diff --git a/2025.4/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml b/2025.4/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml index 895ba9f9..75e012d5 100644 --- a/2025.4/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml +++ b/2025.4/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml @@ -5,25 +5,26 @@ channels: dependencies: - _r-mutex=1.0.1 - alabaster=1.0.0 -- altair=5.4.1 -- anyio=4.6.2.post1 +- altair=5.5.0 +- annotated-types=0.7.0 +- anyio=4.7.0 - appdirs=1.4.4 - appnope=0.1.4 -- argcomplete=3.5.1 +- argcomplete=3.5.2 - argh=0.31.3 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - aria2=1.37.0 - arrow=1.3.0 - astor=0.8.1 -- asttokens=2.4.1 +- asttokens=3.0.0 - atpublic=5.0 - attrs=24.2.0 - augustus=3.5.0 -- babel=2.14.0 +- babel=2.16.0 - bamtools=2.5.2 -- bbmap=39.10 -- bcrypt=4.2.0 +- bbmap=39.13 +- bcrypt=4.2.1 - beautifulsoup4=4.12.3 - bedtools=2.31.1 - bibtexparser=1.4.2 @@ -93,11 +94,11 @@ dependencies: - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 -- busco=5.8.0 +- busco=5.8.2 - bwa=0.7.18 -- bwidget=1.9.14 +- bwidget=1.10.1 - bzip2=1.0.8 -- c-ares=1.34.2 +- c-ares=1.34.3 - ca-certificates=2024.8.30 - cached-property=1.5.2 - cached_property=1.5.2 @@ -109,28 +110,28 @@ dependencies: - cffi=1.17.1 - charset-normalizer=3.4.0 - 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=18.1.7 +- clang-18=18.1.7 +- clang_impl_osx-64=18.1.7 +- clang_osx-64=18.1.7 +- clangxx=18.1.7 +- clangxx_impl_osx-64=18.1.7 +- clangxx_osx-64=18.1.7 - click=8.1.7 - clustalw=2.1 - colorama=0.4.6 - comm=0.2.2 - commonmark=0.9.1 -- compiler-rt=17.0.6 -- compiler-rt_osx-64=17.0.6 +- compiler-rt=18.1.7 +- compiler-rt_osx-64=18.1.7 - conda-pack=0.7.0 -- contourpy=1.3.0 -- cryptography=43.0.3 +- contourpy=1.3.1 +- cryptography=44.0.0 - curl=8.8.0 - cutadapt=4.9 - cycler=0.12.1 - cython=3.0.11 -- debugpy=1.8.7 +- debugpy=1.8.10 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=5.0.1 @@ -148,7 +149,7 @@ dependencies: - entrypoints=0.4 - exceptiongroup=1.2.2 - executing=2.1.0 -- expat=2.6.3 +- expat=2.6.4 - fastcluster=1.2.6 - fasttree=2.1.11 - feedparser=6.0.11 @@ -161,7 +162,7 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.54.1 +- fonttools=4.55.3 - formulaic=1.0.2 - fqdn=1.5.1 - freetype=2.12.1 @@ -176,19 +177,22 @@ dependencies: - gfortran_osx-64=12.3.0 - giflib=5.2.2 - glimmerhmm=3.0.4 -- globus-sdk=3.46.0 +- globus-sdk=3.49.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 - graphlib-backport=1.0.3 - gridss=2.11.1 - gsl=2.7 +- h2=4.1.0 - h5py=3.11.0 - harfbuzz=8.5.0 - hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.4 +- hpack=4.0.0 - htslib=1.21 +- hyperframe=6.0.1 - icu=73.2 - idna=3.10 - ijson=3.3.0 @@ -206,7 +210,7 @@ dependencies: - isa-l=2.31.0 - isl=0.26 - isoduration=20.11.0 -- jedi=0.19.1 +- jedi=0.19.2 - jinja2=3.1.4 - joblib=1.4.2 - jq=1.7.1 @@ -243,14 +247,13 @@ dependencies: - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 -- libclang-cpp17=17.0.6 +- libclang-cpp18.1=18.1.7 - libcurl=8.8.0 -- libcxx=19.1.3 -- libcxx-devel=17.0.6 +- libcxx=19.1.5 - libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 -- libexpat=2.6.3 +- libexpat=2.6.4 - libffi=3.4.2 - libgd=2.3.3 - libgettextpo=0.22.5 @@ -259,7 +262,7 @@ dependencies: - libgfortran-devel_osx-64=12.3.0 - libgfortran5=13.2.0 - libglib=2.80.2 -- libhwloc=2.11.1 +- libhwloc=2.11.2 - libiconv=1.17 - libidn2=2.3.7 - libintl=0.22.5 @@ -268,10 +271,12 @@ dependencies: - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 -- libllvm17=17.0.6 +- libllvm18=18.1.7 +- liblzma=5.6.3 +- liblzma-devel=5.6.3 - libnghttp2=1.58.0 - libopenblas=0.3.28 -- libopenssl-static=3.3.2 +- libopenssl-static=3.4.0 - libpng=1.6.43 - libprotobuf=3.20.3 - libsodium=1.0.18 @@ -286,13 +291,13 @@ dependencies: - libxml2=2.12.7 - libxslt=1.1.39 - libzlib=1.2.13 -- llvm-openmp=19.1.3 -- llvm-tools=17.0.6 +- llvm-openmp=19.1.5 +- llvm-tools=18.1.7 - llvmlite=0.42.0 - lp_solve=5.5.2.11 - lxml=5.2.2 - lz4=4.3.3 -- lz4-c=1.9.4 +- lz4-c=1.10.0 - mafft=7.526 - make=4.4.1 - markupsafe=3.0.2 @@ -306,20 +311,22 @@ dependencies: - minimap2=2.28 - miniprot=0.13 - mistune=3.0.2 -- mmseqs2=15.6f452 +- mmseqs2=16.747c6 - mpc=1.3.1 - mpfr=4.2.1 - mpi=1.0.1 +- multimethod=1.9.1 - munkres=1.1.4 - muscle=3.8.1551 +- mypy_extensions=1.0.0 - mysql-connector-c=6.1.11 -- narwhals=1.12.1 +- narwhals=1.17.0 - natsort=8.4.0 - nbclassic=1.1.0 -- nbclient=0.10.0 +- nbclient=0.10.1 - nbconvert-core=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.1 +- ncbi-datasets-pylib=14.25.1 - ncbi-vdb=3.1.1 - ncurses=6.5 - nest-asyncio=1.6.0 @@ -332,11 +339,13 @@ dependencies: - oniguruma=6.9.9 - openjdk=22.0.1 - openjpeg=2.5.2 -- openssl=3.3.2 +- openssl=3.4.0 - overrides=7.7.0 -- packaging=24.1 +- packaging=24.2 - pandas=2.2.2 -- pandoc=3.5 +- pandera=0.21.1 +- pandera-base=0.21.1 +- pandoc=3.6 - pandocfilters=1.5.0 - pango=1.54.0 - parameterized=0.9.0 @@ -394,12 +403,12 @@ dependencies: - perl-number-format=1.76 - perl-parallel-forkmanager=2.03 - perl-params-validate=1.31 -- perl-parent=0.242 +- perl-parent=0.243 - perl-pathtools=3.75 - perl-readonly=2.05 - perl-regexp-common=2017060201 - perl-role-tiny=2.002004 -- perl-scalar-list-utils=1.63 +- perl-scalar-list-utils=1.68 - perl-set-intspan=1.19 - perl-statistics-basic=1.6611 - perl-storable=3.15 @@ -417,7 +426,7 @@ dependencies: - pigz=2.8 - pillow=10.3.0 - pip=24.3.1 -- pixman=0.43.4 +- pixman=0.44.2 - pkgutil-resolve-name=1.3.10 - platformdirs=4.3.6 - pluggy=1.5.0 @@ -425,7 +434,7 @@ dependencies: - popt=1.16 - prank=170427 - prodigal=2.6.3 -- prometheus_client=0.21.0 +- prometheus_client=0.21.1 - prompt-toolkit=3.0.48 - protobuf=3.20.3 - psutil=6.1.0 @@ -433,23 +442,25 @@ dependencies: - ptyprocess=0.7.0 - pure_eval=0.2.3 - pycparser=2.22 +- pydantic=2.10.3 +- pydantic-core=2.27.1 - pyfaidx=0.8.1.3 - pygments=2.18.0 - pyhmmer=0.10.15 -- pyjwt=2.9.0 +- pyjwt=2.10.1 - pymongo=4.10.1 - pynacl=1.5.0 - pynndescent=0.5.13 -- pyobjc-core=10.3.1 -- pyobjc-framework-cocoa=10.3.1 +- pyobjc-core=10.3.2 +- pyobjc-framework-cocoa=10.3.2 - pyparsing=3.2.0 - pysam=0.22.1 - pysocks=1.7.1 -- pytest=8.3.3 +- pytest=8.3.4 - python=3.10.14 -- python-dateutil=2.8.2 +- python-dateutil=2.9.0.post0 - python-dotenv=1.0.1 -- python-fastjsonschema=2.20.0 +- python-fastjsonschema=2.21.1 - python-isal=1.7.1 - python-json-logger=2.0.7 - python-tzdata=2024.2 @@ -459,8 +470,9 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- pyzotero=1.5.25 -- q2-assembly=2025.4.0.dev0 +- pyzotero=1.5.27 +- q2-alignment=2025.4.0.dev0 +- q2-assembly=2025.4.0.dev0+2.g3a645f4 - q2-composition=2025.4.0.dev0 - q2-cutadapt=2025.4.0.dev0 - q2-demux=2025.4.0.dev0 @@ -468,11 +480,11 @@ dependencies: - q2-diversity-lib=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 -- q2-fondue=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 +- q2-fondue=2025.4.0.dev0+1.g4bc2add - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 -- q2-moshpit=2025.4.0.dev0 +- q2-moshpit=2025.4.0.dev0+9.gf09a381 - q2-mystery-stew=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 - q2-quality-filter=2025.4.0.dev0 @@ -481,12 +493,12 @@ dependencies: - q2-sourmash=2025.4.0.dev0 - q2-taxa=2025.4.0.dev0 - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0 +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+1.gab00603 -- quast=5.2.0 +- qiime2=2025.4.0.dev0+5.gdb970dd +- quast=5.3.0 - r-abind=1.4_5 - r-ade4=1.7_22 - r-ape=5.8 @@ -499,7 +511,7 @@ dependencies: - r-beeswarm=0.4.0 - r-bh=1.84.0_0 - r-bibtex=0.5.1 -- r-bit=4.5.0 +- r-bit=4.5.0.1 - r-bit64=4.5.2 - r-bitops=1.0_9 - r-blob=1.2.4 @@ -515,20 +527,20 @@ dependencies: - r-class=7.3_22 - r-cli=3.6.3 - r-clipr=0.8.0 -- r-cluster=2.1.6 +- r-cluster=2.1.7 - r-codetools=0.2_20 - r-colorspace=2.1_1 - r-conflicted=1.2.0 -- r-cpp11=0.5.0 +- r-cpp11=0.5.1 - r-crayon=1.5.3 -- r-curl=5.2.1 -- r-cvxr=1.0_13 +- r-curl=6.0.1 +- r-cvxr=1.0_15 - r-data.table=1.15.2 - r-dbi=1.2.3 - r-dbplyr=2.5.0 - r-deldir=2.0_4 - r-desc=1.4.3 -- r-desctools=0.99.57 +- r-desctools=0.99.58 - r-diffobj=0.3.5 - r-digest=0.6.37 - r-doparallel=1.0.17 @@ -548,7 +560,7 @@ dependencies: - r-fastmap=1.2.0 - r-filelock=1.0.3 - r-fnn=1.1.4.1 -- r-fontawesome=0.5.2 +- r-fontawesome=0.5.3 - r-forcats=1.0.0 - r-foreach=1.5.2 - r-foreign=0.8_87 @@ -578,13 +590,13 @@ dependencies: - r-haven=2.5.4 - r-here=1.0.1 - r-highr=0.11 -- r-hmisc=5.2_0 +- r-hmisc=5.2_1 - r-hms=1.1.3 - r-htmltable=2.4.3 - r-htmltools=0.5.8.1 - r-htmlwidgets=1.6.4 - r-httr=1.4.7 -- r-httr2=1.0.5 +- r-httr2=1.0.7 - r-ids=1.0.1 - r-igraph=2.0.3 - r-interp=1.1_6 @@ -594,7 +606,7 @@ dependencies: - r-jpeg=0.1_10 - r-jquerylib=0.1.4 - r-jsonlite=1.8.9 -- r-knitr=1.48 +- r-knitr=1.49 - r-labeling=0.4.3 - r-lambda.r=1.2.4 - r-lattice=0.22_6 @@ -604,7 +616,7 @@ dependencies: - r-lme4=1.1_35.5 - r-lmertest=3.1_3 - r-lmom=3.2 -- r-lubridate=1.9.3 +- r-lubridate=1.9.4 - r-magrittr=2.0.3 - r-mass=7.3_60.0.1 - r-matrix=1.6_5 @@ -616,7 +628,7 @@ dependencies: - r-modelr=0.1.11 - r-multcomp=1.4_26 - r-munsell=0.5.1 -- r-mvtnorm=1.3_1 +- r-mvtnorm=1.3_2 - r-nlme=3.1_165 - r-nloptr=2.1.1 - r-nnet=7.3_19 @@ -647,7 +659,7 @@ dependencies: - r-rappdirs=0.3.3 - r-rbibutils=2.3 - r-rcolorbrewer=1.1_3 -- r-rcpp=1.0.13 +- r-rcpp=1.0.13_1 - r-rcppannoy=0.0.22 - r-rcppeigen=0.3.4.0.2 - r-rcpphnsw=0.6.0 @@ -655,7 +667,7 @@ dependencies: - r-rcppprogress=0.4.2 - r-rcpptoml=0.2.2 - r-rcurl=1.98_1.16 -- r-rdpack=2.6.1 +- r-rdpack=2.6.2 - r-readr=2.1.5 - r-readxl=1.4.3 - r-registry=0.5_1 @@ -667,13 +679,13 @@ dependencies: - r-reticulate=1.36.0 - r-rjson=0.2.23 - r-rlang=1.1.4 -- r-rmarkdown=2.28 -- r-rmpfr=0.9_5 +- r-rmarkdown=2.29 +- r-rmpfr=1.0_0 - r-rngtools=1.5.2 - r-rootsolve=1.8.2.4 - r-rpart=4.1.23 - r-rprojroot=2.0.4 -- r-rsqlite=2.3.7 +- r-rsqlite=2.3.9 - r-rstudioapi=0.17.1 - r-rsvd=1.0.5 - r-rtsne=0.17 @@ -686,7 +698,7 @@ dependencies: - r-sitmo=2.0.2 - r-snow=0.4_4 - r-sp=2.1_4 -- r-stringdist=0.9.12 +- r-stringdist=0.9.14 - r-stringi=1.8.4 - r-stringr=1.5.1 - r-survival=3.7_0 @@ -701,7 +713,7 @@ dependencies: - r-tidytree=0.4.6 - r-tidyverse=2.0.0 - r-timechange=0.3.0 -- r-tinytex=0.53 +- r-tinytex=0.54 - r-tzdb=0.4.0 - r-utf8=1.2.4 - r-uuid=1.2_1 @@ -712,26 +724,27 @@ dependencies: - r-viridis=0.6.5 - r-viridislite=0.4.2 - r-vroom=1.6.5 -- r-waldo=0.5.3 +- r-waldo=0.6.1 - r-withr=3.0.2 -- r-xfun=0.48 +- r-xfun=0.49 - r-xml=3.99_0.17 - r-xml2=1.3.6 - r-xtable=1.8_4 - r-yaml=2.3.10 -- r-yulab.utils=0.1.7 +- r-yulab.utils=0.1.8 - r-zoo=1.8_12 - raxml=8.2.13 - readline=8.2 - recommonmark=0.7.1 - referencing=0.35.1 - requests=2.32.3 -- rescript=2025.4.0.dev0 +- rescript=2025.4.0.dev0+2.g16a48fa - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 -- rpds-py=0.20.0 +- rnanorm=2.1.0 +- rpds-py=0.22.3 - rpsbproc=0.5.0 -- rsync=3.3.0 +- rsync=3.1.3 - samtools=1.21 - scikit-bio=0.6.0 - scikit-learn=1.4.2 @@ -742,17 +755,17 @@ dependencies: - send2trash=1.8.3 - sepp=4.5.5 - seqtk=1.4 -- setproctitle=1.3.3 -- setuptools=75.3.0 +- setproctitle=1.3.4 +- setuptools=75.6.0 - sgmllib3k=1.0.0 - shortuuid=1.0.13 - sigtool=0.1.3 - simplejson=3.19.3 -- six=1.16.0 +- six=1.17.0 - sniffio=1.3.1 - snowballstemmer=2.2.0 - soupsieve=2.5 -- sourmash-minimal=4.8.11 +- sourmash-minimal=4.8.12 - spades=3.15.2 - sphinx=8.1.3 - sphinxcontrib-applehelp=2.0.0 @@ -763,12 +776,12 @@ dependencies: - sphinxcontrib-qthelp=2.0.0 - sphinxcontrib-serializinghtml=1.1.10 - sqlite=3.46.0 -- stack_data=0.6.2 +- stack_data=0.6.3 - statsmodels=0.14.4 - suitesparse=5.10.1 -- tapi=1300.6.5 +- tapi=1100.0.11 - tar=1.34 -- tbb=2021.13.0 +- tbb=2022.0.0 - tblib=3.0.0 - terminado=0.18.1 - threadpoolctl=3.5.0 @@ -776,15 +789,16 @@ dependencies: - tk=8.6.13 - tktable=2.10 - toml=0.10.2 -- tomli=2.0.2 +- tomli=2.2.1 - tomlkit=0.13.2 -- tornado=6.4.1 +- tornado=6.4.2 - tqdm=4.62.3 - traitlets=5.9.0 -- typeguard=4.4.0 -- types-python-dateutil=2.9.0.20241003 +- typeguard=4.4.1 +- types-python-dateutil=2.9.0.20241206 - typing-extensions=4.12.2 - typing_extensions=4.12.2 +- typing_inspect=0.9.0 - typing_utils=0.1.0 - tzdata=2024b - tzlocal=2.1 @@ -795,27 +809,28 @@ dependencies: - unifrac=1.3 - unifrac-binaries=1.4 - uri-template=1.3.0 -- urllib3=1.26.19 +- urllib3=2.2.3 - vsearch=2.22.1 - wcwidth=0.2.13 -- webcolors=24.8.0 +- webcolors=24.11.1 - webencodings=0.5.1 - websocket-client=1.8.0 - wget=1.21.4 -- wheel=0.44.0 +- wheel=0.45.1 - widgetsnbextension=4.0.13 -- wrapt=1.16.0 +- wrapt=1.17.0 - xlsxwriter=3.2.0 - xmltodict=0.14.2 - xopen=2.0.2 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.5 -- xxhash=0.8.2 -- xz=5.2.6 +- xz=5.6.3 +- xz-gpl-tools=5.6.3 +- xz-tools=5.6.3 - yaml=0.2.5 - yq=3.4.3 - zeromq=4.3.5 -- zipp=3.20.2 +- zipp=3.21.0 - zlib=1.2.13 - zlib-ng=2.2.2 - zstandard=0.23.0 diff --git a/2025.4/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml b/2025.4/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml index 136f22d8..3902002e 100644 --- a/2025.4/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml +++ b/2025.4/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml @@ -8,27 +8,28 @@ dependencies: - _r-mutex=1.0.1 - alabaster=1.0.0 - alsa-lib=1.2.11 -- altair=5.4.1 -- anyio=4.6.2.post1 +- altair=5.5.0 +- annotated-types=0.7.0 +- anyio=4.7.0 - appdirs=1.4.4 -- argcomplete=3.5.1 +- argcomplete=3.5.2 - argh=0.31.3 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - aria2=1.37.0 - arrow=1.3.0 - astor=0.8.1 -- asttokens=2.4.1 +- asttokens=3.0.0 - atpublic=5.0 - attr=2.5.1 - attrs=24.2.0 - augustus=3.5.0 -- babel=2.14.0 +- babel=2.16.0 - bamtools=2.5.2 -- bbmap=39.10 +- bbmap=39.13 - bc=1.07.1 - bcftools=1.21 -- bcrypt=4.2.0 +- bcrypt=4.2.1 - beautifulsoup4=4.12.3 - bedtools=2.31.1 - bibtexparser=1.4.2 @@ -99,11 +100,11 @@ dependencies: - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 -- busco=5.8.0 +- busco=5.8.2 - bwa=0.7.18 -- bwidget=1.9.14 +- bwidget=1.10.1 - bzip2=1.0.8 -- c-ares=1.34.2 +- c-ares=1.34.3 - ca-certificates=2024.8.30 - cached-property=1.5.2 - cached_property=1.5.2 @@ -120,14 +121,14 @@ dependencies: - comm=0.2.2 - commonmark=0.9.1 - conda-pack=0.7.0 -- contourpy=1.3.0 -- cryptography=43.0.3 +- contourpy=1.3.1 +- cryptography=44.0.0 - curl=8.8.0 - cutadapt=4.9 - cycler=0.12.1 - cython=3.0.11 - dbus=1.13.6 -- debugpy=1.8.7 +- debugpy=1.8.10 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=5.0.1 @@ -145,7 +146,7 @@ dependencies: - entrypoints=0.4 - exceptiongroup=1.2.2 - executing=2.1.0 -- expat=2.6.3 +- expat=2.6.4 - fastcluster=1.2.6 - fasttree=2.1.11 - feedparser=6.0.11 @@ -158,7 +159,7 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.54.1 +- fonttools=4.55.3 - formulaic=1.0.2 - fqdn=1.5.1 - freetype=2.12.1 @@ -175,7 +176,7 @@ dependencies: - glib=2.80.2 - glib-tools=2.80.2 - glimmerhmm=3.0.4 -- globus-sdk=3.46.0 +- globus-sdk=3.49.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 @@ -185,12 +186,15 @@ dependencies: - gst-plugins-base=1.24.4 - gstreamer=1.24.4 - gxx_impl_linux-64=14.2.0 +- h2=4.1.0 - h5py=3.11.0 - harfbuzz=8.5.0 - hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.4 +- hpack=4.0.0 - htslib=1.21 +- hyperframe=6.0.1 - icu=73.2 - idna=3.10 - ijson=3.3.0 @@ -207,7 +211,7 @@ dependencies: - ipywidgets=8.1.5 - isa-l=2.31.0 - isoduration=20.11.0 -- jedi=0.19.1 +- jedi=0.19.2 - jinja2=3.1.4 - joblib=1.4.2 - jq=1.7.1 @@ -244,7 +248,7 @@ dependencies: - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 -- libcap=2.69 +- libcap=2.71 - libcblas=3.9.0 - libclang-cpp15=15.0.7 - libclang13=18.1.7 @@ -254,13 +258,13 @@ dependencies: - libedit=3.1.20191231 - libev=4.33 - libevent=2.1.12 -- libexpat=2.6.3 +- libexpat=2.6.4 - libffi=3.4.2 - libflac=1.4.3 - libgcc=14.2.0 - libgcc-devel_linux-64=14.2.0 - libgcc-ng=14.2.0 -- libgcrypt=1.11.0 +- libgcrypt-lib=1.11.0 - libgd=2.3.3 - libgettextpo=0.22.5 - libgettextpo-devel=0.22.5 @@ -269,8 +273,8 @@ dependencies: - libgfortran5=14.2.0 - libglib=2.80.2 - libgomp=14.2.0 -- libgpg-error=1.50 -- libhwloc=2.11.1 +- libgpg-error=1.51 +- libhwloc=2.11.2 - libiconv=1.17 - libidn2=2.3.7 - libjpeg-turbo=3.0.0 @@ -279,14 +283,16 @@ dependencies: - libllvm14=14.0.6 - libllvm15=15.0.7 - libllvm18=18.1.7 +- liblzma=5.6.3 +- liblzma-devel=5.6.3 - libnghttp2=1.58.0 - libnsl=2.0.1 - libogg=1.3.5 - libopenblas=0.3.28 -- libopenssl-static=3.3.2 +- libopenssl-static=3.4.0 - libopus=1.3.1 - libpng=1.6.43 -- libpq=16.4 +- libpq=16.6 - libprotobuf=3.20.3 - libsanitizer=14.2.0 - libsndfile=1.2.2 @@ -296,7 +302,7 @@ dependencies: - libstdcxx=14.2.0 - libstdcxx-devel_linux-64=14.2.0 - libstdcxx-ng=14.2.0 -- libsystemd0=256.7 +- libsystemd0=256.9 - libtiff=4.6.0 - libunistring=0.9.10 - libuuid=2.38.1 @@ -314,7 +320,7 @@ dependencies: - lp_solve=5.5.2.11 - lxml=5.2.2 - lz4=4.3.3 -- lz4-c=1.9.4 +- lz4-c=1.10.0 - mafft=7.526 - make=4.4.1 - markupsafe=3.0.2 @@ -328,22 +334,24 @@ dependencies: - minimap2=2.28 - miniprot=0.13 - mistune=3.0.2 -- mmseqs2=15.6f452 +- mmseqs2=16.747c6 - mpfr=4.2.1 -- mpg123=1.32.8 +- mpg123=1.32.9 - mpi=1.0.1 +- multimethod=1.9.1 - munkres=1.1.4 - muscle=3.8.1551 +- mypy_extensions=1.0.0 - mysql-common=8.3.0 - mysql-connector-c=6.1.11 - mysql-libs=8.3.0 -- narwhals=1.12.1 +- narwhals=1.17.0 - natsort=8.4.0 - nbclassic=1.1.0 -- nbclient=0.10.0 +- nbclient=0.10.1 - nbconvert-core=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.1 +- ncbi-datasets-pylib=14.25.1 - ncbi-vdb=3.1.1 - ncurses=6.5 - nest-asyncio=1.6.0 @@ -359,11 +367,13 @@ dependencies: - openjdk=22.0.1 - openjpeg=2.5.2 - openmp=8.0.1 -- openssl=3.3.2 +- openssl=3.4.0 - overrides=7.7.0 -- packaging=24.1 +- packaging=24.2 - pandas=2.2.2 -- pandoc=3.5 +- pandera=0.21.1 +- pandera-base=0.21.1 +- pandoc=3.6 - pandocfilters=1.5.0 - pango=1.54.0 - parameterized=0.9.0 @@ -421,12 +431,12 @@ dependencies: - perl-number-format=1.76 - perl-parallel-forkmanager=2.03 - perl-params-validate=1.31 -- perl-parent=0.242 +- perl-parent=0.243 - perl-pathtools=3.75 - perl-readonly=2.05 - perl-regexp-common=2017060201 - perl-role-tiny=2.002004 -- perl-scalar-list-utils=1.63 +- perl-scalar-list-utils=1.68 - perl-set-intspan=1.19 - perl-statistics-basic=1.6611 - perl-storable=3.15 @@ -444,7 +454,7 @@ dependencies: - pigz=2.8 - pillow=10.3.0 - pip=24.3.1 -- pixman=0.43.2 +- pixman=0.44.2 - pkgutil-resolve-name=1.3.10 - platformdirs=4.3.6 - pluggy=1.5.0 @@ -453,7 +463,7 @@ dependencies: - popt=1.16 - prank=170427 - prodigal=2.6.3 -- prometheus_client=0.21.0 +- prometheus_client=0.21.1 - prompt-toolkit=3.0.48 - protobuf=3.20.3 - psutil=6.1.0 @@ -462,10 +472,12 @@ dependencies: - pulseaudio-client=17.0 - pure_eval=0.2.3 - pycparser=2.22 +- pydantic=2.10.3 +- pydantic-core=2.27.1 - pyfaidx=0.8.1.3 - pygments=2.18.0 - pyhmmer=0.10.15 -- pyjwt=2.9.0 +- pyjwt=2.10.1 - pymongo=4.10.1 - pynacl=1.5.0 - pynndescent=0.5.13 @@ -474,11 +486,11 @@ dependencies: - pyqt5-sip=12.12.2 - pysam=0.22.1 - pysocks=1.7.1 -- pytest=8.3.3 +- pytest=8.3.4 - python=3.10.14 -- python-dateutil=2.8.2 +- python-dateutil=2.9.0.post0 - python-dotenv=1.0.1 -- python-fastjsonschema=2.20.0 +- python-fastjsonschema=2.21.1 - python-isal=1.7.1 - python-json-logger=2.0.7 - python-tzdata=2024.2 @@ -488,8 +500,9 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- pyzotero=1.5.25 -- q2-assembly=2025.4.0.dev0 +- pyzotero=1.5.27 +- q2-alignment=2025.4.0.dev0 +- q2-assembly=2025.4.0.dev0+2.g3a645f4 - q2-composition=2025.4.0.dev0 - q2-cutadapt=2025.4.0.dev0 - q2-demux=2025.4.0.dev0 @@ -497,11 +510,11 @@ dependencies: - q2-diversity-lib=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 -- q2-fondue=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 +- q2-fondue=2025.4.0.dev0+1.g4bc2add - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 -- q2-moshpit=2025.4.0.dev0 +- q2-moshpit=2025.4.0.dev0+9.gf09a381 - q2-mystery-stew=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 - q2-quality-filter=2025.4.0.dev0 @@ -510,13 +523,13 @@ dependencies: - q2-sourmash=2025.4.0.dev0 - q2-taxa=2025.4.0.dev0 - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0 +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+1.gab00603 +- qiime2=2025.4.0.dev0+5.gdb970dd - qt-main=5.15.8 -- quast=5.2.0 +- quast=5.3.0 - r-abind=1.4_5 - r-ade4=1.7_22 - r-ape=5.8 @@ -529,7 +542,7 @@ dependencies: - r-beeswarm=0.4.0 - r-bh=1.84.0_0 - r-bibtex=0.5.1 -- r-bit=4.5.0 +- r-bit=4.5.0.1 - r-bit64=4.5.2 - r-bitops=1.0_9 - r-blob=1.2.4 @@ -545,20 +558,20 @@ dependencies: - r-class=7.3_22 - r-cli=3.6.3 - r-clipr=0.8.0 -- r-cluster=2.1.6 +- r-cluster=2.1.7 - r-codetools=0.2_20 - r-colorspace=2.1_1 - r-conflicted=1.2.0 -- r-cpp11=0.5.0 +- r-cpp11=0.5.1 - r-crayon=1.5.3 -- r-curl=5.2.1 -- r-cvxr=1.0_13 +- r-curl=6.0.1 +- r-cvxr=1.0_15 - r-data.table=1.15.2 - r-dbi=1.2.3 - r-dbplyr=2.5.0 - r-deldir=2.0_4 - r-desc=1.4.3 -- r-desctools=0.99.57 +- r-desctools=0.99.58 - r-diffobj=0.3.5 - r-digest=0.6.37 - r-doparallel=1.0.17 @@ -578,7 +591,7 @@ dependencies: - r-fastmap=1.2.0 - r-filelock=1.0.3 - r-fnn=1.1.4.1 -- r-fontawesome=0.5.2 +- r-fontawesome=0.5.3 - r-forcats=1.0.0 - r-foreach=1.5.2 - r-foreign=0.8_87 @@ -608,13 +621,13 @@ dependencies: - r-haven=2.5.4 - r-here=1.0.1 - r-highr=0.11 -- r-hmisc=5.2_0 +- r-hmisc=5.2_1 - r-hms=1.1.3 - r-htmltable=2.4.3 - r-htmltools=0.5.8.1 - r-htmlwidgets=1.6.4 - r-httr=1.4.7 -- r-httr2=1.0.5 +- r-httr2=1.0.7 - r-ids=1.0.1 - r-igraph=2.0.3 - r-interp=1.1_6 @@ -624,7 +637,7 @@ dependencies: - r-jpeg=0.1_10 - r-jquerylib=0.1.4 - r-jsonlite=1.8.9 -- r-knitr=1.48 +- r-knitr=1.49 - r-labeling=0.4.3 - r-lambda.r=1.2.4 - r-lattice=0.22_6 @@ -634,7 +647,7 @@ dependencies: - r-lme4=1.1_35.5 - r-lmertest=3.1_3 - r-lmom=3.2 -- r-lubridate=1.9.3 +- r-lubridate=1.9.4 - r-magrittr=2.0.3 - r-mass=7.3_60.0.1 - r-matrix=1.6_5 @@ -646,7 +659,7 @@ dependencies: - r-modelr=0.1.11 - r-multcomp=1.4_26 - r-munsell=0.5.1 -- r-mvtnorm=1.3_1 +- r-mvtnorm=1.3_2 - r-nlme=3.1_165 - r-nloptr=2.1.1 - r-nnet=7.3_19 @@ -677,7 +690,7 @@ dependencies: - r-rappdirs=0.3.3 - r-rbibutils=2.3 - r-rcolorbrewer=1.1_3 -- r-rcpp=1.0.13 +- r-rcpp=1.0.13_1 - r-rcppannoy=0.0.22 - r-rcppeigen=0.3.4.0.2 - r-rcpphnsw=0.6.0 @@ -685,7 +698,7 @@ dependencies: - r-rcppprogress=0.4.2 - r-rcpptoml=0.2.2 - r-rcurl=1.98_1.16 -- r-rdpack=2.6.1 +- r-rdpack=2.6.2 - r-readr=2.1.5 - r-readxl=1.4.3 - r-registry=0.5_1 @@ -697,13 +710,13 @@ dependencies: - r-reticulate=1.36.0 - r-rjson=0.2.23 - r-rlang=1.1.4 -- r-rmarkdown=2.28 -- r-rmpfr=0.9_5 +- r-rmarkdown=2.29 +- r-rmpfr=1.0_0 - r-rngtools=1.5.2 - r-rootsolve=1.8.2.4 - r-rpart=4.1.23 - r-rprojroot=2.0.4 -- r-rsqlite=2.3.7 +- r-rsqlite=2.3.9 - r-rstudioapi=0.17.1 - r-rsvd=1.0.5 - r-rtsne=0.17 @@ -716,7 +729,7 @@ dependencies: - r-sitmo=2.0.2 - r-snow=0.4_4 - r-sp=2.1_4 -- r-stringdist=0.9.12 +- r-stringdist=0.9.14 - r-stringi=1.8.4 - r-stringr=1.5.1 - r-survival=3.7_0 @@ -731,7 +744,7 @@ dependencies: - r-tidytree=0.4.6 - r-tidyverse=2.0.0 - r-timechange=0.3.0 -- r-tinytex=0.53 +- r-tinytex=0.54 - r-tzdb=0.4.0 - r-utf8=1.2.4 - r-uuid=1.2_1 @@ -742,14 +755,14 @@ dependencies: - r-viridis=0.6.5 - r-viridislite=0.4.2 - r-vroom=1.6.5 -- r-waldo=0.5.3 +- r-waldo=0.6.1 - r-withr=3.0.2 -- r-xfun=0.48 +- r-xfun=0.49 - r-xml=3.99_0.17 - r-xml2=1.3.6 - r-xtable=1.8_4 - r-yaml=2.3.10 -- r-yulab.utils=0.1.7 +- r-yulab.utils=0.1.8 - r-zoo=1.8_12 - raxml=8.2.13 - readline=8.2 @@ -757,13 +770,14 @@ dependencies: - referencing=0.35.1 - repeatmasker=4.1.7p1 - requests=2.32.3 -- rescript=2025.4.0.dev0 +- rescript=2025.4.0.dev0+2.g16a48fa - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rmblast=2.14.1 -- rpds-py=0.20.0 +- rnanorm=2.1.0 +- rpds-py=0.22.3 - rpsbproc=0.5.0 -- rsync=3.3.0 +- rsync=3.1.3 - samtools=1.21 - scikit-bio=0.6.0 - scikit-learn=1.4.2 @@ -775,17 +789,17 @@ dependencies: - send2trash=1.8.3 - sepp=4.5.5 - seqtk=1.4 -- setproctitle=1.3.3 -- setuptools=75.3.0 +- setproctitle=1.3.4 +- setuptools=75.6.0 - sgmllib3k=1.0.0 - shortuuid=1.0.13 - simplejson=3.19.3 - sip=6.7.12 -- six=1.16.0 +- six=1.17.0 - sniffio=1.3.1 - snowballstemmer=2.2.0 - soupsieve=2.5 -- sourmash-minimal=4.8.11 +- sourmash-minimal=4.8.12 - spades=3.15.2 - sphinx=8.1.3 - sphinxcontrib-applehelp=2.0.0 @@ -796,13 +810,13 @@ dependencies: - sphinxcontrib-qthelp=2.0.0 - sphinxcontrib-serializinghtml=1.1.10 - sqlite=3.46.0 -- stack_data=0.6.2 +- stack_data=0.6.3 - statsmodels=0.14.4 - suitesparse=5.10.1 - sysroot_linux-64=2.17 - tapi=1300.6.5 - tar=1.34 -- tbb=2021.13.0 +- tbb=2022.0.0 - tblib=3.0.0 - terminado=0.18.1 - threadpoolctl=3.5.0 @@ -810,16 +824,17 @@ dependencies: - tk=8.6.13 - tktable=2.10 - toml=0.10.2 -- tomli=2.0.2 +- tomli=2.2.1 - tomlkit=0.13.2 -- tornado=6.4.1 +- tornado=6.4.2 - tqdm=4.62.3 - traitlets=5.9.0 - trf=4.09.1 -- typeguard=4.4.0 -- types-python-dateutil=2.9.0.20241003 +- typeguard=4.4.1 +- types-python-dateutil=2.9.0.20241206 - typing-extensions=4.12.2 - typing_extensions=4.12.2 +- typing_inspect=0.9.0 - typing_utils=0.1.0 - tzdata=2024b - tzlocal=2.1 @@ -830,16 +845,16 @@ dependencies: - unifrac=1.3 - unifrac-binaries=1.4 - uri-template=1.3.0 -- urllib3=1.26.19 +- urllib3=2.2.3 - vsearch=2.22.1 - wcwidth=0.2.13 -- webcolors=24.8.0 +- webcolors=24.11.1 - webencodings=0.5.1 - websocket-client=1.8.0 - wget=1.21.4 -- wheel=0.44.0 +- wheel=0.45.1 - widgetsnbextension=4.0.13 -- wrapt=1.16.0 +- wrapt=1.17.0 - xcb-util=0.4.0 - xcb-util-image=0.4.0 - xcb-util-keysyms=0.4.0 @@ -868,12 +883,13 @@ dependencies: - xorg-xextproto=7.3.0 - xorg-xf86vidmodeproto=2.3.1 - xorg-xproto=7.0.31 -- xxhash=0.8.2 -- xz=5.2.6 +- xz=5.6.3 +- xz-gpl-tools=5.6.3 +- xz-tools=5.6.3 - yaml=0.2.5 - yq=3.4.3 - zeromq=4.3.5 -- zipp=3.20.2 +- zipp=3.21.0 - zlib=1.2.13 - zlib-ng=2.2.2 - zstandard=0.23.0 diff --git a/2025.4/metagenome/passed/seed-environment-conda.yml b/2025.4/metagenome/passed/seed-environment-conda.yml index 2fd289e2..8257d3ee 100644 --- a/2025.4/metagenome/passed/seed-environment-conda.yml +++ b/2025.4/metagenome/passed/seed-environment-conda.yml @@ -9,6 +9,7 @@ dependencies: - entrezpy=2.1.2 - h5py=3.11.0 - hdf5=1.14.3 +- mafft=7.526 - matplotlib=3.8.4 - notebook=6.5.5 - numpy=1.26.4 @@ -17,7 +18,8 @@ dependencies: - patsy=0.5.6 - pysam=0.22.1 - python=3.10 -- q2-assembly=2025.4.0.dev0 +- q2-alignment=2025.4.0.dev0 +- q2-assembly=2025.4.0.dev0+2.g3a645f4 - q2-composition=2025.4.0.dev0 - q2-cutadapt=2025.4.0.dev0 - q2-demux=2025.4.0.dev0 @@ -25,11 +27,11 @@ dependencies: - q2-diversity=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 -- q2-fondue=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 +- q2-fondue=2025.4.0.dev0+1.g4bc2add - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 -- q2-moshpit=2025.4.0.dev0 +- q2-moshpit=2025.4.0.dev0+9.gf09a381 - q2-mystery-stew=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 - q2-quality-filter=2025.4.0.dev0 @@ -38,14 +40,14 @@ dependencies: - q2-sourmash=2025.4.0.dev0 - q2-taxa=2025.4.0.dev0 - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0 +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+1.gab00603 +- qiime2=2025.4.0.dev0+5.gdb970dd - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2025.4.0.dev0 +- rescript=2025.4.0.dev0+2.g16a48fa - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0 diff --git a/2025.4/metagenome/staged/seed-environment-conda.yml b/2025.4/metagenome/staged/seed-environment-conda.yml index 36b90452..cadce64e 100644 --- a/2025.4/metagenome/staged/seed-environment-conda.yml +++ b/2025.4/metagenome/staged/seed-environment-conda.yml @@ -10,6 +10,7 @@ dependencies: - entrezpy=2.1.2 - h5py=3.11.0 - hdf5=1.14.3 +- mafft=7.526 - matplotlib=3.8.4 - notebook=6.5.5 - numpy=1.26.4 @@ -19,7 +20,8 @@ dependencies: - pysam=0.22.1 - python=3.10 - python_abi=3.9 -- q2-assembly=2025.4.0.dev0 +- q2-alignment=2025.4.0.dev0 +- q2-assembly=2025.4.0.dev0+2.g3a645f4 - q2-composition=2025.4.0.dev0 - q2-cutadapt=2025.4.0.dev0 - q2-demux=2025.4.0.dev0 @@ -27,11 +29,11 @@ dependencies: - q2-diversity=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 -- q2-fondue=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 +- q2-fondue=2025.4.0.dev0+1.g4bc2add - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 -- q2-moshpit=2025.4.0.dev0 +- q2-moshpit=2025.4.0.dev0+9.gf09a381 - q2-mystery-stew=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 - q2-quality-filter=2025.4.0.dev0 @@ -41,14 +43,14 @@ dependencies: - q2-taxa=2025.4.0.dev0 - q2-types-genomics=2023.11.0.dev0+8.g3b993ed - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0 +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+1.gab00603 +- qiime2=2025.4.0.dev0+5.gdb970dd - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2025.4.0.dev0 +- rescript=2025.4.0.dev0+2.g16a48fa - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0