 -- bioconductor-genomicranges=1.50.0 -- bioconductor-iranges=2.32.0 -- bioconductor-keggrest=1.38.0 -- bioconductor-matrixgenerics=1.10.0 -- bioconductor-mia=1.6.0 -- bioconductor-multiassayexperiment=1.24.0 -- bioconductor-multtest=2.54.0 -- bioconductor-phyloseq=1.42.0 -- bioconductor-rhdf5=2.42.0 -- bioconductor-rhdf5filters=1.10.0 -- bioconductor-rhdf5lib=1.20.0 -- bioconductor-rhtslib=2.0.0 -- bioconductor-rsamtools=2.14.0 -- bioconductor-rtracklayer=1.58.0 -- bioconductor-s4vectors=0.36.0 -- bioconductor-scaledmatrix=1.6.0 -- bioconductor-scater=1.26.0 -- bioconductor-scuttle=1.8.0 -- bioconductor-singlecellexperiment=1.20.0 -- bioconductor-sparsematrixstats=1.10.0 -- bioconductor-structuralvariantannotation=1.13.0 -- bioconductor-summarizedexperiment=1.28.0 -- bioconductor-treeio=1.22.0 -- bioconductor-treesummarizedexperiment=2.6.0 -- bioconductor-variantannotation=1.44.0 -- bioconductor-xvector=0.38.0 -- bioconductor-zlibbioc=1.44.0 -- biom-format=2.1.14 -- biopython=1.78 +- bioconductor-decipher=2.30.0 +- bioconductor-decontam=1.22.0 +- bioconductor-delayedarray=0.28.0 +- bioconductor-delayedmatrixstats=1.24.0 +- bioconductor-dirichletmultinomial=1.44.0 +- bioconductor-genomeinfodb=1.38.1 +- bioconductor-genomeinfodbdata=1.2.11 +- bioconductor-genomicalignments=1.38.0 +- bioconductor-genomicfeatures=1.54.1 +- bioconductor-genomicranges=1.54.1 +- bioconductor-iranges=2.36.0 +- bioconductor-keggrest=1.42.0 +- bioconductor-matrixgenerics=1.14.0 +- bioconductor-mia=1.10.0 +- bioconductor-multiassayexperiment=1.28.0 +- bioconductor-multtest=2.58.0 +- bioconductor-phyloseq=1.46.0 +- bioconductor-rhdf5=2.46.1 +- bioconductor-rhdf5filters=1.14.1 +- bioconductor-rhdf5lib=1.24.0 +- bioconductor-rhtslib=2.4.0 +- bioconductor-rsamtools=2.18.0 +- bioconductor-rtracklayer=1.62.0 +- bioconductor-s4arrays=1.2.0 +- bioconductor-s4vectors=0.40.2 +- bioconductor-scaledmatrix=1.10.0 +- bioconductor-scater=1.30.1 +- bioconductor-scuttle=1.12.0 +- bioconductor-singlecellexperiment=1.24.0 +- bioconductor-sparsearray=1.2.2 +- bioconductor-sparsematrixstats=1.14.0 +- bioconductor-structuralvariantannotation=1.18.0 +- bioconductor-summarizedexperiment=1.32.0 +- bioconductor-treeio=1.26.0 +- bioconductor-treesummarizedexperiment=2.10.0 +- bioconductor-variantannotation=1.48.1 +- bioconductor-xvector=0.42.0 +- bioconductor-zlibbioc=1.48.0 +- biom-format=2.1.15 +- biopython=1.83 - blast=2.15.0 - bleach=6.1.0 -- boost-cpp=1.74.0 +- boost-cpp=1.78.0 - bowtie2=2.5.1 -- bracken=2.6.1 +- bracken=1.0.0 - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 @@ -95,32 +97,31 @@ dependencies: - bzip2=1.0.8 - c-ares=1.28.1 - ca-certificates=2024.2.2 -- cachecontrol=0.14.0 - cached-property=1.5.2 - cached_property=1.5.2 -- cairo=1.16.0 +- cairo=1.18.0 - cctools_osx-64=986 - cdbtools=0.99 - certifi=2024.2.2 - cffi=1.16.0 - charset-normalizer=3.3.2 - circos=0.69.9 -- clang=17.0.6 -- clang-17=17.0.6 -- clang_impl_osx-64=17.0.6 -- clang_osx-64=17.0.6 -- clangxx=17.0.6 -- clangxx_impl_osx-64=17.0.6 -- clangxx_osx-64=17.0.6 +- clang=18.1.5 +- clang-18=18.1.5 +- clang_impl_osx-64=18.1.5 +- clang_osx-64=18.1.5 +- clangxx=18.1.5 +- clangxx_impl_osx-64=18.1.5 +- clangxx_osx-64=18.1.5 - click=8.1.7 - colorama=0.4.6 - comm=0.2.2 -- compiler-rt=17.0.6 -- compiler-rt_osx-64=17.0.6 +- compiler-rt=18.1.5 +- compiler-rt_osx-64=18.1.5 - conda-pack=0.7.0 -- contourpy=1.1.1 -- cryptography=42.0.5 -- curl=7.88.1 +- contourpy=1.2.1 +- cryptography=42.0.6 +- curl=8.7.1 - cutadapt=4.8 - cycler=0.12.1 - debugpy=1.8.1 @@ -134,13 +135,14 @@ dependencies: - eggnog-mapper=2.1.12 - emperor=1.0.4 - entrez-direct=21.6 -- entrezpy=2.1.3 +- entrezpy=2.1.2 - entrypoints=0.4 - exceptiongroup=1.2.0 - executing=2.0.1 - expat=2.6.2 - fastcluster=1.2.6 - feedparser=6.0.11 +- filelock=3.14.0 - flufl.lock=7.1 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 @@ -159,50 +161,52 @@ dependencies: - gettext=0.22.5 - gettext-tools=0.22.5 - gffutils=0.10.1 -- gfortran_impl_osx-64=11.4.0 -- gfortran_osx-64=11.4.0 +- gfortran_impl_osx-64=12.3.0 +- gfortran_osx-64=12.3.0 +- giflib=5.2.2 - glimmerhmm=3.0.4 -- globus-sdk=3.40.0 +- globus-sdk=3.41.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 - graphlib-backport=1.0.3 - gridss=2.11.1 - gsl=2.7 -- h5py=3.8.0 -- harfbuzz=6.0.0 -- hdf5=1.14.0 +- h5py=3.11.0 +- harfbuzz=8.4.0 +- hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.1b2 -- htslib=1.17 -- icu=70.1 +- htslib=1.20 +- icu=73.2 - idna=3.7 - ijson=3.2.3 - importlib-metadata=7.1.0 +- importlib-resources=6.4.0 +- importlib_metadata=7.1.0 - importlib_resources=6.4.0 - iniconfig=2.0.0 -- insilicoseq=1.5.4 +- insilicoseq=1.3.5 - interface_meta=1.3.0 - iow=1.0.5 - ipykernel=6.29.3 -- ipython=8.12.2 +- ipython=8.18.1 - ipython_genutils=0.2.0 - ipywidgets=8.1.2 - isa-l=2.31.0 -- isl=0.25 +- isl=0.26 - isoduration=20.11.0 - jedi=0.19.1 - jinja2=3.1.3 -- joblib=1.4.0 -- jpeg=9e +- joblib=1.4.2 - jq=1.7.1 - jsonlines=3.0.0 - jsonpointer=2.4 -- jsonschema=4.21.1 +- jsonschema=4.22.0 - jsonschema-specifications=2023.12.1 -- jsonschema-with-format-nongpl=4.21.1 +- jsonschema-with-format-nongpl=4.22.0 - jupyter_client=7.4.9 -- jupyter_core=5.7.2 +- jupyter_core=5.7.1 - jupyter_events=0.10.0 - jupyter_server=2.14.0 - jupyter_server_terminals=0.5.3 @@ -211,9 +215,11 @@ dependencies: - k8=0.2.5 - kaiju=1.10.1 - kiwisolver=1.4.5 +- kmer-jellyfish=1.1.12 +- kraken=1.1.1 - kraken2=2.1.3 -- krb5=1.20.1 -- lcms2=2.14 +- krb5=1.21.2 +- lcms2=2.16 - ld64_osx-64=711 - lerc=4.0.0 - libaec=1.1.3 @@ -224,60 +230,62 @@ dependencies: - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 -- libclang-cpp17=17.0.6 -- libcurl=7.88.1 -- libcxx=16.0.6 -- libdeflate=1.13 +- libclang-cpp18.1=18.1.5 +- libcurl=8.7.1 +- libcxx=17.0.6 +- libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 - libexpat=2.6.2 -- libffi=3.4.4 +- libffi=3.4.2 - libgd=2.3.3 - libgettextpo=0.22.5 - libgettextpo-devel=0.22.5 - libgfortran=5.0.0 -- libgfortran-devel_osx-64=11.4.0 +- libgfortran-devel_osx-64=12.3.0 - libgfortran5=13.2.0 -- libglib=2.78.1 +- libglib=2.80.0 +- libhwloc=2.10.0 - libiconv=1.17 - libidn2=2.3.7 - libintl=0.22.5 - libintl-devel=0.22.5 +- libjpeg-turbo=3.0.0 - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 -- libllvm17=17.0.6 +- libllvm18=18.1.5 - libnghttp2=1.58.0 -- libopenblas=0.3.25 +- libopenblas=0.3.27 - libpng=1.6.43 - libprotobuf=3.20.3 - libsodium=1.0.18 - libsqlite=3.45.3 - libssh2=1.11.0 -- libtiff=4.4.0 +- libtiff=4.6.0 - libunistring=0.9.10 +- libwebp=1.4.0 - libwebp-base=1.4.0 -- libxcb=1.13 -- libxml2=2.10.3 -- libxslt=1.1.37 +- libxcb=1.15 +- libxml2=2.12.6 +- libxslt=1.1.39 - libzlib=1.2.13 -- llvm-openmp=18.1.3 -- llvm-tools=17.0.6 -- llvmlite=0.41.1 -- lockfile=0.12.2 +- llvm-openmp=18.1.5 +- llvm-tools=18.1.5 +- llvmlite=0.42.0 - lp_solve=5.5.2.11 -- lxml=4.9.2 +- lxml=5.2.1 - lz4=4.3.3 - lz4-c=1.9.4 - make=4.3 - markupsafe=2.1.5 -- matplotlib=3.6.0 -- matplotlib-base=3.6.0 +- matplotlib=3.8.4 +- matplotlib-base=3.8.4 - matplotlib-inline=0.1.7 - megahit=1.2.9 - metabat2=2.15 - metaeuk=6.a5d39d9 -- metis=5.1.1 +- metis=5.1.0 - minimap2=2.28 - miniprot=0.13 - mistune=3.0.2 @@ -285,16 +293,15 @@ dependencies: - mpc=1.3.1 - mpfr=4.2.1 - mpi=1.0 -- msgpack-python=1.0.7 - munkres=1.1.4 - natsort=8.4.0 - nbclassic=1.0.0 - nbclient=0.10.0 -- nbconvert=7.16.3 -- nbconvert-core=7.16.3 -- nbconvert-pandoc=7.16.3 +- nbconvert=7.16.4 +- nbconvert-core=7.16.4 +- nbconvert-pandoc=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.0 +- ncbi-datasets-pylib=16.6.1 - ncbi-vdb=3.1.0 - ncurses=6.4.20240210 - nest-asyncio=1.6.0 @@ -302,26 +309,26 @@ dependencies: - nlopt=2.7.1 - notebook=6.5.5 - notebook-shim=0.2.4 -- numba=0.58.1 -- numpy=1.24.4 +- numba=0.59.1 +- numpy=1.26.4 - oniguruma=6.9.9 -- openjdk=21.0.3 -- openjpeg=2.5.0 -- openssl=3.2.1 +- openjdk=22.0.1 +- openjpeg=2.5.2 +- openssl=3.3.0 - overrides=7.7.0 - packaging=24.0 -- pandas=1.5.3 +- pandas=2.2.2 - pandoc=3.1.13 - pandocfilters=1.5.0 -- pango=1.50.14 +- pango=1.52.2 - paramiko=3.4.0 -- parsl=2023.12.4 +- parsl=2024.4.15 - parso=0.8.4 - pathlib=1.0.1 -- patsy=0.5.3 +- patsy=0.5.6 - pbzip2=1.1.13 - pcre=8.45 -- pcre2=10.40 +- pcre2=10.43 - perl=5.32.1 - perl-app-cpanminus=1.7047 - perl-archive-tar=2.40 @@ -360,7 +367,7 @@ dependencies: - perl-math-bezier=0.01 - perl-math-round=0.07 - perl-math-vecstat=0.08 -- perl-module-build=0.4232 +- perl-module-build=0.4234 - perl-module-build-tiny=0.039 - perl-module-implementation=0.09 - perl-module-runtime=0.016 @@ -389,17 +396,16 @@ dependencies: - pexpect=4.9.0 - pickleshare=0.7.5 - pigz=2.8 -- pillow=9.2.0 +- pillow=10.3.0 - pip=24.0 - pixman=0.43.4 - pkgutil-resolve-name=1.3.10 -- platformdirs=4.2.0 +- platformdirs=4.2.1 - pluggy=1.5.0 -- pooch=1.8.1 +- popt=1.16 - prodigal=2.6.3 - prometheus_client=0.20.0 - prompt-toolkit=3.0.42 -- prompt_toolkit=3.0.42 - protobuf=3.20.3 - psutil=5.9.8 - pthread-stubs=0.4 @@ -407,61 +413,62 @@ dependencies: - pure_eval=0.2.2 - pycparser=2.22 - pyfaidx=0.8.1.1 -- pygments=2.17.2 +- pygments=2.18.0 - pyjwt=2.8.0 - pynacl=1.5.0 - pynndescent=0.5.12 - pyobjc-core=10.2 - pyobjc-framework-cocoa=10.2 - pyparsing=3.1.2 -- pysam=0.21.0 - pysocks=1.7.1 -- pytest=8.1.1 -- python=3.8.19 +- pytest=8.2.0 +- python=3.9.19 - python-dateutil=2.8.2 - python-dotenv=1.0.1 - python-fastjsonschema=2.19.1 - python-isal=1.6.1 - python-json-logger=2.0.7 +- python-tzdata=2024.1 - python-zlib-ng=0.4.3 -- python_abi=3.8 +- python_abi=3.9 - pytz=2024.1 - pyvcf3=1.0.3 - pyyaml=6.0.1 - pyzmq=24.0.1 - pyzotero=1.5.18 -- q2-assembly=2024.5.0.dev0+2.gea8f24f -- q2-composition=2024.5.0.dev0 +- q2-assembly=2024.5.0.dev0+7.g1d87e60 +- q2-composition=2024.5.0.dev0+24.g33e8a9e - q2-cutadapt=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca -- q2-diversity-lib=2024.5.0.dev0 +- q2-diversity=2024.5.0.dev0+4.gf6b6556 +- q2-diversity-lib=2024.5.0.dev0+7.g7738698 - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fondue=2024.5.0.dev0+1.gbc30858 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 -- q2-moshpit=2024.5.0.dev0+7.gd45c699 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad +- q2-moshpit=2024.5.0.dev0+11.g2b3b03d - q2-mystery-stew=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c - q2-sapienns=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-taxa=2024.5.0.dev0+1.g127c848 +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 +- q2cli=2024.5.0.dev0+1.gafe71da +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa - quast=5.2.0 +- r-abind=1.4_5 - r-ade4=1.7_22 -- r-ape=5.7_1 +- r-ape=5.8 - r-argparser=0.7.2 - r-askpass=1.2.0 - r-assertthat=0.2.1 - r-backports=1.4.1 -- r-base=4.2.2 +- r-base=4.3.3 - r-base64enc=0.1_3 - r-beeswarm=0.4.0 - r-bh=1.84.0_0 @@ -471,11 +478,11 @@ dependencies: - r-bitops=1.0_7 - r-blob=1.2.4 - r-boot=1.3_30 -- r-brio=1.1.4 +- r-brio=1.1.5 - r-broom=1.0.5 - r-bslib=0.7.0 - r-cachem=1.0.8 -- r-cairo=1.6_0 +- r-cairo=1.6_2 - r-callr=3.7.6 - r-cellranger=1.1.0 - r-checkmate=2.3.1 @@ -485,16 +492,17 @@ dependencies: - r-cluster=2.1.6 - r-codetools=0.2_20 - r-colorspace=2.1_0 +- r-conflicted=1.2.0 - r-cpp11=0.4.7 - r-crayon=1.5.2 -- r-curl=4.3.3 +- r-curl=5.1.0 - r-cvxr=1.0_12 - r-data.table=1.15.2 - r-dbi=1.2.2 -- r-dbplyr=2.4.0 +- r-dbplyr=2.5.0 - r-deldir=2.0_4 - r-desc=1.4.3 -- r-desctools=0.99.51 +- r-desctools=0.99.54 - r-diffobj=0.3.5 - r-digest=0.6.35 - r-doparallel=1.0.17 @@ -505,9 +513,7 @@ dependencies: - r-e1071=1.7_14 - r-ecosolver=0.5.5 - r-ellipsis=0.3.2 -- r-emmeans=1.10.1 - r-energy=1.7_11 -- r-estimability=1.4.1 - r-evaluate=0.23 - r-exact=3.2 - r-expm=0.999_9 @@ -523,7 +529,7 @@ dependencies: - r-formatr=1.14 - r-formula=1.2_5 - r-frictionless=1.1.0 -- r-fs=1.6.3 +- r-fs=1.6.4 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 - r-gargle=1.5.2 @@ -531,7 +537,7 @@ dependencies: - r-generics=0.1.3 - r-getopt=1.20.4 - r-ggbeeswarm=0.7.2 -- r-ggplot2=3.5.0 +- r-ggplot2=3.5.1 - r-ggrastr=1.0.2 - r-ggrepel=0.9.5 - r-gld=2.6.6 @@ -541,8 +547,10 @@ dependencies: - r-googlesheets4=1.1.1 - r-gridextra=2.3 - r-gsl=2.1_8 -- r-gtable=0.3.4 +- r-gtable=0.3.5 +- r-gtools=3.9.5 - r-haven=2.5.4 +- r-here=1.0.1 - r-highr=0.10 - r-hmisc=5.1_2 - r-hms=1.1.3 @@ -551,7 +559,7 @@ dependencies: - r-htmlwidgets=1.6.4 - r-httr=1.4.7 - r-ids=1.0.1 -- r-igraph=1.4.2 +- r-igraph=2.0.3 - r-interp=1.1_6 - r-irlba=2.3.5.1 - r-isoband=0.2.7 @@ -571,7 +579,7 @@ dependencies: - r-lmom=3.0 - r-lubridate=1.9.3 - r-magrittr=2.0.3 -- r-mass=7.3_60.0.1 +- r-mass=7.3_60 - r-matrix=1.6_5 - r-matrixstats=1.3.0 - r-memoise=2.0.1 @@ -579,19 +587,20 @@ dependencies: - r-mime=0.12 - r-minqa=1.2.6 - r-modelr=0.1.11 +- r-multcomp=1.4_25 - r-munsell=0.5.1 - r-mvtnorm=1.2_4 - r-nlme=3.1_164 - r-nloptr=2.0.3 - r-nnet=7.3_19 - r-numderiv=2016.8_1.1 -- r-openssl=2.1.1 +- r-openssl=2.1.2 - r-optparse=1.7.5 - r-osqp=0.6.3.2 - r-permute=0.9_7 - r-pheatmap=1.0.12 - r-pillar=1.9.0 -- r-pixmap=0.4_12 +- r-pixmap=0.4_13 - r-pkgbuild=1.4.4 - r-pkgconfig=2.0.3 - r-pkgload=1.3.4 @@ -607,7 +616,7 @@ dependencies: - r-ps=1.7.6 - r-purrr=1.0.2 - r-r6=2.5.1 -- r-ragg=1.2.4 +- r-ragg=1.3.0 - r-rappdirs=0.3.3 - r-rbibutils=2.2.16 - r-rcolorbrewer=1.1_3 @@ -617,7 +626,8 @@ dependencies: - r-rcpphnsw=0.6.0 - r-rcppml=0.3.7 - r-rcppprogress=0.4.2 -- r-rcurl=1.98_1.12 +- r-rcpptoml=0.2.2 +- r-rcurl=1.98_1.14 - r-rdpack=2.6 - r-readr=2.1.5 - r-readxl=1.4.3 @@ -627,9 +637,10 @@ dependencies: - r-reprex=2.1.0 - r-reshape2=1.4.4 - r-restfulr=0.0.15 +- r-reticulate=1.36.0 - r-rjson=0.2.21 - r-rlang=1.1.3 -- r-rmarkdown=2.25 +- r-rmarkdown=2.26 - r-rmpfr=0.9_5 - r-rngtools=1.5.2 - r-rootsolve=1.8.2.4 @@ -640,26 +651,28 @@ dependencies: - r-rsvd=1.0.5 - r-rtsne=0.17 - r-rvest=1.0.4 +- r-sandwich=3.1_0 - r-sass=0.4.9 - r-scales=1.3.0 - r-scs=3.2.4 - r-selectr=0.4_2 - r-sitmo=2.0.2 - r-snow=0.4_4 -- r-sp=2.1_3 +- r-sp=2.1_4 - r-stringdist=0.9.10 -- r-stringi=1.7.12 +- r-stringi=1.8.4 - r-stringr=1.5.1 -- r-survival=3.5_8 +- r-survival=3.6_4 - r-sys=3.4.2 - r-systemfonts=1.0.5 - r-testthat=3.2.1.1 -- r-textshaping=0.3.6 +- r-textshaping=0.3.7 +- r-th.data=1.1_2 - r-tibble=3.2.1 - r-tidyr=1.3.1 -- r-tidyselect=1.2.0 +- r-tidyselect=1.2.1 - r-tidytree=0.4.6 -- r-tidyverse=1.3.2 +- r-tidyverse=2.0.0 - r-timechange=0.3.0 - r-tinytex=0.50 - r-tzdb=0.4.0 @@ -675,26 +688,28 @@ dependencies: - r-waldo=0.5.2 - r-withr=3.0.0 - r-xfun=0.43 -- r-xml=3.99_0.14 -- r-xml2=1.3.3 +- r-xml=3.99_0.16.1 +- r-xml2=1.3.6 - r-xtable=1.8_4 - r-yaml=2.3.8 - r-yulab.utils=0.1.4 +- r-zoo=1.8_12 - readline=8.2 -- referencing=0.34.0 +- referencing=0.35.1 - requests=2.31.0 - rescript=2024.5.0.dev0+3.g6e87cfe - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rpds-py=0.18.0 -- samtools=1.18 -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 +- rsync=3.3.0 +- samtools=1.20 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 - seaborn=0.12.2 - seaborn-base=0.12.2 - send2trash=1.8.3 -- sepp=4.3.10 +- sepp=4.4.0 - setproctitle=1.3.3 - setuptools=69.5.1 - sgmllib3k=1.0.0 @@ -706,15 +721,15 @@ dependencies: - spades=3.15.2 - sqlite=3.45.3 - stack_data=0.6.2 -- statsmodels=0.14.0 +- statsmodels=0.14.1 - suitesparse=5.10.1 - tapi=1100.0.11 - tar=1.34 -- tbb=2021.10.0 +- tbb=2021.12.0 - tblib=3.0.0 - terminado=0.18.1 -- threadpoolctl=3.4.0 -- tinycss2=1.2.1 +- threadpoolctl=3.5.0 +- tinycss2=1.3.0 - tk=8.6.13 - tktable=2.10 - toml=0.10.2 @@ -722,27 +737,28 @@ dependencies: - tomlkit=0.12.4 - toolz=0.12.1 - tornado=6.4 -- tqdm=4.66.2 +- tqdm=4.62.3 - traitlets=5.9.0 -- typeguard=2.13.3 +- typeguard=4.2.1 - types-python-dateutil=2.9.0.20240316 - typing-extensions=4.11.0 - typing_extensions=4.11.0 - typing_utils=0.1.0 +- tzdata=2024a - tzlocal=2.1 - ucsc-fatotwobit=366 - ucsc-twobitinfo=366 - umap-learn=0.5.4 - unicodedata2=15.1.0 - unifrac=1.3 -- unifrac-binaries=1.3.2 +- unifrac-binaries=1.4 - uri-template=1.3.0 - urllib3=1.26.18 -- vsearch=2.27.1 +- vsearch=2.28.1 - wcwidth=0.2.13 - webcolors=1.13 - webencodings=0.5.1 -- websocket-client=1.7.0 +- websocket-client=1.8.0 - wget=1.21.4 - wheel=0.43.0 - widgetsnbextension=4.0.10 @@ -750,21 +766,15 @@ dependencies: - xlsxwriter=3.1.9 - xmltodict=0.13.0 - xopen=2.0.1 -- xorg-kbproto=1.0.7 -- xorg-libice=1.0.10 -- xorg-libsm=1.2.3 -- xorg-libx11=1.8.4 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 -- xorg-libxt=1.3.0 -- xorg-xextproto=7.3.0 -- xorg-xproto=7.0.31 +- xxhash=0.8.2 - xz=5.2.6 - yaml=0.2.5 -- yq=3.4.1 +- yq=3.4.3 - zeromq=4.3.5 - zipp=3.17.0 - zlib=1.2.13 - zlib-ng=2.0.7 -- zstandard=0.22.0 -- zstd=1.5.5 +- zstandard=0.19.0 +- zstd=1.5.6 diff --git a/2024.5/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml b/2024.5/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml index 0565bab3..746ec3d1 100644 --- a/2024.5/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml +++ b/2024.5/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml @@ -8,7 +8,7 @@ dependencies: - _openmp_mutex=4.5 - _r-mutex=1.0.1 - _sysroot_linux-64_curr_repodata_hack=3 -- alsa-lib=1.2.8 +- alsa-lib=1.2.11 - altair=5.3.0 - anyio=4.3.0 - appdirs=1.4.4 @@ -16,7 +16,7 @@ dependencies: - argh=0.31.2 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 -- aria2=1.36.0 +- aria2=1.37.0 - arrow=1.3.0 - astor=0.8.1 - asttokens=2.4.1 @@ -24,73 +24,75 @@ dependencies: - attr=2.5.1 - attrs=23.2.0 - augustus=3.5.0 -- backcall=0.2.0 - bamtools=2.5.1 -- bbmap=39.01 +- bbmap=39.06 - bc=1.07.1 -- bcftools=1.17 +- bcftools=1.20 - bcrypt=4.1.2 - beautifulsoup4=4.12.3 - bedtools=2.31.1 - bibtexparser=1.4.1 - binutils_impl_linux-64=2.40 -- bioconductor-ancombc=2.0.1 -- bioconductor-annotationdbi=1.60.0 -- bioconductor-beachmat=2.14.0 -- bioconductor-biobase=2.58.0 -- bioconductor-biocbaseutils=1.0.0 -- bioconductor-biocfilecache=2.6.0 -- bioconductor-biocgenerics=0.44.0 -- bioconductor-biocio=1.8.0 -- bioconductor-biocneighbors=1.16.0 -- bioconductor-biocparallel=1.32.5 -- bioconductor-biocsingular=1.14.0 -- bioconductor-biomart=2.54.0 -- bioconductor-biomformat=1.26.0 -- bioconductor-biostrings=2.66.0 -- bioconductor-bsgenome=1.66.3 +- bioconductor-ancombc=2.4.0 +- bioconductor-annotationdbi=1.64.1 +- bioconductor-beachmat=2.18.0 +- bioconductor-biobase=2.62.0 +- bioconductor-biocbaseutils=1.4.0 +- bioconductor-biocfilecache=2.10.1 +- bioconductor-biocgenerics=0.48.1 +- bioconductor-biocio=1.12.0 +- bioconductor-biocneighbors=1.20.0 +- bioconductor-biocparallel=1.36.0 +- bioconductor-biocsingular=1.18.0 +- bioconductor-biomart=2.58.0 +- bioconductor-biomformat=1.30.0 +- bioconductor-biostrings=2.70.1 +- bioconductor-bluster=1.12.0 +- bioconductor-bsgenome=1.70.1 - bioconductor-data-packages=20231203 -- bioconductor-decipher=2.26.0 -- bioconductor-decontam=1.18.0 -- bioconductor-delayedarray=0.24.0 -- bioconductor-delayedmatrixstats=1.20.0 -- bioconductor-dirichletmultinomial=1.40.0 -- bioconductor-genomeinfodb=1.34.9 -- bioconductor-genomeinfodbdata=1.2.9 -- bioconductor-genomicalignments=1.34.0 -- bioconductor-genomicfeatures=1.50.2 -- bioconductor-genomicranges=1.50.0 -- bioconductor-iranges=2.32.0 -- bioconductor-keggrest=1.38.0 -- bioconductor-matrixgenerics=1.10.0 -- bioconductor-mia=1.6.0 -- bioconductor-multiassayexperiment=1.24.0 -- bioconductor-multtest=2.54.0 -- bioconductor-phyloseq=1.42.0 -- bioconductor-rhdf5=2.42.0 -- bioconductor-rhdf5filters=1.10.0 -- bioconductor-rhdf5lib=1.20.0 -- bioconductor-rhtslib=2.0.0 -- bioconductor-rsamtools=2.14.0 -- bioconductor-rtracklayer=1.58.0 -- bioconductor-s4vectors=0.36.0 -- bioconductor-scaledmatrix=1.6.0 -- bioconductor-scater=1.26.0 -- bioconductor-scuttle=1.8.0 -- bioconductor-singlecellexperiment=1.20.0 -- bioconductor-sparsematrixstats=1.10.0 -- bioconductor-structuralvariantannotation=1.13.0 -- bioconductor-summarizedexperiment=1.28.0 -- bioconductor-treeio=1.22.0 -- bioconductor-treesummarizedexperiment=2.6.0 -- bioconductor-variantannotation=1.44.0 -- bioconductor-xvector=0.38.0 -- bioconductor-zlibbioc=1.44.0 -- biom-format=2.1.14 -- biopython=1.78 +- bioconductor-decipher=2.30.0 +- bioconductor-decontam=1.22.0 +- bioconductor-delayedarray=0.28.0 +- bioconductor-delayedmatrixstats=1.24.0 +- bioconductor-dirichletmultinomial=1.44.0 +- bioconductor-genomeinfodb=1.38.1 +- bioconductor-genomeinfodbdata=1.2.11 +- bioconductor-genomicalignments=1.38.0 +- bioconductor-genomicfeatures=1.54.1 +- bioconductor-genomicranges=1.54.1 +- bioconductor-iranges=2.36.0 +- bioconductor-keggrest=1.42.0 +- bioconductor-matrixgenerics=1.14.0 +- bioconductor-mia=1.10.0 +- bioconductor-multiassayexperiment=1.28.0 +- bioconductor-multtest=2.58.0 +- bioconductor-phyloseq=1.46.0 +- bioconductor-rhdf5=2.46.1 +- bioconductor-rhdf5filters=1.14.1 +- bioconductor-rhdf5lib=1.24.0 +- bioconductor-rhtslib=2.4.0 +- bioconductor-rsamtools=2.18.0 +- bioconductor-rtracklayer=1.62.0 +- bioconductor-s4arrays=1.2.0 +- bioconductor-s4vectors=0.40.2 +- bioconductor-scaledmatrix=1.10.0 +- bioconductor-scater=1.30.1 +- bioconductor-scuttle=1.12.0 +- bioconductor-singlecellexperiment=1.24.0 +- bioconductor-sparsearray=1.2.2 +- bioconductor-sparsematrixstats=1.14.0 +- bioconductor-structuralvariantannotation=1.18.0 +- bioconductor-summarizedexperiment=1.32.0 +- bioconductor-treeio=1.26.0 +- bioconductor-treesummarizedexperiment=2.10.0 +- bioconductor-variantannotation=1.48.1 +- bioconductor-xvector=0.42.0 +- bioconductor-zlibbioc=1.48.0 +- biom-format=2.1.15 +- biopython=1.83 - blast=2.15.0 - bleach=6.1.0 -- boost-cpp=1.74.0 +- boost-cpp=1.78.0 - bowtie2=2.5.1 - bracken=2.9 - brotli=1.1.0 @@ -102,10 +104,9 @@ dependencies: - bzip2=1.0.8 - c-ares=1.28.1 - ca-certificates=2024.2.2 -- cachecontrol=0.14.0 - cached-property=1.5.2 - cached_property=1.5.2 -- cairo=1.16.0 +- cairo=1.18.0 - cdbtools=0.99 - certifi=2024.2.2 - cffi=1.16.0 @@ -115,9 +116,9 @@ dependencies: - colorama=0.4.6 - comm=0.2.2 - conda-pack=0.7.0 -- contourpy=1.1.1 -- cryptography=39.0.0 -- curl=7.87.0 +- contourpy=1.2.1 +- cryptography=42.0.6 +- curl=8.7.1 - cutadapt=4.8 - cycler=0.12.1 - dbus=1.13.6 @@ -132,14 +133,14 @@ dependencies: - eggnog-mapper=2.1.12 - emperor=1.0.4 - entrez-direct=21.6 -- entrezpy=2.1.3 +- entrezpy=2.1.2 - entrypoints=0.4 - exceptiongroup=1.2.0 - executing=2.0.1 - expat=2.6.2 - fastcluster=1.2.6 - feedparser=6.0.11 -- fftw=3.3.10 +- filelock=3.14.0 - flufl.lock=7.1 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 @@ -161,52 +162,51 @@ dependencies: - gffutils=0.10.1 - gfortran_impl_linux-64=13.2.0 - giflib=5.2.2 -- glib=2.78.1 -- glib-tools=2.78.1 +- glib=2.80.0 +- glib-tools=2.80.0 - glimmerhmm=3.0.4 -- globus-sdk=3.40.0 +- globus-sdk=3.41.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 - graphlib-backport=1.0.3 - gridss=2.13.2 - gsl=2.7 -- gst-plugins-base=1.21.3 -- gstreamer=1.21.3 -- gstreamer-orc=0.4.38 +- gst-plugins-base=1.24.3 +- gstreamer=1.24.3 - gxx_impl_linux-64=13.2.0 -- h5py=3.8.0 -- harfbuzz=6.0.0 -- hdf5=1.14.0 +- h5py=3.11.0 +- harfbuzz=8.4.0 +- hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.1b2 -- htslib=1.17 -- icu=70.1 +- htslib=1.20 +- icu=73.2 - idna=3.7 - ijson=3.2.3 - importlib-metadata=7.1.0 +- importlib-resources=6.4.0 +- importlib_metadata=7.1.0 - importlib_resources=6.4.0 - iniconfig=2.0.0 -- insilicoseq=1.5.4 +- insilicoseq=1.3.5 - interface_meta=1.3.0 - iow=1.0.5 - ipykernel=6.29.3 -- ipython=8.12.2 +- ipython=8.18.1 - ipython_genutils=0.2.0 - ipywidgets=8.1.2 - isa-l=2.31.0 - isoduration=20.11.0 -- jack=1.9.22 - jedi=0.19.1 - jinja2=3.1.3 -- joblib=1.4.0 -- jpeg=9e +- joblib=1.4.2 - jq=1.7.1 - jsonlines=3.0.0 - jsonpointer=2.4 -- jsonschema=4.21.1 +- jsonschema=4.22.0 - jsonschema-specifications=2023.12.1 -- jsonschema-with-format-nongpl=4.21.1 +- jsonschema-with-format-nongpl=4.22.0 - jupyter_client=7.4.9 - jupyter_core=5.7.2 - jupyter_events=0.10.0 @@ -220,9 +220,9 @@ dependencies: - keyutils=1.6.1 - kiwisolver=1.4.5 - kraken2=2.1.3 -- krb5=1.20.1 +- krb5=1.21.2 - lame=3.100 -- lcms2=2.14 +- lcms2=2.16 - ld_impl_linux-64=2.40 - lerc=4.0.0 - libaec=1.1.3 @@ -232,17 +232,16 @@ dependencies: - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 -- libcap=2.66 +- libcap=2.69 - libcblas=3.9.0 -- libclang=15.0.7 -- libclang13=15.0.7 +- libclang-cpp15=15.0.7 +- libclang13=18.1.5 - libcups=2.3.3 -- libcurl=7.87.0 -- libdb=6.2.32 -- libdeflate=1.13 +- libcurl=8.7.1 +- libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 -- libevent=2.1.10 +- libevent=2.1.12 - libexpat=2.6.2 - libffi=3.4.2 - libflac=1.4.3 @@ -254,56 +253,56 @@ dependencies: - libgettextpo-devel=0.22.5 - libgfortran-ng=13.2.0 - libgfortran5=13.2.0 -- libglib=2.78.1 +- libglib=2.80.0 - libgomp=13.2.0 -- libgpg-error=1.48 -- libhwloc=2.9.1 +- libgpg-error=1.49 +- libhwloc=2.10.0 - libiconv=1.17 - libidn2=2.3.7 +- libjpeg-turbo=3.0.0 - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 - libllvm15=15.0.7 -- libnghttp2=1.51.0 +- libllvm18=18.1.5 +- libnghttp2=1.58.0 - libnsl=2.0.1 - libogg=1.3.4 -- libopenblas=0.3.25 +- libopenblas=0.3.27 - libopus=1.3.1 - libpng=1.6.43 -- libpq=15.1 +- libpq=16.2 - libprotobuf=3.20.3 - libsanitizer=13.2.0 - libsndfile=1.2.2 - libsodium=1.0.18 - libsqlite=3.45.3 -- libssh2=1.10.0 +- libssh2=1.11.0 - libstdcxx-devel_linux-64=13.2.0 - libstdcxx-ng=13.2.0 -- libsystemd0=252 -- libtiff=4.4.0 -- libtool=2.4.7 -- libudev1=253 +- libsystemd0=255 +- libtiff=4.6.0 - libunistring=0.9.10 - libuuid=2.38.1 - libvorbis=1.3.7 +- libwebp=1.4.0 - libwebp-base=1.4.0 -- libxcb=1.13 +- libxcb=1.15 - libxcrypt=4.4.36 -- libxkbcommon=1.5.0 -- libxml2=2.10.3 -- libxslt=1.1.37 +- libxkbcommon=1.7.0 +- libxml2=2.12.6 +- libxslt=1.1.39 - libzlib=1.2.13 - llvm-openmp=8.0.1 -- llvmlite=0.41.1 -- lockfile=0.12.2 +- llvmlite=0.42.0 - lp_solve=5.5.2.11 -- lxml=4.9.2 +- lxml=5.2.1 - lz4=4.3.3 - lz4-c=1.9.4 - make=4.3 - markupsafe=2.1.5 -- matplotlib=3.6.0 -- matplotlib-base=3.6.0 +- matplotlib=3.8.4 +- matplotlib-base=3.8.4 - matplotlib-inline=0.1.7 - megahit=1.2.9 - metabat2=2.15 @@ -316,19 +315,18 @@ dependencies: - mpfr=4.2.1 - mpg123=1.32.6 - mpi=1.0 -- msgpack-python=1.0.7 - munkres=1.1.4 -- mysql-common=8.0.32 +- mysql-common=8.3.0 - mysql-connector-c=6.1.11 -- mysql-libs=8.0.32 +- mysql-libs=8.3.0 - natsort=8.4.0 - nbclassic=1.0.0 - nbclient=0.10.0 -- nbconvert=7.16.3 -- nbconvert-core=7.16.3 -- nbconvert-pandoc=7.16.3 +- nbconvert=7.16.4 +- nbconvert-core=7.16.4 +- nbconvert-pandoc=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.0 +- ncbi-datasets-pylib=16.6.1 - ncbi-vdb=3.1.0 - ncurses=6.4.20240210 - nest-asyncio=1.6.0 @@ -338,27 +336,27 @@ dependencies: - notebook-shim=0.2.4 - nspr=4.35 - nss=3.98 -- numba=0.58.1 -- numpy=1.24.4 +- numba=0.59.1 +- numpy=1.26.4 - oniguruma=6.9.9 -- openjdk=17.0.3 -- openjpeg=2.5.0 +- openjdk=22.0.1 +- openjpeg=2.5.2 - openmp=8.0.1 -- openssl=1.1.1w +- openssl=3.3.0 - overrides=7.7.0 - packaging=24.0 -- pandas=1.5.3 +- pandas=2.2.2 - pandoc=3.1.13 - pandocfilters=1.5.0 -- pango=1.50.14 +- pango=1.52.2 - paramiko=3.4.0 -- parsl=2023.12.4 +- parsl=2024.4.15 - parso=0.8.4 - pathlib=1.0.1 -- patsy=0.5.3 +- patsy=0.5.6 - pbzip2=1.1.13 - pcre=8.45 -- pcre2=10.40 +- pcre2=10.43 - perl=5.32.1 - perl-app-cpanminus=1.7047 - perl-archive-tar=2.40 @@ -397,7 +395,7 @@ dependencies: - perl-math-bezier=0.01 - perl-math-round=0.07 - perl-math-vecstat=0.08 -- perl-module-build=0.4232 +- perl-module-build=0.4234 - perl-module-build-tiny=0.039 - perl-module-implementation=0.09 - perl-module-runtime=0.016 @@ -426,82 +424,81 @@ dependencies: - pexpect=4.9.0 - pickleshare=0.7.5 - pigz=2.8 -- pillow=9.2.0 +- pillow=10.3.0 - pip=24.0 - pixman=0.43.2 - pkgutil-resolve-name=1.3.10 -- platformdirs=4.2.0 +- platformdirs=4.2.1 - pluggy=1.5.0 - ply=3.11 -- pooch=1.8.1 - prodigal=2.6.3 - prometheus_client=0.20.0 - prompt-toolkit=3.0.42 -- prompt_toolkit=3.0.42 - protobuf=3.20.3 - psutil=5.9.8 - pthread-stubs=0.4 - ptyprocess=0.7.0 -- pulseaudio=16.1 +- pulseaudio-client=17.0 - pure_eval=0.2.2 - pycparser=2.22 - pyfaidx=0.8.1.1 -- pygments=2.17.2 +- pygments=2.18.0 - pyjwt=2.8.0 - pynacl=1.5.0 - pynndescent=0.5.12 - pyparsing=3.1.2 -- pyqt=5.15.7 -- pyqt5-sip=12.11.0 -- pysam=0.21.0 +- pyqt=5.15.9 +- pyqt5-sip=12.12.2 - pysocks=1.7.1 -- pytest=8.1.1 -- python=3.8.15 +- pytest=8.2.0 +- python=3.9.19 - python-dateutil=2.8.2 - python-dotenv=1.0.1 - python-fastjsonschema=2.19.1 - python-isal=1.6.1 - python-json-logger=2.0.7 +- python-tzdata=2024.1 - python-zlib-ng=0.4.3 -- python_abi=3.8 +- python_abi=3.9 - pytz=2024.1 - pyvcf3=1.0.3 - pyyaml=6.0.1 - pyzmq=24.0.1 - pyzotero=1.5.18 -- q2-assembly=2024.5.0.dev0+2.gea8f24f -- q2-composition=2024.5.0.dev0 +- q2-assembly=2024.5.0.dev0+7.g1d87e60 +- q2-composition=2024.5.0.dev0+24.g33e8a9e - q2-cutadapt=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca -- q2-diversity-lib=2024.5.0.dev0 +- q2-diversity=2024.5.0.dev0+4.gf6b6556 +- q2-diversity-lib=2024.5.0.dev0+7.g7738698 - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fondue=2024.5.0.dev0+1.gbc30858 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 -- q2-moshpit=2024.5.0.dev0+7.gd45c699 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad +- q2-moshpit=2024.5.0.dev0+11.g2b3b03d - q2-mystery-stew=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c - q2-sapienns=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-taxa=2024.5.0.dev0+1.g127c848 +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 -- qt-main=5.15.6 +- q2cli=2024.5.0.dev0+1.gafe71da +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa +- qt-main=5.15.8 - quast=5.2.0 +- r-abind=1.4_5 - r-ade4=1.7_22 -- r-ape=5.7_1 +- r-ape=5.8 - r-argparser=0.7.2 - r-askpass=1.2.0 - r-assertthat=0.2.1 - r-backports=1.4.1 -- r-base=4.2.2 +- r-base=4.3.3 - r-base64enc=0.1_3 - r-beeswarm=0.4.0 - r-bh=1.84.0_0 @@ -511,11 +508,11 @@ dependencies: - r-bitops=1.0_7 - r-blob=1.2.4 - r-boot=1.3_30 -- r-brio=1.1.4 +- r-brio=1.1.5 - r-broom=1.0.5 - r-bslib=0.7.0 - r-cachem=1.0.8 -- r-cairo=1.6_0 +- r-cairo=1.6_2 - r-callr=3.7.6 - r-cellranger=1.1.0 - r-checkmate=2.3.0 @@ -525,16 +522,17 @@ dependencies: - r-cluster=2.1.6 - r-codetools=0.2_20 - r-colorspace=2.1_0 +- r-conflicted=1.2.0 - r-cpp11=0.4.7 - r-crayon=1.5.2 -- r-curl=4.3.3 +- r-curl=5.1.0 - r-cvxr=1.0_12 - r-data.table=1.15.2 - r-dbi=1.2.2 -- r-dbplyr=2.4.0 +- r-dbplyr=2.5.0 - r-deldir=2.0_4 - r-desc=1.4.3 -- r-desctools=0.99.51 +- r-desctools=0.99.54 - r-diffobj=0.3.5 - r-digest=0.6.35 - r-doparallel=1.0.17 @@ -545,9 +543,7 @@ dependencies: - r-e1071=1.7_14 - r-ecosolver=0.5.5 - r-ellipsis=0.3.2 -- r-emmeans=1.10.1 - r-energy=1.7_11 -- r-estimability=1.4.1 - r-evaluate=0.23 - r-exact=3.2 - r-expm=0.999_9 @@ -563,7 +559,7 @@ dependencies: - r-formatr=1.14 - r-formula=1.2_5 - r-frictionless=1.1.0 -- r-fs=1.6.3 +- r-fs=1.6.4 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 - r-gargle=1.5.2 @@ -571,7 +567,7 @@ dependencies: - r-generics=0.1.3 - r-getopt=1.20.4 - r-ggbeeswarm=0.7.2 -- r-ggplot2=3.5.0 +- r-ggplot2=3.5.1 - r-ggrastr=1.0.2 - r-ggrepel=0.9.5 - r-gld=2.6.6 @@ -581,8 +577,10 @@ dependencies: - r-googlesheets4=1.1.1 - r-gridextra=2.3 - r-gsl=2.1_8 -- r-gtable=0.3.4 +- r-gtable=0.3.5 +- r-gtools=3.9.5 - r-haven=2.5.4 +- r-here=1.0.1 - r-highr=0.10 - r-hmisc=5.1_2 - r-hms=1.1.3 @@ -591,7 +589,7 @@ dependencies: - r-htmlwidgets=1.6.4 - r-httr=1.4.7 - r-ids=1.0.1 -- r-igraph=1.4.2 +- r-igraph=2.0.3 - r-interp=1.1_6 - r-irlba=2.3.5.1 - r-isoband=0.2.7 @@ -611,7 +609,7 @@ dependencies: - r-lmom=3.0 - r-lubridate=1.9.3 - r-magrittr=2.0.3 -- r-mass=7.3_60.0.1 +- r-mass=7.3_60 - r-matrix=1.6_5 - r-matrixstats=1.3.0 - r-memoise=2.0.1 @@ -619,19 +617,20 @@ dependencies: - r-mime=0.12 - r-minqa=1.2.6 - r-modelr=0.1.11 +- r-multcomp=1.4_25 - r-munsell=0.5.1 - r-mvtnorm=1.2_4 - r-nlme=3.1_164 - r-nloptr=2.0.3 - r-nnet=7.3_19 - r-numderiv=2016.8_1.1 -- r-openssl=2.0.5 +- r-openssl=2.1.2 - r-optparse=1.7.5 - r-osqp=0.6.3.2 - r-permute=0.9_7 - r-pheatmap=1.0.12 - r-pillar=1.9.0 -- r-pixmap=0.4_12 +- r-pixmap=0.4_13 - r-pkgbuild=1.4.4 - r-pkgconfig=2.0.3 - r-pkgload=1.3.4 @@ -647,7 +646,7 @@ dependencies: - r-ps=1.7.6 - r-purrr=1.0.2 - r-r6=2.5.1 -- r-ragg=1.2.4 +- r-ragg=1.3.0 - r-rappdirs=0.3.3 - r-rbibutils=2.2.16 - r-rcolorbrewer=1.1_3 @@ -657,7 +656,8 @@ dependencies: - r-rcpphnsw=0.6.0 - r-rcppml=0.3.7 - r-rcppprogress=0.4.2 -- r-rcurl=1.98_1.10 +- r-rcpptoml=0.2.2 +- r-rcurl=1.98_1.14 - r-rdpack=2.6 - r-readr=2.1.5 - r-readxl=1.4.3 @@ -667,9 +667,10 @@ dependencies: - r-reprex=2.1.0 - r-reshape2=1.4.4 - r-restfulr=0.0.15 +- r-reticulate=1.36.0 - r-rjson=0.2.21 - r-rlang=1.1.3 -- r-rmarkdown=2.25 +- r-rmarkdown=2.26 - r-rmpfr=0.9_5 - r-rngtools=1.5.2 - r-rootsolve=1.8.2.4 @@ -680,26 +681,28 @@ dependencies: - r-rsvd=1.0.5 - r-rtsne=0.17 - r-rvest=1.0.4 +- r-sandwich=3.1_0 - r-sass=0.4.9 - r-scales=1.3.0 - r-scs=3.2.4 - r-selectr=0.4_2 - r-sitmo=2.0.2 - r-snow=0.4_4 -- r-sp=2.1_3 +- r-sp=2.1_4 - r-stringdist=0.9.10 -- r-stringi=1.7.12 +- r-stringi=1.8.4 - r-stringr=1.5.1 -- r-survival=3.5_8 +- r-survival=3.6_4 - r-sys=3.4.2 - r-systemfonts=1.0.5 - r-testthat=3.2.1.1 -- r-textshaping=0.3.6 +- r-textshaping=0.3.7 +- r-th.data=1.1_2 - r-tibble=3.2.1 - r-tidyr=1.3.1 -- r-tidyselect=1.2.0 +- r-tidyselect=1.2.1 - r-tidytree=0.4.6 -- r-tidyverse=1.3.2 +- r-tidyverse=2.0.0 - r-timechange=0.3.0 - r-tinytex=0.50 - r-tzdb=0.4.0 @@ -715,13 +718,14 @@ dependencies: - r-waldo=0.5.2 - r-withr=3.0.0 - r-xfun=0.43 -- r-xml=3.99_0.14 -- r-xml2=1.3.3 +- r-xml=3.99_0.16.1 +- r-xml2=1.3.6 - r-xtable=1.8_4 - r-yaml=2.3.8 - r-yulab.utils=0.1.4 +- r-zoo=1.8_12 - readline=8.2 -- referencing=0.34.0 +- referencing=0.35.1 - repeatmasker=4.1.5 - requests=2.31.0 - rescript=2024.5.0.dev0+3.g6e87cfe @@ -729,15 +733,15 @@ dependencies: - rfc3986-validator=0.1.1 - rmblast=2.14.1 - rpds-py=0.18.0 -- samtools=1.18 -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 +- samtools=1.20 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 - seaborn=0.12.2 - seaborn-base=0.12.2 - sed=4.8 - send2trash=1.8.3 -- sepp=4.3.10 +- sepp=4.4.0 - setproctitle=1.3.3 - setuptools=69.5.1 - sgmllib3k=1.0.0 @@ -749,15 +753,15 @@ dependencies: - spades=3.15.2 - sqlite=3.45.3 - stack_data=0.6.2 -- statsmodels=0.14.0 +- statsmodels=0.14.1 - suitesparse=5.10.1 - sysroot_linux-64=2.17 - tar=1.34 -- tbb=2021.9.0 +- tbb=2021.12.0 - tblib=3.0.0 - terminado=0.18.1 -- threadpoolctl=3.4.0 -- tinycss2=1.2.1 +- threadpoolctl=3.5.0 +- tinycss2=1.3.0 - tk=8.6.13 - tktable=2.10 - toml=0.10.2 @@ -765,29 +769,30 @@ dependencies: - tomlkit=0.12.4 - toolz=0.12.1 - tornado=6.4 -- tqdm=4.66.2 +- tqdm=4.62.3 - traitlets=5.9.0 - trf=4.09.1 -- typeguard=2.13.3 +- typeguard=4.2.1 - types-python-dateutil=2.9.0.20240316 - typing-extensions=4.11.0 - typing_extensions=4.11.0 - typing_utils=0.1.0 +- tzdata=2024a - tzlocal=2.1 -- ucsc-fatotwobit=447 -- ucsc-twobitinfo=447 +- ucsc-fatotwobit=455 +- ucsc-twobitinfo=455 - umap-learn=0.5.4 - unicodedata2=15.1.0 - unifrac=1.3 -- unifrac-binaries=1.3.2 +- unifrac-binaries=1.4 - uri-template=1.3.0 - urllib3=1.26.18 -- vsearch=2.27.1 +- vsearch=2.28.1 - wcwidth=0.2.13 - webcolors=1.13 - webencodings=0.5.1 -- websocket-client=1.7.0 -- wget=1.20.3 +- websocket-client=1.8.0 +- wget=1.21.4 - wheel=0.43.0 - widgetsnbextension=4.0.10 - wrapt=1.16.0 @@ -796,34 +801,35 @@ dependencies: - xcb-util-keysyms=0.4.0 - xcb-util-renderutil=0.3.9 - xcb-util-wm=0.4.1 -- xkeyboard-config=2.38 +- xkeyboard-config=2.41 - xlsxwriter=3.1.9 - xmltodict=0.13.0 - xopen=2.0.1 - xorg-fixesproto=5.0 - xorg-inputproto=2.3.2 - xorg-kbproto=1.0.7 -- xorg-libice=1.0.10 -- xorg-libsm=1.2.3 -- xorg-libx11=1.8.4 +- xorg-libice=1.1.1 +- xorg-libsm=1.2.4 +- xorg-libx11=1.8.9 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - xorg-libxext=1.3.4 - xorg-libxfixes=5.0.3 - xorg-libxi=1.7.10 -- xorg-libxrender=0.9.10 +- xorg-libxrender=0.9.11 - xorg-libxt=1.3.0 - xorg-libxtst=1.2.3 - xorg-recordproto=1.14.2 - xorg-renderproto=0.11.1 - xorg-xextproto=7.3.0 +- xorg-xf86vidmodeproto=2.3.1 - xorg-xproto=7.0.31 - xz=5.2.6 - yaml=0.2.5 -- yq=3.4.1 +- yq=3.4.3 - zeromq=4.3.5 - zipp=3.17.0 - zlib=1.2.13 - zlib-ng=2.0.7 -- zstandard=0.22.0 -- zstd=1.5.5 +- zstandard=0.19.0 +- zstd=1.5.6 diff --git a/2024.5/metagenome/passed/seed-environment-conda.yml b/2024.5/metagenome/passed/seed-environment-conda.yml index 482c3187..d4260686 100644 --- a/2024.5/metagenome/passed/seed-environment-conda.yml +++ b/2024.5/metagenome/passed/seed-environment-conda.yml @@ -6,8 +6,8 @@ channels: dependencies: - biom-format=2.1.15 - biopython=1.83 -- busco=5.5.0 - bowtie2=2.5.1 +- busco=5.5.0 - entrezpy=2.1.2 - h5py=3.11.0 - hdf5=1.14.3 @@ -19,30 +19,30 @@ dependencies: - patsy=0.5.6 - python=3.9.19 - python_abi=3.9 -- q2-assembly=2024.5.0.dev0+2.gea8f24f -- q2-composition=2024.5.0.dev0 +- q2-assembly=2024.5.0.dev0+7.g1d87e60 +- q2-composition=2024.5.0.dev0+24.g33e8a9e - q2-cutadapt=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity-lib=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca +- q2-diversity-lib=2024.5.0.dev0+7.g7738698 +- q2-diversity=2024.5.0.dev0+4.gf6b6556 - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fondue=2024.5.0.dev0+1.gbc30858 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 -- q2-moshpit=2024.5.0.dev0+7.gd45c699 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad +- q2-moshpit=2024.5.0.dev0+11.g2b3b03d - q2-mystery-stew=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c - q2-sapienns=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-taxa=2024.5.0.dev0+1.g127c848 +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 +- q2cli=2024.5.0.dev0+1.gafe71da +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa - r-base=4.3.3 - r-reticulate=1.36.0 - rescript=2024.5.0.dev0+3.g6e87cfe diff --git a/2024.5/metagenome/staged/seed-environment-conda.yml b/2024.5/metagenome/staged/seed-environment-conda.yml index 1d5bb0c8..f514ddfa 100644 --- a/2024.5/metagenome/staged/seed-environment-conda.yml +++ b/2024.5/metagenome/staged/seed-environment-conda.yml @@ -4,50 +4,57 @@ channels: - bioconda - defaults dependencies: -- biom-format=2.1.14 +- biom-format=2.1.15 +- biopython=1.83 - bowtie2=2.5.1 -- h5py=3.8.0 -- hdf5=1.14.0 -- matplotlib=3.6.0 +- busco=5.5.0 +- entrezpy=2.1.2 +- h5py=3.11.0 +- hdf5=1.14.3 +- matplotlib=3.8.4 - notebook=6.5.5 -- numpy=1.24.4 -- pandas=1.5.3 -- parsl=2023.12.04 -- patsy=0.5.3 -- python=3.8 -- q2-assembly=2024.5.0.dev0+2.gea8f24f -- q2-composition=2024.5.0.dev0 +- numpy=1.26.4 +- pandas=2.2.2 +- parsl=2024.4.15 +- patsy=0.5.6 +- python=3.9.19 +- python_abi=3.9 +- q2-assembly=2024.5.0.dev0+7.g1d87e60 +- q2-composition=2024.5.0.dev0+24.g33e8a9e - q2-cutadapt=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity-lib=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca +- q2-diversity-lib=2024.5.0.dev0+7.g7738698 +- q2-diversity=2024.5.0.dev0+4.gf6b6556 - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fondue=2024.5.0.dev0+1.gbc30858 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 -- q2-moshpit=2024.5.0.dev0+7.gd45c699 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad +- q2-moshpit=2024.5.0.dev0+11.g2b3b03d - q2-mystery-stew=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c - q2-sapienns=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 +- q2-taxa=2024.5.0.dev0+1.g127c848 - q2-types-genomics=2023.11.0.dev0+8.g3b993ed -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 -- r-base=4.2.2 +- q2cli=2024.5.0.dev0+1.gafe71da +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa +- r-base=4.3.3 +- r-reticulate=1.36.0 - rescript=2024.5.0.dev0+3.g6e87cfe -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 - seaborn=0.12.2 +- sepp=4.4.0 +- tqdm=4.62.3 - umap-learn=0.5.4 -- unifrac-binaries=1.3.2 +- unifrac-binaries=1.4 - unifrac=1.3 extras: variant_override: