diff --git a/2024.5/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml b/2024.5/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml new file mode 100644 index 00000000..352d504f --- /dev/null +++ b/2024.5/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml @@ -0,0 +1,663 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.2/amplicon/passed +- bioconda +- conda-forge +- defaults +dependencies: +- _r-mutex=1.0.1 +- altair=5.2.0 +- anyio=4.2.0 +- appdirs=1.4.4 +- appnope=0.1.4 +- argcomplete=3.2.2 +- argh=0.31.2 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- arrow=1.3.0 +- astor=0.8.1 +- asttokens=2.4.1 +- atpublic=3.0.1 +- attrs=23.2.0 +- backcall=0.2.0 +- bcrypt=4.1.2 +- beautifulsoup4=4.12.3 +- bibtexparser=1.4.1 +- bioconductor-ancombc=2.0.1 +- bioconductor-beachmat=2.14.0 +- bioconductor-biobase=2.58.0 +- bioconductor-biocbaseutils=1.0.0 +- bioconductor-biocgenerics=0.44.0 +- bioconductor-biocneighbors=1.16.0 +- bioconductor-biocparallel=1.32.5 +- bioconductor-biocsingular=1.14.0 +- bioconductor-biomformat=1.26.0 +- bioconductor-biostrings=2.66.0 +- bioconductor-dada2=1.26.0 +- 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-genomicranges=1.50.0 +- bioconductor-iranges=2.32.0 +- 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-s4vectors=0.36.0 +- bioconductor-scaledmatrix=1.6.0 +- bioconductor-scater=1.26.0 +- bioconductor-scuttle=1.8.0 +- bioconductor-shortread=1.56.0 +- bioconductor-singlecellexperiment=1.20.0 +- bioconductor-sparsematrixstats=1.10.0 +- bioconductor-summarizedexperiment=1.28.0 +- bioconductor-treeio=1.22.0 +- bioconductor-treesummarizedexperiment=2.6.0 +- bioconductor-xvector=0.38.0 +- bioconductor-zlibbioc=1.44.0 +- biom-format=2.1.14 +- biopython=1.83 +- blast=2.15.0 +- bleach=6.1.0 +- bowtie2=2.5.2 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.26.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.16.0 +- cctools_osx-64=973.0.1 +- certifi=2024.2.2 +- cffi=1.16.0 +- charset-normalizer=3.3.2 +- 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 +- click=8.1.7 +- colorama=0.4.6 +- comm=0.2.1 +- compiler-rt=17.0.6 +- compiler-rt_osx-64=17.0.6 +- conda-pack=0.7.0 +- contourpy=1.1.1 +- cryptography=42.0.3 +- curl=7.88.1 +- cutadapt=4.6 +- cycler=0.12.1 +- cython=3.0.8 +- deblur=1.1.1 +- debugpy=1.8.1 +- decorator=4.4.2 +- defusedxml=0.7.1 +- dendropy=4.5.2 +- dill=0.3.8 +- dnaio=1.2.0 +- emperor=1.0.4 +- entrez-direct=16.2 +- entrypoints=0.4 +- exceptiongroup=1.2.0 +- executing=2.0.1 +- expat=2.5.0 +- fastcluster=1.2.6 +- fasttree=2.1.11 +- flufl.lock=7.1 +- font-ttf-dejavu-sans-mono=2.37 +- font-ttf-inconsolata=3.000 +- font-ttf-source-code-pro=2.038 +- font-ttf-ubuntu=0.83 +- fontconfig=2.14.2 +- fonts-conda-ecosystem=1 +- fonts-conda-forge=1 +- fonttools=4.49.0 +- formulaic=1.0.1 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- future=0.18.3 +- gawk=5.3.0 +- gettext=0.21.1 +- gffutils=0.10.1 +- gfortran_impl_osx-64=11.4.0 +- gfortran_osx-64=11.4.0 +- globus-sdk=3.37.0 +- glpk=5.0 +- gmp=6.3.0 +- graphite2=1.3.13 +- graphlib-backport=1.0.3 +- gsl=2.7 +- h5py=3.8.0 +- harfbuzz=6.0.0 +- hdf5=1.14.0 +- hdmedians=0.14.2 +- hmmer=3.1b2 +- htslib=1.17 +- icu=70.1 +- idna=3.6 +- ijson=3.2.3 +- importlib-metadata=7.0.1 +- importlib_resources=6.1.1 +- iniconfig=2.0.0 +- interface_meta=1.3.0 +- iow=1.0.5 +- ipykernel=6.29.2 +- ipython=8.12.2 +- ipython_genutils=0.2.0 +- ipywidgets=8.1.2 +- iqtree=2.2.6 +- isa-l=2.31.0 +- isl=0.25 +- isoduration=20.11.0 +- jedi=0.19.1 +- jinja2=3.1.3 +- joblib=1.3.2 +- jpeg=9e +- jq=1.7.1 +- jsonlines=3.0.0 +- jsonpointer=2.4 +- jsonschema=4.21.1 +- jsonschema-specifications=2023.12.1 +- jsonschema-with-format-nongpl=4.21.1 +- jupyter_client=7.4.9 +- jupyter_core=5.7.1 +- jupyter_events=0.9.0 +- jupyter_server=2.12.5 +- jupyter_server_terminals=0.5.2 +- jupyterlab_pygments=0.3.0 +- jupyterlab_widgets=3.0.10 +- kiwisolver=1.4.5 +- krb5=1.20.1 +- lcms2=2.15 +- ld64_osx-64=609 +- lerc=4.0.0 +- libaec=1.1.2 +- libblas=3.9.0 +- libbrotlicommon=1.1.0 +- 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=1.17 +- libedit=3.1.20191231 +- libev=4.33 +- libexpat=2.5.0 +- libffi=3.4.4 +- libgfortran=5.0.0 +- libgfortran-devel_osx-64=11.4.0 +- libgfortran5=13.2.0 +- libglib=2.78.1 +- libiconv=1.17 +- libidn2=2.3.7 +- liblapack=3.9.0 +- liblapacke=3.9.0 +- libllvm14=14.0.6 +- libllvm17=17.0.6 +- libnghttp2=1.58.0 +- libopenblas=0.3.25 +- libpng=1.6.42 +- libprotobuf=3.20.3 +- libsodium=1.0.18 +- libsqlite=3.45.1 +- libssh2=1.11.0 +- libtiff=4.5.0 +- libunistring=0.9.10 +- libwebp-base=1.3.2 +- libxcb=1.13 +- libxml2=2.10.3 +- libxslt=1.1.37 +- libzlib=1.2.13 +- llvm-openmp=17.0.6 +- llvm-tools=17.0.6 +- llvmlite=0.41.1 +- lockfile=0.12.2 +- lxml=4.9.2 +- lz4=4.3.3 +- lz4-c=1.9.4 +- mafft=7.520 +- make=4.3 +- markupsafe=2.1.5 +- matplotlib=3.6.0 +- matplotlib-base=3.6.0 +- matplotlib-inline=0.1.6 +- mistune=3.0.2 +- 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=0.8.0 +- nbconvert=7.16.0 +- nbconvert-core=7.16.0 +- nbconvert-pandoc=7.16.0 +- nbformat=5.9.2 +- ncbi-datasets-pylib=16.4.8 +- ncbi-vdb=3.0.0 +- ncurses=6.4 +- nest-asyncio=1.6.0 +- networkx=3.1 +- nlopt=2.7.1 +- notebook=6.5.5 +- notebook-shim=0.2.4 +- numba=0.58.1 +- numpy=1.24.4 +- oniguruma=6.9.9 +- openjdk=21.0.2 +- openjpeg=2.5.0 +- openssl=3.2.1 +- overrides=7.7.0 +- packaging=23.2 +- pandas=1.5.3 +- pandoc=3.1.12 +- pandocfilters=1.5.0 +- pango=1.50.14 +- paramiko=3.4.0 +- parsl=2023.12.4 +- parso=0.8.3 +- patsy=0.5.3 +- pbzip2=1.1.13 +- pcre=8.45 +- pcre2=10.40 +- perl=5.32.1 +- perl-archive-tar=2.40 +- perl-carp=1.50 +- perl-common-sense=3.75 +- perl-compress-raw-bzip2=2.201 +- perl-compress-raw-zlib=2.202 +- perl-encode=3.19 +- perl-exporter=5.74 +- perl-exporter-tiny=1.002002 +- perl-extutils-makemaker=7.70 +- perl-io-compress=2.201 +- perl-io-zlib=1.14 +- perl-json=4.10 +- perl-json-xs=2.34 +- perl-list-moreutils=0.430 +- perl-list-moreutils-xs=0.430 +- perl-parent=0.241 +- perl-pathtools=3.75 +- perl-scalar-list-utils=1.63 +- perl-storable=3.15 +- perl-types-serialiser=1.01 +- pexpect=4.9.0 +- pickleshare=0.7.5 +- pigz=2.8 +- pillow=9.4.0 +- pip=24.0 +- pixman=0.43.2 +- pkgutil-resolve-name=1.3.10 +- platformdirs=4.2.0 +- pluggy=1.4.0 +- pooch=1.8.0 +- 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 +- pure_eval=0.2.2 +- pycparser=2.21 +- pyfaidx=0.8.1.1 +- pygments=2.17.2 +- pyjwt=2.8.0 +- pynacl=1.5.0 +- pynndescent=0.5.11 +- pyobjc-core=10.1 +- pyobjc-framework-cocoa=10.1 +- pyparsing=3.1.1 +- pysocks=1.7.1 +- pytest=8.0.0 +- python=3.8.18 +- python-dateutil=2.8.2 +- python-fastjsonschema=2.19.1 +- python-isal=1.5.3 +- python-json-logger=2.0.7 +- python_abi=3.8 +- pytz=2024.1 +- pyvcf3=1.0.3 +- pyyaml=6.0.1 +- pyzmq=24.0.1 +- q2-alignment=2024.2.0 +- q2-composition=2024.2.0 +- q2-cutadapt=2024.2.0 +- q2-dada2=2024.2.0 +- q2-deblur=2024.2.0 +- q2-demux=2024.2.0 +- q2-diversity=2024.2.0 +- q2-diversity-lib=2024.2.0 +- q2-emperor=2024.2.0 +- q2-feature-classifier=2024.2.0 +- q2-feature-table=2024.2.0 +- q2-fragment-insertion=2024.2.0 +- q2-longitudinal=2024.2.0 +- q2-metadata=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-phylogeny=2024.2.0 +- q2-quality-control=2024.2.0 +- q2-quality-filter=2024.2.0 +- q2-sample-classifier=2024.2.0 +- q2-taxa=2024.2.0 +- q2-types=2024.2.0 +- q2-vsearch=2024.2.0 +- q2cli=2024.2.0 +- q2galaxy=2024.2.0 +- q2templates=2024.2.0 +- qiime2=2024.2.0 +- r-ade4=1.7_22 +- r-ape=5.7_1 +- r-askpass=1.2.0 +- r-assertthat=0.2.1 +- r-backports=1.4.1 +- r-base=4.2.2 +- r-base64enc=0.1_3 +- r-beeswarm=0.4.0 +- r-bh=1.84.0_0 +- r-bibtex=0.5.1 +- r-bit=4.0.5 +- r-bit64=4.0.5 +- r-bitops=1.0_7 +- r-blob=1.2.4 +- r-boot=1.3_28.1 +- r-broom=1.0.5 +- r-bslib=0.6.1 +- r-cachem=1.0.8 +- r-cairo=1.6_0 +- r-callr=3.7.3 +- r-cellranger=1.1.0 +- r-checkmate=2.3.1 +- r-class=7.3_22 +- r-cli=3.6.2 +- r-clipr=0.8.0 +- r-cluster=2.1.6 +- r-codetools=0.2_19 +- 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r-googlesheets4=1.1.1 +- r-gridextra=2.3 +- r-gsl=2.1_8 +- r-gtable=0.3.4 +- r-haven=2.5.4 +- r-highr=0.10 +- r-hmisc=5.1_1 +- r-hms=1.1.3 +- r-htmltable=2.4.2 +- r-htmltools=0.5.7 +- r-htmlwidgets=1.6.4 +- r-httr=1.4.7 +- r-hwriter=1.3.2.1 +- r-ids=1.0.1 +- r-igraph=1.4.2 +- r-interp=1.1_6 +- r-irlba=2.3.5.1 +- r-isoband=0.2.7 +- r-iterators=1.0.14 +- r-jpeg=0.1_10 +- r-jquerylib=0.1.4 +- r-jsonlite=1.8.8 +- r-knitr=1.45 +- r-labeling=0.4.3 +- r-lambda.r=1.2.4 +- r-lattice=0.22_5 +- r-latticeextra=0.6_30 +- r-lazyeval=0.2.2 +- r-lifecycle=1.0.4 +- r-lme4=1.1_35.1 +- r-lmertest=3.1_3 +- r-lmom=3.0 +- r-lubridate=1.9.3 +- r-magrittr=2.0.3 +- r-mass=7.3_60.0.1 +- r-matrix=1.6_5 +- r-matrixstats=1.2.0 +- r-memoise=2.0.1 +- r-mgcv=1.9_1 +- r-mime=0.12 +- r-minqa=1.2.6 +- r-modelr=0.1.11 +- r-munsell=0.5.0 +- 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-optparse=1.7.4 +- 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-pkgconfig=2.0.3 +- r-pkgmaker=0.32.10 +- r-plogr=0.2.0 +- r-plyr=1.8.9 +- r-png=0.1_8 +- r-prettyunits=1.2.0 +- r-processx=3.8.3 +- r-progress=1.2.3 +- r-proxy=0.4_27 +- r-ps=1.7.6 +- r-purrr=1.0.2 +- r-r6=2.5.1 +- r-ragg=1.2.5 +- r-rappdirs=0.3.3 +- r-rbibutils=2.2.16 +- r-rcolorbrewer=1.1_3 +- r-rcpp=1.0.12 +- r-rcppannoy=0.0.22 +- r-rcppeigen=0.3.3.9.4 +- r-rcpphnsw=0.6.0 +- r-rcppml=0.3.7 +- r-rcppparallel=5.1.6 +- r-rcppprogress=0.4.2 +- r-rcurl=1.98_1.12 +- r-rdpack=2.6 +- r-readr=2.1.5 +- r-readxl=1.4.3 +- r-registry=0.5_1 +- r-rematch=2.0.0 +- r-rematch2=2.1.2 +- r-reprex=2.1.0 +- r-reshape2=1.4.4 +- r-rlang=1.1.3 +- r-rmarkdown=2.25 +- r-rmpfr=0.9_5 +- r-rngtools=1.5.2 +- r-rootsolve=1.8.2.4 +- r-rpart=4.1.23 +- r-rsqlite=2.3.4 +- r-rstudioapi=0.15.0 +- r-rsvd=1.0.5 +- r-rtsne=0.17 +- r-rvest=1.0.4 +- r-sass=0.4.8 +- 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-statmod=1.5.0 +- r-stringi=1.7.12 +- r-stringr=1.5.1 +- r-survival=3.5_8 +- r-sys=3.4.2 +- r-systemfonts=1.0.5 +- r-textshaping=0.3.6 +- r-tibble=3.2.1 +- r-tidyr=1.3.1 +- r-tidyselect=1.2.0 +- r-tidytree=0.4.6 +- r-tidyverse=2.0.0 +- r-timechange=0.3.0 +- r-tinytex=0.49 +- r-tzdb=0.4.0 +- r-utf8=1.2.4 +- r-uuid=1.2_0 +- r-uwot=0.1.16 +- r-vctrs=0.6.5 +- r-vegan=2.6_4 +- r-vipor=0.4.7 +- r-viridis=0.6.5 +- r-viridislite=0.4.2 +- r-vroom=1.6.5 +- r-withr=3.0.0 +- r-xfun=0.42 +- r-xml2=1.3.3 +- r-xtable=1.8_4 +- r-yaml=2.3.8 +- r-yulab.utils=0.1.4 +- raxml=8.2.13 +- readline=8.2 +- referencing=0.33.0 +- requests=2.31.0 +- rescript=2024.2.0 +- 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 +- seaborn=0.12.2 +- seaborn-base=0.12.2 +- send2trash=1.8.2 +- sepp=4.3.10 +- setproctitle=1.3.3 +- setuptools=69.0.3 +- sigtool=0.1.3 +- simplejson=3.19.2 +- six=1.16.0 +- sniffio=1.3.0 +- sortmerna=2.0 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bioconductor-beachmat=2.14.0 +- bioconductor-biobase=2.58.0 +- bioconductor-biocbaseutils=1.0.0 +- bioconductor-biocgenerics=0.44.0 +- bioconductor-biocneighbors=1.16.0 +- bioconductor-biocparallel=1.32.5 +- bioconductor-biocsingular=1.14.0 +- bioconductor-biomformat=1.26.0 +- bioconductor-biostrings=2.66.0 +- bioconductor-dada2=1.26.0 +- 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-genomicranges=1.50.0 +- bioconductor-iranges=2.32.0 +- 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 +- 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r-rcppparallel=5.1.6 +- r-rcppprogress=0.4.2 +- r-rcurl=1.98_1.12 +- r-rdpack=2.6 +- r-readr=2.1.5 +- r-readxl=1.4.3 +- r-registry=0.5_1 +- r-rematch=2.0.0 +- r-rematch2=2.1.2 +- r-reprex=2.1.0 +- r-reshape2=1.4.4 +- r-rlang=1.1.3 +- r-rmarkdown=2.25 +- r-rmpfr=0.9_5 +- r-rngtools=1.5.2 +- r-rootsolve=1.8.2.4 +- r-rpart=4.1.23 +- r-rsqlite=2.3.4 +- r-rstudioapi=0.15.0 +- r-rsvd=1.0.5 +- r-rtsne=0.17 +- r-rvest=1.0.4 +- r-sass=0.4.8 +- 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-statmod=1.5.0 +- r-stringi=1.7.12 +- r-stringr=1.5.1 +- r-survival=3.5_8 +- r-sys=3.4.2 +- r-systemfonts=1.0.5 +- r-textshaping=0.3.6 +- r-tibble=3.2.1 +- r-tidyr=1.3.1 +- r-tidyselect=1.2.0 +- r-tidytree=0.4.6 +- r-tidyverse=2.0.0 +- r-timechange=0.3.0 +- r-tinytex=0.49 +- r-tzdb=0.4.0 +- r-utf8=1.2.4 +- r-uuid=1.2_0 +- r-uwot=0.1.16 +- r-vctrs=0.6.5 +- r-vegan=2.6_4 +- r-vipor=0.4.7 +- r-viridis=0.6.5 +- r-viridislite=0.4.2 +- r-vroom=1.6.5 +- r-withr=3.0.0 +- r-xfun=0.42 +- r-xml2=1.3.3 +- r-xtable=1.8_4 +- r-yaml=2.3.8 +- r-yulab.utils=0.1.4 +- raxml=8.2.13 +- readline=8.2 +- referencing=0.33.0 +- requests=2.31.0 +- rescript=2024.2.0 +- 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 +- seaborn=0.12.2 +- seaborn-base=0.12.2 +- sed=4.8 +- send2trash=1.8.2 +- sepp=4.3.10 +- setproctitle=1.3.3 +- setuptools=69.0.3 +- simplejson=3.19.2 +- sip=6.7.12 +- six=1.16.0 +- sniffio=1.3.0 +- sortmerna=2.0 +- soupsieve=2.5 +- stack_data=0.6.2 +- statsmodels=0.14.0 +- sysroot_linux-64=2.12 +- tbb=2021.9.0 +- tblib=3.0.0 +- terminado=0.18.0 +- threadpoolctl=3.3.0 +- tinycss2=1.2.1 +- tk=8.6.13 +- tktable=2.10 +- toml=0.10.2 +- tomli=2.0.1 +- tomlkit=0.12.3 +- toolz=0.12.1 +- tornado=6.3.3 +- tqdm=4.66.2 +- traitlets=5.9.0 +- typeguard=2.13.3 +- types-python-dateutil=2.8.19.20240106 +- typing-extensions=4.9.0 +- typing_extensions=4.9.0 +- typing_utils=0.1.0 +- tzlocal=2.1 +- umap-learn=0.5.5 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.3.2 +- uri-template=1.3.0 +- urllib3=1.26.18 +- vsearch=2.22.1 +- wcwidth=0.2.13 +- webcolors=1.13 +- webencodings=0.5.1 +- websocket-client=1.7.0 +- wget=1.20.3 +- wheel=0.42.0 +- widgetsnbextension=4.0.10 +- wrapt=1.16.0 +- xcb-util=0.4.0 +- xcb-util-image=0.4.0 +- xcb-util-keysyms=0.4.0 +- xcb-util-renderutil=0.3.9 +- xcb-util-wm=0.4.1 +- xkeyboard-config=2.38 +- xmltodict=0.13.0 +- xopen=1.9.0 +- 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-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-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-xproto=7.0.31 +- xz=5.2.6 +- yaml=0.2.5 +- yq=3.2.3 +- zeromq=4.3.5 +- zipp=3.17.0 +- zlib=1.2.13 +- zstandard=0.22.0 +- zstd=1.5.5 diff --git a/2024.5/amplicon/passed/seed-environment-conda.yml b/2024.5/amplicon/passed/seed-environment-conda.yml new file mode 100644 index 00000000..7027c8e0 --- /dev/null +++ b/2024.5/amplicon/passed/seed-environment-conda.yml @@ -0,0 +1,54 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/amplicon/passed +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- h5py=3.8.0 +- hdf5=1.14.0 +- matplotlib=3.6.0 +- notebook=6.5.5 +- numpy=1.24.4 +- pandas=1.5.3 +- parsl=2023.12.04 +- patsy=0.5.3 +- pillow=9.4.0 +- python=3.8 +- q2-alignment=2024.2.0 +- q2-composition=2024.2.0 +- q2-cutadapt=2024.2.0 +- q2-dada2=2024.2.0 +- q2-deblur=2024.2.0 +- q2-demux=2024.2.0 +- q2-diversity-lib=2024.2.0 +- q2-diversity=2024.2.0 +- q2-emperor=2024.2.0 +- q2-feature-classifier=2024.2.0 +- q2-feature-table=2024.2.0 +- q2-fragment-insertion=2024.2.0 +- q2-longitudinal=2024.2.0 +- q2-metadata=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-phylogeny=2024.2.0 +- q2-quality-control=2024.2.0 +- q2-quality-filter=2024.2.0 +- q2-sample-classifier=2024.2.0 +- q2-taxa=2024.2.0 +- q2-types=2024.2.0 +- q2-vsearch=2024.2.0 +- q2cli=2024.2.0 +- q2galaxy=2024.2.0 +- q2templates=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- rescript=2024.2.0 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- seaborn=0.12.2 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2' diff --git a/2024.5/amplicon/staged/seed-environment-conda.yml b/2024.5/amplicon/staged/seed-environment-conda.yml new file mode 100644 index 00000000..0212515d --- /dev/null +++ b/2024.5/amplicon/staged/seed-environment-conda.yml @@ -0,0 +1,54 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/amplicon/staged +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- h5py=3.8.0 +- hdf5=1.14.0 +- matplotlib=3.6.0 +- notebook=6.5.5 +- numpy=1.24.4 +- pandas=1.5.3 +- parsl=2023.12.04 +- patsy=0.5.3 +- pillow=9.4.0 +- python=3.8 +- q2-alignment=2024.2.0 +- q2-composition=2024.2.0 +- q2-cutadapt=2024.2.0 +- q2-dada2=2024.2.0 +- q2-deblur=2024.2.0 +- q2-demux=2024.2.0 +- q2-diversity-lib=2024.2.0 +- q2-diversity=2024.2.0 +- q2-emperor=2024.2.0 +- q2-feature-classifier=2024.2.0 +- q2-feature-table=2024.2.0 +- q2-fragment-insertion=2024.2.0 +- q2-longitudinal=2024.2.0 +- q2-metadata=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-phylogeny=2024.2.0 +- q2-quality-control=2024.2.0 +- q2-quality-filter=2024.2.0 +- q2-sample-classifier=2024.2.0 +- q2-taxa=2024.2.0 +- q2-types=2024.2.0 +- q2-vsearch=2024.2.0 +- q2cli=2024.2.0 +- q2galaxy=2024.2.0 +- q2templates=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- rescript=2024.2.0 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- seaborn=0.12.2 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2' diff --git a/2024.5/fmt/passed/qiime2-fmt-macos-latest-conda.yml b/2024.5/fmt/passed/qiime2-fmt-macos-latest-conda.yml new file mode 100644 index 00000000..34ef772f --- /dev/null +++ b/2024.5/fmt/passed/qiime2-fmt-macos-latest-conda.yml @@ -0,0 +1,305 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.2/fmt/passed +- bioconda +- conda-forge +- defaults +dependencies: +- _r-mutex=1.0.1 +- anyio=4.2.0 +- appdirs=1.4.4 +- appnope=0.1.4 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- arrow=1.3.0 +- asttokens=2.4.1 +- atpublic=3.0.1 +- attrs=23.2.0 +- backcall=0.2.0 +- bcrypt=4.1.2 +- beautifulsoup4=4.12.3 +- bibtexparser=1.4.1 +- biom-format=2.1.14 +- bleach=6.1.0 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.26.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.16.0 +- cctools_osx-64=973.0.1 +- certifi=2024.2.2 +- cffi=1.16.0 +- chardet=5.2.0 +- charset-normalizer=3.3.2 +- 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 +- click=8.1.7 +- colorama=0.4.6 +- comm=0.2.1 +- compiler-rt=17.0.6 +- compiler-rt_osx-64=17.0.6 +- conda-pack=0.7.0 +- contourpy=1.1.1 +- cryptography=42.0.3 +- curl=7.88.1 +- cycler=0.12.1 +- cython=3.0.8 +- debugpy=1.8.1 +- decorator=4.4.2 +- defusedxml=0.7.1 +- dill=0.3.8 +- entrypoints=0.4 +- exceptiongroup=1.2.0 +- executing=2.0.1 +- expat=2.5.0 +- flufl.lock=7.1 +- font-ttf-dejavu-sans-mono=2.37 +- font-ttf-inconsolata=3.000 +- font-ttf-source-code-pro=2.038 +- font-ttf-ubuntu=0.83 +- fontconfig=2.14.2 +- fonts-conda-ecosystem=1 +- fonts-conda-forge=1 +- fonttools=4.49.0 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- frictionless=5.5.0 +- gettext=0.21.1 +- gfortran_impl_osx-64=11.4.0 +- gfortran_osx-64=11.4.0 +- globus-sdk=3.37.0 +- gmp=6.3.0 +- graphite2=1.3.13 +- gsl=2.7 +- h5py=3.8.0 +- harfbuzz=6.0.0 +- hdf5=1.14.0 +- hdmedians=0.14.2 +- htslib=1.17 +- humanize=4.9.0 +- icu=70.1 +- idna=3.6 +- ijson=3.2.3 +- importlib-resources=6.1.1 +- importlib_resources=6.1.1 +- iniconfig=2.0.0 +- iow=1.0.5 +- ipykernel=6.29.2 +- ipython=8.12.2 +- ipython_genutils=0.2.0 +- isl=0.25 +- isodate=0.6.1 +- isoduration=20.11.0 +- jedi=0.19.1 +- jinja2=3.1.3 +- joblib=1.3.2 +- jpeg=9e +- jsonpointer=2.4 +- jsonschema=4.21.1 +- jsonschema-specifications=2023.12.1 +- jsonschema-with-format-nongpl=4.21.1 +- jupyter_client=7.4.9 +- jupyter_core=5.7.1 +- jupyter_events=0.9.0 +- jupyter_server=2.12.5 +- jupyter_server_terminals=0.5.2 +- jupyterlab_pygments=0.3.0 +- kiwisolver=1.4.5 +- krb5=1.20.1 +- lcms2=2.15 +- ld64_osx-64=609 +- lerc=4.0.0 +- libaec=1.1.2 +- libblas=3.9.0 +- libbrotlicommon=1.1.0 +- 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=1.17 +- libedit=3.1.20191231 +- libev=4.33 +- libexpat=2.5.0 +- libffi=3.4.4 +- libgfortran=5.0.0 +- libgfortran-devel_osx-64=11.4.0 +- libgfortran5=13.2.0 +- libglib=2.78.1 +- libiconv=1.17 +- liblapack=3.9.0 +- liblapacke=3.9.0 +- libllvm17=17.0.6 +- libnghttp2=1.58.0 +- libopenblas=0.3.25 +- libpng=1.6.42 +- libsodium=1.0.18 +- libsqlite=3.45.1 +- libssh2=1.11.0 +- libtiff=4.5.0 +- libwebp-base=1.3.2 +- libxcb=1.13 +- libxml2=2.10.3 +- libxslt=1.1.37 +- libzlib=1.2.13 +- llvm-openmp=17.0.6 +- llvm-tools=17.0.6 +- lockfile=0.12.2 +- lxml=4.9.2 +- lz4=4.3.3 +- lz4-c=1.9.4 +- make=4.3 +- markdown-it-py=3.0.0 +- marko=2.0.2 +- markupsafe=2.1.5 +- matplotlib-base=3.7.3 +- matplotlib-inline=0.1.6 +- mdurl=0.1.2 +- mistune=3.0.2 +- 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=0.8.0 +- nbconvert=7.16.0 +- nbconvert-core=7.16.0 +- nbconvert-pandoc=7.16.0 +- nbformat=5.9.2 +- ncurses=6.4 +- nest-asyncio=1.6.0 +- networkx=3.1 +- notebook=6.5.5 +- notebook-shim=0.2.4 +- numpy=1.24.4 +- openjpeg=2.5.0 +- openssl=3.2.1 +- overrides=7.7.0 +- packaging=23.2 +- pandas=1.5.3 +- pandoc=3.1.12 +- pandocfilters=1.5.0 +- pango=1.50.14 +- paramiko=3.4.0 +- parsl=2023.12.4 +- parso=0.8.3 +- pcre2=10.40 +- petl=1.7.14 +- pexpect=4.9.0 +- pickleshare=0.7.5 +- pillow=9.4.0 +- pip=24.0 +- pixman=0.43.2 +- pkgutil-resolve-name=1.3.10 +- platformdirs=4.2.0 +- pluggy=1.4.0 +- pooch=1.8.0 +- prometheus_client=0.20.0 +- prompt-toolkit=3.0.42 +- prompt_toolkit=3.0.42 +- psutil=5.9.8 +- pthread-stubs=0.4 +- ptyprocess=0.7.0 +- pure_eval=0.2.2 +- pycparser=2.21 +- pygments=2.17.2 +- pyjwt=2.8.0 +- pynacl=1.5.0 +- pyobjc-core=10.1 +- pyobjc-framework-cocoa=10.1 +- pyparsing=3.1.1 +- pysocks=1.7.1 +- pytest=8.0.0 +- python=3.8.18 +- python-dateutil=2.8.2 +- python-fastjsonschema=2.19.1 +- python-json-logger=2.0.7 +- python-slugify=8.0.4 +- python_abi=3.8 +- pytz=2024.1 +- pyyaml=6.0.1 +- pyzmq=24.0.1 +- q2-fmt=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-stats=2024.2.0 +- q2-types=2024.2.0 +- q2-vizard=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.3 +- readline=8.2 +- referencing=0.33.0 +- requests=2.31.0 +- rfc3339-validator=0.1.4 +- rfc3986=2.0.0 +- rfc3986-validator=0.1.1 +- rich=13.7.0 +- rpds-py=0.18.0 +- samtools=1.18 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- send2trash=1.8.2 +- setproctitle=1.3.3 +- setuptools=69.0.3 +- shellingham=1.5.4 +- sigtool=0.1.3 +- simpleeval=0.9.13 +- six=1.16.0 +- sniffio=1.3.0 +- soupsieve=2.5 +- stack_data=0.6.2 +- stringcase=1.2.0 +- tabulate=0.9.0 +- tapi=1100.0.11 +- tblib=3.0.0 +- terminado=0.18.0 +- text-unidecode=1.3 +- threadpoolctl=3.3.0 +- tinycss2=1.2.1 +- tk=8.6.13 +- tktable=2.10 +- tomli=2.0.1 +- tomlkit=0.12.3 +- tornado=6.3.3 +- traitlets=5.9.0 +- typeguard=2.13.3 +- typer=0.9.0 +- types-python-dateutil=2.8.19.20240106 +- typing-extensions=4.9.0 +- typing_extensions=4.9.0 +- typing_utils=0.1.0 +- tzlocal=2.1 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.3.2 +- uri-template=1.3.0 +- urllib3=2.2.0 +- validators=0.22.0 +- wcwidth=0.2.13 +- webcolors=1.13 +- webencodings=0.5.1 +- websocket-client=1.7.0 +- wheel=0.42.0 +- xorg-libxau=1.0.11 +- xorg-libxdmcp=1.1.3 +- xz=5.2.6 +- yaml=0.2.5 +- zeromq=4.3.5 +- zipp=3.17.0 +- zlib=1.2.13 +- zstd=1.5.5 diff --git a/2024.5/fmt/passed/qiime2-fmt-ubuntu-latest-conda.yml b/2024.5/fmt/passed/qiime2-fmt-ubuntu-latest-conda.yml new file mode 100644 index 00000000..77dea2e1 --- /dev/null +++ b/2024.5/fmt/passed/qiime2-fmt-ubuntu-latest-conda.yml @@ -0,0 +1,306 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.2/fmt/passed +- bioconda +- conda-forge +- defaults +dependencies: +- _libgcc_mutex=0.1 +- _openmp_mutex=4.5 +- _r-mutex=1.0.1 +- anyio=4.2.0 +- appdirs=1.4.4 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- arrow=1.3.0 +- asttokens=2.4.1 +- atpublic=3.0.1 +- attrs=23.2.0 +- backcall=0.2.0 +- bcrypt=4.1.2 +- beautifulsoup4=4.12.3 +- bibtexparser=1.4.1 +- binutils_impl_linux-64=2.40 +- biom-format=2.1.14 +- bleach=6.1.0 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.26.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.16.0 +- certifi=2024.2.2 +- cffi=1.16.0 +- chardet=5.2.0 +- charset-normalizer=3.3.2 +- click=8.1.7 +- colorama=0.4.6 +- comm=0.2.1 +- conda-pack=0.7.0 +- contourpy=1.1.1 +- cryptography=42.0.3 +- curl=8.1.2 +- cycler=0.12.1 +- cython=3.0.8 +- debugpy=1.8.1 +- decorator=4.4.2 +- defusedxml=0.7.1 +- dill=0.3.8 +- entrypoints=0.4 +- exceptiongroup=1.2.0 +- executing=2.0.1 +- expat=2.5.0 +- flufl.lock=7.1 +- font-ttf-dejavu-sans-mono=2.37 +- font-ttf-inconsolata=3.000 +- font-ttf-source-code-pro=2.038 +- font-ttf-ubuntu=0.83 +- fontconfig=2.14.2 +- fonts-conda-ecosystem=1 +- fonts-conda-forge=1 +- fonttools=4.49.0 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- frictionless=5.5.0 +- gcc_impl_linux-64=13.2.0 +- gettext=0.21.1 +- gfortran_impl_linux-64=13.2.0 +- globus-sdk=3.37.0 +- graphite2=1.3.13 +- gsl=2.7 +- gxx_impl_linux-64=13.2.0 +- h5py=3.8.0 +- harfbuzz=6.0.0 +- hdf5=1.14.0 +- hdmedians=0.14.2 +- humanize=4.9.0 +- icu=70.1 +- idna=3.6 +- ijson=3.2.3 +- importlib-resources=6.1.1 +- importlib_resources=6.1.1 +- iniconfig=2.0.0 +- iow=1.0.5 +- ipykernel=6.29.2 +- ipython=8.12.2 +- ipython_genutils=0.2.0 +- isodate=0.6.1 +- isoduration=20.11.0 +- jedi=0.19.1 +- jinja2=3.1.3 +- joblib=1.3.2 +- jpeg=9e +- jsonpointer=2.4 +- jsonschema=4.21.1 +- jsonschema-specifications=2023.12.1 +- jsonschema-with-format-nongpl=4.21.1 +- jupyter_client=7.4.9 +- jupyter_core=5.7.1 +- jupyter_events=0.9.0 +- jupyter_server=2.12.5 +- jupyter_server_terminals=0.5.2 +- jupyterlab_pygments=0.3.0 +- kernel-headers_linux-64=2.6.32 +- keyutils=1.6.1 +- kiwisolver=1.4.5 +- krb5=1.20.1 +- lcms2=2.15 +- ld_impl_linux-64=2.40 +- lerc=4.0.0 +- libaec=1.1.2 +- libblas=3.9.0 +- libbrotlicommon=1.1.0 +- libbrotlidec=1.1.0 +- libbrotlienc=1.1.0 +- libcblas=3.9.0 +- libcurl=8.1.2 +- libdeflate=1.17 +- libedit=3.1.20191231 +- libev=4.33 +- libexpat=2.5.0 +- libffi=3.4.2 +- libgcc-devel_linux-64=13.2.0 +- libgcc-ng=13.2.0 +- libgfortran-ng=13.2.0 +- libgfortran5=13.2.0 +- libglib=2.78.1 +- libgomp=13.2.0 +- libiconv=1.17 +- liblapack=3.9.0 +- liblapacke=3.9.0 +- libnghttp2=1.58.0 +- libnsl=2.0.1 +- libopenblas=0.3.25 +- libpng=1.6.42 +- libsanitizer=13.2.0 +- libsodium=1.0.18 +- libsqlite=3.45.1 +- libssh2=1.11.0 +- libstdcxx-devel_linux-64=13.2.0 +- libstdcxx-ng=13.2.0 +- libtiff=4.5.0 +- libuuid=2.38.1 +- libwebp-base=1.3.2 +- libxcb=1.13 +- libxcrypt=4.4.36 +- libxml2=2.10.3 +- libxslt=1.1.37 +- libzlib=1.2.13 +- lockfile=0.12.2 +- lxml=4.9.2 +- lz4=4.3.3 +- lz4-c=1.9.4 +- make=4.3 +- markdown-it-py=3.0.0 +- marko=2.0.2 +- markupsafe=2.1.5 +- matplotlib-base=3.7.3 +- matplotlib-inline=0.1.6 +- mdurl=0.1.2 +- mistune=3.0.2 +- mpi=1.0 +- msgpack-python=1.0.7 +- munkres=1.1.4 +- natsort=8.4.0 +- nbclassic=1.0.0 +- nbclient=0.8.0 +- nbconvert=7.16.0 +- nbconvert-core=7.16.0 +- nbconvert-pandoc=7.16.0 +- nbformat=5.9.2 +- ncurses=6.4 +- nest-asyncio=1.6.0 +- networkx=3.1 +- notebook=6.5.5 +- notebook-shim=0.2.4 +- numpy=1.24.4 +- openjpeg=2.5.0 +- openssl=3.2.1 +- overrides=7.7.0 +- packaging=23.2 +- pandas=1.5.3 +- pandoc=3.1.12 +- pandocfilters=1.5.0 +- pango=1.50.14 +- paramiko=3.4.0 +- parsl=2023.12.4 +- parso=0.8.3 +- pcre2=10.40 +- petl=1.7.14 +- pexpect=4.9.0 +- pickleshare=0.7.5 +- pillow=9.4.0 +- pip=24.0 +- pixman=0.43.2 +- pkgutil-resolve-name=1.3.10 +- platformdirs=4.2.0 +- pluggy=1.4.0 +- pooch=1.8.0 +- prometheus_client=0.20.0 +- prompt-toolkit=3.0.42 +- prompt_toolkit=3.0.42 +- psutil=5.9.8 +- pthread-stubs=0.4 +- ptyprocess=0.7.0 +- pure_eval=0.2.2 +- pycparser=2.21 +- pygments=2.17.2 +- pyjwt=2.8.0 +- pynacl=1.5.0 +- pyparsing=3.1.1 +- pysocks=1.7.1 +- pytest=8.0.0 +- python=3.8.18 +- python-dateutil=2.8.2 +- python-fastjsonschema=2.19.1 +- python-json-logger=2.0.7 +- python-slugify=8.0.4 +- python_abi=3.8 +- pytz=2024.1 +- pyyaml=6.0.1 +- pyzmq=24.0.1 +- q2-fmt=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-stats=2024.2.0 +- q2-types=2024.2.0 +- q2-vizard=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.3 +- readline=8.2 +- referencing=0.33.0 +- requests=2.31.0 +- rfc3339-validator=0.1.4 +- rfc3986=2.0.0 +- rfc3986-validator=0.1.1 +- rich=13.7.0 +- rpds-py=0.18.0 +- samtools=1.6 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- sed=4.8 +- send2trash=1.8.2 +- setproctitle=1.3.3 +- setuptools=69.0.3 +- shellingham=1.5.4 +- simpleeval=0.9.13 +- six=1.16.0 +- sniffio=1.3.0 +- soupsieve=2.5 +- stack_data=0.6.2 +- stringcase=1.2.0 +- sysroot_linux-64=2.12 +- tabulate=0.9.0 +- tblib=3.0.0 +- terminado=0.18.0 +- text-unidecode=1.3 +- threadpoolctl=3.3.0 +- tinycss2=1.2.1 +- tk=8.6.13 +- tktable=2.10 +- tomli=2.0.1 +- tomlkit=0.12.3 +- tornado=6.3.3 +- traitlets=5.9.0 +- typeguard=2.13.3 +- typer=0.9.0 +- types-python-dateutil=2.8.19.20240106 +- typing-extensions=4.9.0 +- typing_extensions=4.9.0 +- typing_utils=0.1.0 +- tzlocal=2.1 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.3.2 +- uri-template=1.3.0 +- urllib3=2.2.0 +- validators=0.22.0 +- wcwidth=0.2.13 +- webcolors=1.13 +- webencodings=0.5.1 +- websocket-client=1.7.0 +- wheel=0.42.0 +- 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-libxext=1.3.4 +- xorg-libxrender=0.9.10 +- xorg-libxt=1.3.0 +- xorg-renderproto=0.11.1 +- xorg-xextproto=7.3.0 +- xorg-xproto=7.0.31 +- xz=5.2.6 +- yaml=0.2.5 +- zeromq=4.3.5 +- zipp=3.17.0 +- zlib=1.2.13 +- zstd=1.5.5 diff --git a/2024.5/fmt/passed/seed-environment-conda.yml b/2024.5/fmt/passed/seed-environment-conda.yml new file mode 100644 index 00000000..fedfacb9 --- /dev/null +++ b/2024.5/fmt/passed/seed-environment-conda.yml @@ -0,0 +1,30 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/fmt/passed +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- h5py=3.8.0 +- hdf5=1.14.0 +- notebook=6.5.5 +- numpy=1.24.4 +- pandas=1.5.3 +- parsl=2023.12.04 +- python=3.8 +- q2-fmt=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-stats=2024.2.0 +- q2-types=2024.2.0 +- q2-vizard=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2' diff --git a/2024.5/fmt/staged/seed-environment-conda.yml b/2024.5/fmt/staged/seed-environment-conda.yml new file mode 100644 index 00000000..96b7abd6 --- /dev/null +++ b/2024.5/fmt/staged/seed-environment-conda.yml @@ -0,0 +1,30 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/fmt/staged +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- h5py=3.8.0 +- hdf5=1.14.0 +- notebook=6.5.5 +- numpy=1.24.4 +- pandas=1.5.3 +- parsl=2023.12.04 +- python=3.8 +- q2-fmt=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-stats=2024.2.0 +- q2-types=2024.2.0 +- q2-vizard=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2' diff --git a/2024.5/shotgun/passed/qiime2-shotgun-macos-latest-conda.yml b/2024.5/shotgun/passed/qiime2-shotgun-macos-latest-conda.yml new file mode 100644 index 00000000..733d4ed5 --- /dev/null +++ b/2024.5/shotgun/passed/qiime2-shotgun-macos-latest-conda.yml @@ -0,0 +1,765 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.2/shotgun/passed +- bioconda +- conda-forge +- defaults +dependencies: +- _r-mutex=1.0.1 +- altair=5.2.0 +- anyio=4.2.0 +- appdirs=1.4.4 +- appnope=0.1.4 +- argcomplete=3.2.2 +- argh=0.31.2 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- aria2=1.36.0 +- 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 +- 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-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 +- blast=2.15.0 +- bleach=6.1.0 +- boost-cpp=1.74.0 +- bowtie2=2.5.1 +- bracken=2.6.1 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- busco=5.5.0 +- bwa=0.7.17 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.26.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.16.0 +- cctools_osx-64=973.0.1 +- 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 +- click=8.1.7 +- colorama=0.4.6 +- comm=0.2.1 +- compiler-rt=17.0.6 +- compiler-rt_osx-64=17.0.6 +- conda-pack=0.7.0 +- contourpy=1.1.1 +- cryptography=42.0.3 +- curl=7.88.1 +- cutadapt=4.6 +- cycler=0.12.1 +- cython=3.0.8 +- debugpy=1.8.1 +- decorator=4.4.2 +- defusedxml=0.7.1 +- dendropy=4.5.2 +- diamond=2.1.9 +- dill=0.3.8 +- dnaio=1.2.0 +- easel=0.49 +- eggnog-mapper=2.1.12 +- emperor=1.0.4 +- entrez-direct=16.2 +- entrezpy=2.1.3 +- entrypoints=0.4 +- exceptiongroup=1.2.0 +- executing=2.0.1 +- expat=2.5.0 +- fastcluster=1.2.6 +- feedparser=6.0.11 +- flufl.lock=7.1 +- font-ttf-dejavu-sans-mono=2.37 +- font-ttf-inconsolata=3.000 +- font-ttf-source-code-pro=2.038 +- font-ttf-ubuntu=0.83 +- fontconfig=2.14.2 +- fonts-conda-ecosystem=1 +- fonts-conda-forge=1 +- fonttools=4.49.0 +- formulaic=1.0.1 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- future=0.18.3 +- gawk=5.3.0 +- gettext=0.21.1 +- gffutils=0.10.1 +- gfortran_impl_osx-64=11.4.0 +- gfortran_osx-64=11.4.0 +- giflib=5.2.1 +- glimmerhmm=3.0.4 +- globus-sdk=3.37.0 +- 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 +- hdmedians=0.14.2 +- hmmer=3.1b2 +- 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typeguard=2.13.3 +- types-python-dateutil=2.8.19.20240106 +- typing-extensions=4.9.0 +- typing_extensions=4.9.0 +- typing_utils=0.1.0 +- 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 +- uri-template=1.3.0 +- urllib3=1.26.18 +- vsearch=2.27.0 +- wcwidth=0.2.13 +- webcolors=1.13 +- webencodings=0.5.1 +- websocket-client=1.7.0 +- wget=1.20.3 +- wheel=0.42.0 +- widgetsnbextension=4.0.10 +- wrapt=1.16.0 +- xlsxwriter=3.1.9 +- xmltodict=0.13.0 +- xopen=1.9.0 +- 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 +- xz=5.2.6 +- yaml=0.2.5 +- yq=3.2.3 +- zeromq=4.3.5 +- zipp=3.17.0 +- zlib=1.2.13 +- zstandard=0.22.0 +- zstd=1.5.5 diff --git a/2024.5/shotgun/passed/qiime2-shotgun-ubuntu-latest-conda.yml b/2024.5/shotgun/passed/qiime2-shotgun-ubuntu-latest-conda.yml new file mode 100644 index 00000000..9ea565e7 --- /dev/null +++ b/2024.5/shotgun/passed/qiime2-shotgun-ubuntu-latest-conda.yml @@ -0,0 +1,825 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.2/shotgun/passed +- bioconda +- conda-forge +- defaults +dependencies: +- _libgcc_mutex=0.1 +- _openmp_mutex=4.5 +- _r-mutex=1.0.1 +- _sysroot_linux-64_curr_repodata_hack=3 +- alsa-lib=1.2.8 +- altair=5.2.0 +- anyio=4.2.0 +- appdirs=1.4.4 +- argcomplete=3.2.2 +- argh=0.31.2 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- aria2=1.36.0 +- arrow=1.3.0 +- astor=0.8.1 +- asttokens=2.4.1 +- atpublic=3.0.1 +- attr=2.5.1 +- attrs=23.2.0 +- augustus=3.5.0 +- backcall=0.2.0 +- bamtools=2.5.1 +- bbmap=39.01 +- bc=1.07.1 +- bcftools=1.17 +- 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-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 +- blast=2.14.1 +- bleach=6.1.0 +- boost-cpp=1.74.0 +- bowtie2=2.5.1 +- bracken=2.9 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- busco=5.5.0 +- bwa=0.7.17 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fonts-conda-forge=1 +- fonttools=4.49.0 +- formulaic=1.0.1 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- future=0.18.3 +- gawk=5.3.0 +- gcc_impl_linux-64=13.2.0 +- gettext=0.21.1 +- gffutils=0.10.1 +- gfortran_impl_linux-64=13.2.0 +- giflib=5.2.1 +- glib=2.78.1 +- glib-tools=2.78.1 +- glimmerhmm=3.0.4 +- globus-sdk=3.37.0 +- 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=0.4.37 +- gxx_impl_linux-64=13.2.0 +- h5py=3.8.0 +- harfbuzz=6.0.0 +- hdf5=1.14.0 +- hdmedians=0.14.2 +- hmmer=3.1b2 +- htslib=1.17 +- icu=70.1 +- idna=3.6 +- ijson=3.2.3 +- importlib-metadata=7.0.1 +- importlib_resources=6.1.1 +- iniconfig=2.0.0 +- insilicoseq=1.5.4 +- interface_meta=1.3.0 +- iow=1.0.5 +- ipykernel=6.29.2 +- ipython=8.12.2 +- 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=1.3.2 +- jpeg=9e +- jq=1.7.1 +- jsonlines=3.0.0 +- jsonpointer=2.4 +- jsonschema=4.21.1 +- jsonschema-specifications=2023.12.1 +- jsonschema-with-format-nongpl=4.21.1 +- jupyter_client=7.4.9 +- jupyter_core=5.7.1 +- jupyter_events=0.9.0 +- jupyter_server=2.12.5 +- jupyter_server_terminals=0.5.2 +- jupyterlab_pygments=0.3.0 +- jupyterlab_widgets=3.0.10 +- k8=0.2.5 +- kaiju=1.10.0 +- kernel-headers_linux-64=3.10.0 +- keyutils=1.6.1 +- kiwisolver=1.4.5 +- kraken2=2.1.3 +- krb5=1.20.1 +- lame=3.100 +- lcms2=2.14 +- ld_impl_linux-64=2.40 +- lerc=4.0.0 +- libaec=1.1.2 +- libblas=3.9.0 +- libbrotlicommon=1.1.0 +- libbrotlidec=1.1.0 +- libbrotlienc=1.1.0 +- libcap=2.66 +- libcblas=3.9.0 +- libclang=15.0.7 +- libclang13=15.0.7 +- libcups=2.3.3 +- libcurl=7.88.1 +- libdb=6.2.32 +- libdeflate=1.13 +- libedit=3.1.20191231 +- libev=4.33 +- libevent=2.1.10 +- libexpat=2.5.0 +- libffi=3.4.2 +- libflac=1.4.3 +- libgcc-devel_linux-64=13.2.0 +- libgcc-ng=13.2.0 +- libgcrypt=1.10.3 +- libgd=2.3.3 +- libgfortran-ng=13.2.0 +- 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matplotlib-inline=0.1.6 +- megahit=1.2.9 +- metabat2=2.15 +- metaeuk=6.a5d39d9 +- metis=5.1.0 +- minimap2=2.26 +- miniprot=0.12 +- mistune=3.0.2 +- mmseqs2=15.6f452 +- mpfr=4.2.1 +- mpg123=1.32.4 +- mpi=1.0 +- msgpack-python=1.0.7 +- munkres=1.1.4 +- mysql-common=8.0.32 +- mysql-connector-c=6.1.11 +- mysql-libs=8.0.32 +- natsort=8.4.0 +- nbclassic=1.0.0 +- nbclient=0.8.0 +- nbconvert=7.16.0 +- nbconvert-core=7.16.0 +- nbconvert-pandoc=7.16.0 +- nbformat=5.9.2 +- ncbi-datasets-pylib=16.4.8 +- ncbi-vdb=3.0.0 +- ncurses=6.4 +- nest-asyncio=1.6.0 +- networkx=3.1 +- nlopt=2.7.1 +- notebook=6.5.5 +- notebook-shim=0.2.4 +- nspr=4.35 +- nss=3.98 +- numba=0.58.1 +- numpy=1.24.4 +- oniguruma=6.9.9 +- openjdk=17.0.3 +- openjpeg=2.5.0 +- openmp=8.0.1 +- openssl=1.1.1w +- overrides=7.7.0 +- packaging=23.2 +- pandas=1.5.3 +- pandoc=3.1.12 +- pandocfilters=1.5.0 +- pango=1.50.14 +- paramiko=3.4.0 +- parsl=2023.12.4 +- parso=0.8.3 +- pathlib=1.0.1 +- patsy=0.5.3 +- pbzip2=1.1.13 +- pcre=8.45 +- pcre2=10.40 +- perl=5.32.1 +- perl-app-cpanminus=1.7047 +- perl-archive-tar=2.40 +- perl-b-cow=0.007 +- perl-carp=1.50 +- perl-class-method-modifiers=2.13 +- perl-clone=0.46 +- perl-common-sense=3.75 +- perl-compress-raw-bzip2=2.201 +- perl-compress-raw-zlib=2.202 +- perl-config-general=2.65 +- perl-constant=1.33 +- perl-dbi=1.643 +- perl-digest-perl-md5=1.9 +- perl-encode=3.19 +- perl-exporter=5.74 +- perl-exporter-tiny=1.002002 +- perl-extutils-config=0.008 +- perl-extutils-helpers=0.026 +- perl-extutils-installpaths=0.012 +- perl-extutils-makemaker=7.70 +- perl-extutils-pl2bat=0.005 +- perl-file-path=2.18 +- perl-file-temp=0.2304 +- perl-file-which=1.24 +- perl-font-ttf=1.06 +- perl-gd=2.76 +- perl-inc-latest=0.500 +- perl-io-compress=2.201 +- perl-io-string=1.08 +- perl-io-zlib=1.14 +- perl-json=4.10 +- perl-json-xs=2.34 +- perl-list-moreutils=0.430 +- perl-list-moreutils-xs=0.430 +- perl-math-bezier=0.01 +- perl-math-round=0.07 +- perl-math-vecstat=0.08 +- perl-module-build=0.4232 +- perl-module-build-tiny=0.039 +- perl-module-implementation=0.09 +- perl-module-runtime=0.016 +- perl-moo=2.005004 +- perl-number-format=1.76 +- perl-parallel-forkmanager=2.02 +- perl-params-validate=1.31 +- perl-parent=0.241 +- perl-pathtools=3.75 +- perl-readonly=2.05 +- perl-regexp-common=2017060201 +- perl-role-tiny=2.002004 +- perl-scalar-list-utils=1.63 +- perl-set-intspan=1.19 +- perl-statistics-basic=1.6611 +- perl-storable=3.15 +- perl-sub-quote=2.006006 +- perl-svg=2.87 +- perl-test-fatal=0.016 +- perl-text-format=0.62 +- perl-time-hires=1.9764 +- perl-try-tiny=0.31 +- perl-types-serialiser=1.01 +- perl-xml-parser=2.44_01 +- perl-yaml=1.30 +- pexpect=4.9.0 +- pickleshare=0.7.5 +- pigz=2.8 +- pillow=9.2.0 +- pip=24.0 +- pixman=0.43.2 +- pkgutil-resolve-name=1.3.10 +- platformdirs=4.2.0 +- pluggy=1.4.0 +- ply=3.11 +- pooch=1.8.0 +- 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 +- pure_eval=0.2.2 +- pycparser=2.21 +- pyfaidx=0.8.1.1 +- pygments=2.17.2 +- pyjwt=2.8.0 +- pynacl=1.5.0 +- pynndescent=0.5.11 +- pyparsing=3.1.1 +- pyqt=5.15.7 +- pyqt5-sip=12.11.0 +- pysam=0.21.0 +- pysocks=1.7.1 +- pytest=8.0.0 +- python=3.8.15 +- python-dateutil=2.8.2 +- python-dotenv=1.0.1 +- python-fastjsonschema=2.19.1 +- python-isal=1.5.3 +- python-json-logger=2.0.7 +- python_abi=3.8 +- pytz=2024.1 +- pyvcf3=1.0.3 +- pyyaml=6.0.1 +- pyzmq=24.0.1 +- pyzotero=1.5.18 +- q2-assembly=2024.2.0 +- q2-composition=2024.2.0 +- q2-cutadapt=2024.2.0 +- q2-demux=2024.2.0 +- q2-diversity=2024.2.0 +- q2-diversity-lib=2024.2.0 +- q2-emperor=2024.2.0 +- q2-feature-classifier=2024.2.0 +- q2-feature-table=2024.2.0 +- q2-fondue=2024.2.0 +- q2-longitudinal=2024.2.0 +- q2-metadata=2024.2.0 +- q2-moshpit=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-quality-control=2024.2.0 +- q2-quality-filter=2024.2.0 +- q2-sample-classifier=2024.2.0 +- q2-sapienns=2024.2.0 +- q2-taxa=2024.2.0 +- q2-types=2024.2.0 +- q2-vsearch=2024.2.0 +- q2cli=2024.2.0 +- q2templates=2024.2.0 +- qiime2=2024.2.0 +- qt-main=5.15.6 +- quast=5.2.0 +- r-ade4=1.7_22 +- r-ape=5.7_1 +- r-argparser=0.7.1 +- r-askpass=1.2.0 +- r-assertthat=0.2.1 +- r-backports=1.4.1 +- r-base=4.2.2 +- r-base64enc=0.1_3 +- r-beeswarm=0.4.0 +- r-bh=1.84.0_0 +- r-bibtex=0.5.1 +- r-bit=4.0.5 +- r-bit64=4.0.5 +- r-bitops=1.0_7 +- r-blob=1.2.4 +- r-boot=1.3_28.1 +- r-brio=1.1.4 +- r-broom=1.0.5 +- r-bslib=0.6.1 +- r-cachem=1.0.8 +- r-cairo=1.6_0 +- r-callr=3.7.3 +- r-cellranger=1.1.0 +- r-checkmate=2.3.0 +- r-class=7.3_22 +- r-cli=3.6.2 +- r-clipr=0.8.0 +- r-cluster=2.1.6 +- r-codetools=0.2_19 +- r-colorspace=2.1_0 +- r-cpp11=0.4.7 +- r-crayon=1.5.2 +- r-curl=4.3.3 +- r-cvxr=1.0_12 +- r-data.table=1.14.10 +- r-dbi=1.2.2 +- r-dbplyr=2.4.0 +- r-deldir=2.0_2 +- r-desc=1.4.3 +- r-desctools=0.99.51 +- r-diffobj=0.3.5 +- r-digest=0.6.34 +- r-doparallel=1.0.17 +- r-dorng=1.8.6 +- r-dplyr=1.1.4 +- r-dqrng=0.3.2 +- r-dtplyr=1.3.1 +- r-e1071=1.7_14 +- r-ecosolver=0.5.5 +- r-ellipsis=0.3.2 +- r-emmeans=1.10.0 +- r-energy=1.7_11 +- r-estimability=1.4.1 +- r-evaluate=0.23 +- r-exact=3.2 +- r-expm=0.999_9 +- r-fansi=1.0.6 +- r-farver=2.1.1 +- r-fastmap=1.1.1 +- r-filelock=1.0.3 +- r-fnn=1.1.4 +- r-fontawesome=0.5.2 +- r-forcats=1.0.0 +- r-foreach=1.5.2 +- r-foreign=0.8_86 +- r-formatr=1.14 +- r-formula=1.2_5 +- r-frictionless=1.0.2 +- r-fs=1.6.3 +- r-futile.logger=1.4.3 +- r-futile.options=1.0.1 +- r-gargle=1.5.2 +- r-gbrd=0.4_11 +- r-generics=0.1.3 +- r-getopt=1.20.4 +- r-ggbeeswarm=0.7.2 +- r-ggplot2=3.4.4 +- r-ggrastr=1.0.2 +- r-ggrepel=0.9.5 +- r-gld=2.6.6 +- r-glue=1.7.0 +- r-gmp=0.7_4 +- r-googledrive=2.1.1 +- r-googlesheets4=1.1.1 +- r-gridextra=2.3 +- r-gsl=2.1_8 +- r-gtable=0.3.4 +- r-haven=2.5.4 +- r-highr=0.10 +- r-hmisc=5.1_1 +- r-hms=1.1.3 +- r-htmltable=2.4.2 +- r-htmltools=0.5.7 +- r-htmlwidgets=1.6.4 +- r-httr=1.4.7 +- r-ids=1.0.1 +- r-igraph=1.4.2 +- r-interp=1.1_6 +- r-irlba=2.3.5.1 +- r-isoband=0.2.7 +- r-iterators=1.0.14 +- r-jpeg=0.1_10 +- r-jquerylib=0.1.4 +- r-jsonlite=1.8.8 +- r-knitr=1.45 +- r-labeling=0.4.3 +- r-lambda.r=1.2.4 +- r-lattice=0.22_5 +- r-latticeextra=0.6_30 +- r-lazyeval=0.2.2 +- r-lifecycle=1.0.4 +- r-lme4=1.1_35.1 +- r-lmertest=3.1_3 +- r-lmom=3.0 +- r-lubridate=1.9.3 +- r-magrittr=2.0.3 +- r-mass=7.3_60.0.1 +- r-matrix=1.6_5 +- r-matrixstats=1.2.0 +- r-memoise=2.0.1 +- r-mgcv=1.9_1 +- r-mime=0.12 +- r-minqa=1.2.6 +- r-modelr=0.1.11 +- r-munsell=0.5.0 +- 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-optparse=1.7.4 +- 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-pkgbuild=1.4.2 +- r-pkgconfig=2.0.3 +- r-pkgload=1.3.4 +- r-pkgmaker=0.32.10 +- r-plogr=0.2.0 +- r-plyr=1.8.9 +- r-png=0.1_8 +- r-praise=1.0.0 +- r-prettyunits=1.2.0 +- r-processx=3.8.3 +- r-progress=1.2.3 +- r-proxy=0.4_27 +- r-ps=1.7.6 +- r-purrr=1.0.2 +- r-r6=2.5.1 +- r-ragg=1.2.4 +- r-rappdirs=0.3.3 +- r-rbibutils=2.2.16 +- r-rcolorbrewer=1.1_3 +- r-rcpp=1.0.12 +- r-rcppannoy=0.0.22 +- r-rcppeigen=0.3.3.9.4 +- r-rcpphnsw=0.6.0 +- r-rcppml=0.3.7 +- r-rcppprogress=0.4.2 +- r-rcurl=1.98_1.12 +- r-rdpack=2.6 +- r-readr=2.1.5 +- r-readxl=1.4.3 +- r-registry=0.5_1 +- r-rematch=2.0.0 +- r-rematch2=2.1.2 +- r-reprex=2.1.0 +- r-reshape2=1.4.4 +- r-restfulr=0.0.15 +- r-rjson=0.2.21 +- r-rlang=1.1.3 +- r-rmarkdown=2.25 +- r-rmpfr=0.9_5 +- r-rngtools=1.5.2 +- r-rootsolve=1.8.2.4 +- r-rpart=4.1.23 +- r-rprojroot=2.0.4 +- r-rsqlite=2.3.4 +- r-rstudioapi=0.15.0 +- r-rsvd=1.0.5 +- r-rtsne=0.17 +- r-rvest=1.0.4 +- r-sass=0.4.8 +- 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-statmod=1.5.0 +- r-stringdist=0.9.10 +- r-stringi=1.7.12 +- r-stringr=1.5.1 +- r-survival=3.5_8 +- r-sys=3.4.2 +- r-systemfonts=1.0.5 +- r-testthat=3.2.1 +- r-textshaping=0.3.6 +- r-tibble=3.2.1 +- r-tidyr=1.3.1 +- r-tidyselect=1.2.0 +- r-tidytree=0.4.6 +- r-tidyverse=1.3.2 +- r-timechange=0.3.0 +- r-tinytex=0.49 +- r-tzdb=0.4.0 +- r-utf8=1.2.4 +- r-uuid=1.2_0 +- r-uwot=0.1.16 +- r-vctrs=0.6.5 +- r-vegan=2.6_4 +- r-vipor=0.4.7 +- r-viridis=0.6.5 +- r-viridislite=0.4.2 +- r-vroom=1.6.5 +- r-waldo=0.5.2 +- r-withr=3.0.0 +- r-xfun=0.42 +- r-xml=3.99_0.14 +- r-xml2=1.3.3 +- r-xtable=1.8_4 +- r-yaml=2.3.8 +- r-yulab.utils=0.1.4 +- readline=8.2 +- referencing=0.33.0 +- repeatmasker=4.1.5 +- requests=2.31.0 +- rescript=2024.2.0 +- rfc3339-validator=0.1.4 +- 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 +- seaborn=0.12.2 +- seaborn-base=0.12.2 +- sed=4.8 +- send2trash=1.8.2 +- sepp=4.3.10 +- setproctitle=1.3.3 +- setuptools=69.0.3 +- sgmllib3k=1.0.0 +- simplejson=3.19.2 +- sip=6.7.12 +- six=1.16.0 +- sniffio=1.3.0 +- soupsieve=2.5 +- spades=3.15.2 +- sqlite=3.45.1 +- stack_data=0.6.2 +- statsmodels=0.14.0 +- suitesparse=5.10.1 +- sysroot_linux-64=2.17 +- tar=1.34 +- tbb=2021.9.0 +- tblib=3.0.0 +- terminado=0.18.0 +- threadpoolctl=3.3.0 +- tinycss2=1.2.1 +- tk=8.6.13 +- tktable=2.10 +- toml=0.10.2 +- tomli=2.0.1 +- tomlkit=0.12.3 +- toolz=0.12.1 +- tornado=6.3.3 +- tqdm=4.66.2 +- traitlets=5.9.0 +- trf=4.09.1 +- typeguard=2.13.3 +- types-python-dateutil=2.8.19.20240106 +- typing-extensions=4.9.0 +- typing_extensions=4.9.0 +- typing_utils=0.1.0 +- tzlocal=2.1 +- ucsc-fatotwobit=447 +- ucsc-twobitinfo=447 +- umap-learn=0.5.4 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.3.2 +- uri-template=1.3.0 +- urllib3=1.26.18 +- vsearch=2.27.0 +- wcwidth=0.2.13 +- webcolors=1.13 +- webencodings=0.5.1 +- websocket-client=1.7.0 +- wget=1.20.3 +- wheel=0.42.0 +- widgetsnbextension=4.0.10 +- wrapt=1.16.0 +- xcb-util=0.4.0 +- xcb-util-image=0.4.0 +- xcb-util-keysyms=0.4.0 +- xcb-util-renderutil=0.3.9 +- xcb-util-wm=0.4.1 +- xkeyboard-config=2.38 +- xlsxwriter=3.1.9 +- xmltodict=0.13.0 +- xopen=1.9.0 +- 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-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-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-xproto=7.0.31 +- xz=5.2.6 +- yaml=0.2.5 +- yq=3.2.3 +- zeromq=4.3.5 +- zipp=3.17.0 +- zlib=1.2.13 +- zstandard=0.22.0 +- zstd=1.5.5 diff --git a/2024.5/shotgun/passed/seed-environment-conda.yml b/2024.5/shotgun/passed/seed-environment-conda.yml new file mode 100644 index 00000000..e15232aa --- /dev/null +++ b/2024.5/shotgun/passed/seed-environment-conda.yml @@ -0,0 +1,53 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/shotgun/passed +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- bowtie2=2.5.1 +- h5py=3.8.0 +- hdf5=1.14.0 +- matplotlib=3.6.0 +- 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=2024.2.0 +- q2-composition=2024.2.0 +- q2-cutadapt=2024.2.0 +- q2-demux=2024.2.0 +- q2-diversity-lib=2024.2.0 +- q2-diversity=2024.2.0 +- q2-emperor=2024.2.0 +- q2-feature-classifier=2024.2.0 +- q2-feature-table=2024.2.0 +- q2-fondue=2024.2.0 +- q2-longitudinal=2024.2.0 +- q2-metadata=2024.2.0 +- q2-moshpit=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-quality-control=2024.2.0 +- q2-quality-filter=2024.2.0 +- q2-sample-classifier=2024.2.0 +- q2-sapienns=2024.2.0 +- q2-taxa=2024.2.0 +- q2-types=2024.2.0 +- q2-vsearch=2024.2.0 +- q2cli=2024.2.0 +- q2templates=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- rescript=2024.2.0 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- seaborn=0.12.2 +- umap-learn=0.5.4 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2' diff --git a/2024.5/shotgun/staged/seed-environment-conda.yml b/2024.5/shotgun/staged/seed-environment-conda.yml new file mode 100644 index 00000000..36d1f3e3 --- /dev/null +++ b/2024.5/shotgun/staged/seed-environment-conda.yml @@ -0,0 +1,54 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/shotgun/staged +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- bowtie2=2.5.1 +- h5py=3.8.0 +- hdf5=1.14.0 +- matplotlib=3.6.0 +- 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=2024.2.0 +- q2-composition=2024.2.0 +- q2-cutadapt=2024.2.0 +- q2-demux=2024.2.0 +- q2-diversity-lib=2024.2.0 +- q2-diversity=2024.2.0 +- q2-emperor=2024.2.0 +- q2-feature-classifier=2024.2.0 +- q2-feature-table=2024.2.0 +- q2-fondue=2024.2.0 +- q2-longitudinal=2024.2.0 +- q2-metadata=2024.2.0 +- q2-moshpit=2024.2.0 +- q2-mystery-stew=2024.2.0 +- q2-quality-control=2024.2.0 +- q2-quality-filter=2024.2.0 +- q2-sample-classifier=2024.2.0 +- q2-sapienns=2024.2.0 +- q2-taxa=2024.2.0 +- q2-types-genomics=2023.11.0.dev0+8.g3b993ed +- q2-types=2024.2.0 +- q2-vsearch=2024.2.0 +- q2cli=2024.2.0 +- q2templates=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- rescript=2024.2.0 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- seaborn=0.12.2 +- umap-learn=0.5.4 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2' diff --git a/2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml b/2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml new file mode 100644 index 00000000..c7cf3382 --- /dev/null +++ b/2024.5/tiny/passed/qiime2-tiny-macos-latest-conda.yml @@ -0,0 +1,284 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.2/tiny/passed +- bioconda +- conda-forge +- defaults +dependencies: +- _r-mutex=1.0.1 +- anyio=4.2.0 +- appdirs=1.4.4 +- appnope=0.1.4 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- arrow=1.3.0 +- asttokens=2.4.1 +- atpublic=3.0.1 +- attrs=23.2.0 +- backcall=0.2.0 +- bcrypt=4.1.2 +- beautifulsoup4=4.12.3 +- bibtexparser=1.4.1 +- biom-format=2.1.14 +- bleach=6.1.0 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.26.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.16.0 +- cctools_osx-64=973.0.1 +- certifi=2024.2.2 +- cffi=1.16.0 +- charset-normalizer=3.3.2 +- 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 +- click=8.1.7 +- colorama=0.4.6 +- comm=0.2.1 +- compiler-rt=17.0.6 +- compiler-rt_osx-64=17.0.6 +- conda-pack=0.7.0 +- contourpy=1.1.1 +- cryptography=42.0.3 +- curl=7.88.1 +- cycler=0.12.1 +- cython=3.0.8 +- debugpy=1.8.1 +- decorator=4.4.2 +- defusedxml=0.7.1 +- dill=0.3.8 +- entrypoints=0.4 +- exceptiongroup=1.2.0 +- executing=2.0.1 +- expat=2.5.0 +- flufl.lock=7.1 +- font-ttf-dejavu-sans-mono=2.37 +- font-ttf-inconsolata=3.000 +- font-ttf-source-code-pro=2.038 +- font-ttf-ubuntu=0.83 +- fontconfig=2.14.2 +- fonts-conda-ecosystem=1 +- fonts-conda-forge=1 +- fonttools=4.49.0 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- gettext=0.21.1 +- gfortran_impl_osx-64=11.4.0 +- gfortran_osx-64=11.4.0 +- globus-sdk=3.37.0 +- gmp=6.3.0 +- graphite2=1.3.13 +- gsl=2.7 +- h5py=3.8.0 +- harfbuzz=6.0.0 +- hdf5=1.14.0 +- hdmedians=0.14.2 +- htslib=1.17 +- icu=70.1 +- idna=3.6 +- ijson=3.2.3 +- importlib-resources=6.1.1 +- importlib_resources=6.1.1 +- iniconfig=2.0.0 +- iow=1.0.5 +- ipykernel=6.29.2 +- ipython=8.12.2 +- ipython_genutils=0.2.0 +- isl=0.25 +- isoduration=20.11.0 +- jedi=0.19.1 +- jinja2=3.1.3 +- joblib=1.3.2 +- jpeg=9e +- jsonpointer=2.4 +- jsonschema=4.21.1 +- jsonschema-specifications=2023.12.1 +- jsonschema-with-format-nongpl=4.21.1 +- jupyter_client=7.4.9 +- jupyter_core=5.7.1 +- jupyter_events=0.9.0 +- jupyter_server=2.12.5 +- jupyter_server_terminals=0.5.2 +- jupyterlab_pygments=0.3.0 +- kiwisolver=1.4.5 +- krb5=1.20.1 +- lcms2=2.15 +- ld64_osx-64=609 +- lerc=4.0.0 +- libaec=1.1.2 +- libblas=3.9.0 +- libbrotlicommon=1.1.0 +- 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=1.17 +- libedit=3.1.20191231 +- libev=4.33 +- libexpat=2.5.0 +- libffi=3.4.4 +- libgfortran=5.0.0 +- libgfortran-devel_osx-64=11.4.0 +- libgfortran5=13.2.0 +- libglib=2.78.1 +- libiconv=1.17 +- liblapack=3.9.0 +- liblapacke=3.9.0 +- libllvm17=17.0.6 +- libnghttp2=1.58.0 +- libopenblas=0.3.25 +- libpng=1.6.42 +- libsodium=1.0.18 +- libsqlite=3.45.1 +- libssh2=1.11.0 +- libtiff=4.5.0 +- libwebp-base=1.3.2 +- libxcb=1.13 +- libxml2=2.10.3 +- libxslt=1.1.37 +- libzlib=1.2.13 +- llvm-openmp=17.0.6 +- llvm-tools=17.0.6 +- lockfile=0.12.2 +- lxml=4.9.2 +- lz4=4.3.3 +- lz4-c=1.9.4 +- make=4.3 +- markupsafe=2.1.5 +- matplotlib-base=3.7.3 +- matplotlib-inline=0.1.6 +- mistune=3.0.2 +- 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=0.8.0 +- nbconvert=7.16.0 +- nbconvert-core=7.16.0 +- nbconvert-pandoc=7.16.0 +- nbformat=5.9.2 +- ncurses=6.4 +- nest-asyncio=1.6.0 +- networkx=3.1 +- notebook=6.5.5 +- notebook-shim=0.2.4 +- numpy=1.24.4 +- openjpeg=2.5.0 +- openssl=3.2.1 +- overrides=7.7.0 +- packaging=23.2 +- pandas=1.5.3 +- pandoc=3.1.12 +- pandocfilters=1.5.0 +- pango=1.50.14 +- paramiko=3.4.0 +- parsl=2023.12.4 +- parso=0.8.3 +- pcre2=10.40 +- pexpect=4.9.0 +- pickleshare=0.7.5 +- pillow=9.4.0 +- pip=24.0 +- pixman=0.43.2 +- pkgutil-resolve-name=1.3.10 +- platformdirs=4.2.0 +- pluggy=1.4.0 +- pooch=1.8.0 +- prometheus_client=0.20.0 +- prompt-toolkit=3.0.42 +- prompt_toolkit=3.0.42 +- psutil=5.9.8 +- pthread-stubs=0.4 +- ptyprocess=0.7.0 +- pure_eval=0.2.2 +- pycparser=2.21 +- pygments=2.17.2 +- pyjwt=2.8.0 +- pynacl=1.5.0 +- pyobjc-core=10.1 +- pyobjc-framework-cocoa=10.1 +- pyparsing=3.1.1 +- pysocks=1.7.1 +- pytest=8.0.0 +- python=3.8.18 +- python-dateutil=2.8.2 +- python-fastjsonschema=2.19.1 +- python-json-logger=2.0.7 +- python_abi=3.8 +- pytz=2024.1 +- pyyaml=6.0.1 +- pyzmq=24.0.1 +- q2-mystery-stew=2024.2.0 +- q2-types=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.3 +- readline=8.2 +- referencing=0.33.0 +- requests=2.31.0 +- 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 +- send2trash=1.8.2 +- setproctitle=1.3.3 +- setuptools=69.0.3 +- sigtool=0.1.3 +- six=1.16.0 +- sniffio=1.3.0 +- soupsieve=2.5 +- stack_data=0.6.2 +- tapi=1100.0.11 +- tblib=3.0.0 +- terminado=0.18.0 +- threadpoolctl=3.3.0 +- tinycss2=1.2.1 +- tk=8.6.13 +- tktable=2.10 +- tomli=2.0.1 +- tomlkit=0.12.3 +- tornado=6.3.3 +- traitlets=5.9.0 +- typeguard=2.13.3 +- types-python-dateutil=2.8.19.20240106 +- typing-extensions=4.9.0 +- typing_extensions=4.9.0 +- typing_utils=0.1.0 +- tzlocal=2.1 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.3.2 +- uri-template=1.3.0 +- urllib3=2.2.0 +- wcwidth=0.2.13 +- webcolors=1.13 +- webencodings=0.5.1 +- websocket-client=1.7.0 +- wheel=0.42.0 +- xorg-libxau=1.0.11 +- xorg-libxdmcp=1.1.3 +- xz=5.2.6 +- yaml=0.2.5 +- zeromq=4.3.5 +- zipp=3.17.0 +- zlib=1.2.13 +- zstd=1.5.5 diff --git a/2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml b/2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml new file mode 100644 index 00000000..dacb82c1 --- /dev/null +++ b/2024.5/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml @@ -0,0 +1,285 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.2/tiny/passed +- bioconda +- conda-forge +- defaults +dependencies: +- _libgcc_mutex=0.1 +- _openmp_mutex=4.5 +- _r-mutex=1.0.1 +- anyio=4.2.0 +- appdirs=1.4.4 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- arrow=1.3.0 +- asttokens=2.4.1 +- atpublic=3.0.1 +- attrs=23.2.0 +- backcall=0.2.0 +- bcrypt=4.1.2 +- beautifulsoup4=4.12.3 +- bibtexparser=1.4.1 +- binutils_impl_linux-64=2.40 +- biom-format=2.1.14 +- bleach=6.1.0 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.26.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.16.0 +- certifi=2024.2.2 +- cffi=1.16.0 +- charset-normalizer=3.3.2 +- click=8.1.7 +- colorama=0.4.6 +- comm=0.2.1 +- conda-pack=0.7.0 +- contourpy=1.1.1 +- cryptography=42.0.3 +- curl=8.1.2 +- cycler=0.12.1 +- cython=3.0.8 +- debugpy=1.8.1 +- decorator=4.4.2 +- defusedxml=0.7.1 +- dill=0.3.8 +- entrypoints=0.4 +- exceptiongroup=1.2.0 +- executing=2.0.1 +- expat=2.5.0 +- flufl.lock=7.1 +- font-ttf-dejavu-sans-mono=2.37 +- font-ttf-inconsolata=3.000 +- font-ttf-source-code-pro=2.038 +- font-ttf-ubuntu=0.83 +- fontconfig=2.14.2 +- fonts-conda-ecosystem=1 +- fonts-conda-forge=1 +- fonttools=4.49.0 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- gcc_impl_linux-64=13.2.0 +- gettext=0.21.1 +- gfortran_impl_linux-64=13.2.0 +- globus-sdk=3.37.0 +- graphite2=1.3.13 +- gsl=2.7 +- gxx_impl_linux-64=13.2.0 +- h5py=3.8.0 +- harfbuzz=6.0.0 +- hdf5=1.14.0 +- hdmedians=0.14.2 +- icu=70.1 +- idna=3.6 +- ijson=3.2.3 +- importlib-resources=6.1.1 +- importlib_resources=6.1.1 +- iniconfig=2.0.0 +- iow=1.0.5 +- ipykernel=6.29.2 +- ipython=8.12.2 +- ipython_genutils=0.2.0 +- isoduration=20.11.0 +- jedi=0.19.1 +- jinja2=3.1.3 +- joblib=1.3.2 +- jpeg=9e +- jsonpointer=2.4 +- jsonschema=4.21.1 +- jsonschema-specifications=2023.12.1 +- jsonschema-with-format-nongpl=4.21.1 +- jupyter_client=7.4.9 +- jupyter_core=5.7.1 +- jupyter_events=0.9.0 +- jupyter_server=2.12.5 +- jupyter_server_terminals=0.5.2 +- jupyterlab_pygments=0.3.0 +- kernel-headers_linux-64=2.6.32 +- keyutils=1.6.1 +- kiwisolver=1.4.5 +- krb5=1.20.1 +- lcms2=2.15 +- ld_impl_linux-64=2.40 +- lerc=4.0.0 +- libaec=1.1.2 +- libblas=3.9.0 +- libbrotlicommon=1.1.0 +- libbrotlidec=1.1.0 +- libbrotlienc=1.1.0 +- libcblas=3.9.0 +- libcurl=8.1.2 +- libdeflate=1.17 +- libedit=3.1.20191231 +- libev=4.33 +- libexpat=2.5.0 +- libffi=3.4.2 +- libgcc-devel_linux-64=13.2.0 +- libgcc-ng=13.2.0 +- libgfortran-ng=13.2.0 +- libgfortran5=13.2.0 +- libglib=2.78.1 +- libgomp=13.2.0 +- libiconv=1.17 +- liblapack=3.9.0 +- liblapacke=3.9.0 +- libnghttp2=1.58.0 +- libnsl=2.0.1 +- libopenblas=0.3.25 +- libpng=1.6.42 +- libsanitizer=13.2.0 +- libsodium=1.0.18 +- libsqlite=3.45.1 +- libssh2=1.11.0 +- libstdcxx-devel_linux-64=13.2.0 +- libstdcxx-ng=13.2.0 +- libtiff=4.5.0 +- libuuid=2.38.1 +- libwebp-base=1.3.2 +- libxcb=1.13 +- libxcrypt=4.4.36 +- libxml2=2.10.3 +- libxslt=1.1.37 +- libzlib=1.2.13 +- lockfile=0.12.2 +- lxml=4.9.2 +- lz4=4.3.3 +- lz4-c=1.9.4 +- make=4.3 +- markupsafe=2.1.5 +- matplotlib-base=3.7.3 +- matplotlib-inline=0.1.6 +- mistune=3.0.2 +- mpi=1.0 +- msgpack-python=1.0.7 +- munkres=1.1.4 +- natsort=8.4.0 +- nbclassic=1.0.0 +- nbclient=0.8.0 +- nbconvert=7.16.0 +- nbconvert-core=7.16.0 +- nbconvert-pandoc=7.16.0 +- nbformat=5.9.2 +- ncurses=6.4 +- nest-asyncio=1.6.0 +- networkx=3.1 +- notebook=6.5.5 +- notebook-shim=0.2.4 +- numpy=1.24.4 +- openjpeg=2.5.0 +- openssl=3.2.1 +- overrides=7.7.0 +- packaging=23.2 +- pandas=1.5.3 +- pandoc=3.1.12 +- pandocfilters=1.5.0 +- pango=1.50.14 +- paramiko=3.4.0 +- parsl=2023.12.4 +- parso=0.8.3 +- pcre2=10.40 +- pexpect=4.9.0 +- pickleshare=0.7.5 +- pillow=9.4.0 +- pip=24.0 +- pixman=0.43.2 +- pkgutil-resolve-name=1.3.10 +- platformdirs=4.2.0 +- pluggy=1.4.0 +- pooch=1.8.0 +- prometheus_client=0.20.0 +- prompt-toolkit=3.0.42 +- prompt_toolkit=3.0.42 +- psutil=5.9.8 +- pthread-stubs=0.4 +- ptyprocess=0.7.0 +- pure_eval=0.2.2 +- pycparser=2.21 +- pygments=2.17.2 +- pyjwt=2.8.0 +- pynacl=1.5.0 +- pyparsing=3.1.1 +- pysocks=1.7.1 +- pytest=8.0.0 +- python=3.8.18 +- python-dateutil=2.8.2 +- python-fastjsonschema=2.19.1 +- python-json-logger=2.0.7 +- python_abi=3.8 +- pytz=2024.1 +- pyyaml=6.0.1 +- pyzmq=24.0.1 +- q2-mystery-stew=2024.2.0 +- q2-types=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.3 +- readline=8.2 +- referencing=0.33.0 +- requests=2.31.0 +- rfc3339-validator=0.1.4 +- rfc3986-validator=0.1.1 +- rpds-py=0.18.0 +- samtools=1.6 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- sed=4.8 +- send2trash=1.8.2 +- setproctitle=1.3.3 +- setuptools=69.0.3 +- six=1.16.0 +- sniffio=1.3.0 +- soupsieve=2.5 +- stack_data=0.6.2 +- sysroot_linux-64=2.12 +- tblib=3.0.0 +- terminado=0.18.0 +- threadpoolctl=3.3.0 +- tinycss2=1.2.1 +- tk=8.6.13 +- tktable=2.10 +- tomli=2.0.1 +- tomlkit=0.12.3 +- tornado=6.3.3 +- traitlets=5.9.0 +- typeguard=2.13.3 +- types-python-dateutil=2.8.19.20240106 +- typing-extensions=4.9.0 +- typing_extensions=4.9.0 +- typing_utils=0.1.0 +- tzlocal=2.1 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.3.2 +- uri-template=1.3.0 +- urllib3=2.2.0 +- wcwidth=0.2.13 +- webcolors=1.13 +- webencodings=0.5.1 +- websocket-client=1.7.0 +- wheel=0.42.0 +- 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-libxext=1.3.4 +- xorg-libxrender=0.9.10 +- xorg-libxt=1.3.0 +- xorg-renderproto=0.11.1 +- xorg-xextproto=7.3.0 +- xorg-xproto=7.0.31 +- xz=5.2.6 +- yaml=0.2.5 +- zeromq=4.3.5 +- zipp=3.17.0 +- zlib=1.2.13 +- zstd=1.5.5 diff --git a/2024.5/tiny/passed/seed-environment-conda.yml b/2024.5/tiny/passed/seed-environment-conda.yml new file mode 100644 index 00000000..985318af --- /dev/null +++ b/2024.5/tiny/passed/seed-environment-conda.yml @@ -0,0 +1,27 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/tiny/passed +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- h5py=3.8.0 +- hdf5=1.14.0 +- notebook=6.5.5 +- numpy=1.24.4 +- pandas=1.5.3 +- parsl=2023.12.04 +- python=3.8 +- q2-mystery-stew=2024.2.0 +- q2-types=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2' diff --git a/2024.5/tiny/staged/seed-environment-conda.yml b/2024.5/tiny/staged/seed-environment-conda.yml new file mode 100644 index 00000000..3dd35ec0 --- /dev/null +++ b/2024.5/tiny/staged/seed-environment-conda.yml @@ -0,0 +1,27 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.5/tiny/staged +- conda-forge +- bioconda +- defaults +dependencies: +- biom-format=2.1.14 +- h5py=3.8.0 +- hdf5=1.14.0 +- notebook=6.5.5 +- numpy=1.24.4 +- pandas=1.5.3 +- parsl=2023.12.04 +- python=3.8 +- q2-mystery-stew=2024.2.0 +- q2-types=2024.2.0 +- q2cli=2024.2.0 +- qiime2=2024.2.0 +- r-base=4.2.2 +- scikit-bio=0.5.8 +- scikit-learn=0.24.1 +- scipy=1.10.0 +- unifrac-binaries=1.3.2 +- unifrac=1.3 +extras: + variant_override: + qiime2_epoch: '2024.2'