From 7a06fba093b0cd1e189f8c2cabd1c92e6b90219f Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Fri, 1 Nov 2024 11:00:50 -0700 Subject: [PATCH 1/2] PREP: 2025.4 (pathogenome) --- .../qiime2-pathogenome-macos-latest-conda.yml | 591 ++++++++++++++++ ...qiime2-pathogenome-ubuntu-latest-conda.yml | 652 ++++++++++++++++++ .../passed/seed-environment-conda.yml | 47 ++ .../staged/seed-environment-conda.yml | 48 ++ 4 files changed, 1338 insertions(+) create mode 100644 2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml create mode 100644 2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml create mode 100644 2025.4/pathogenome/passed/seed-environment-conda.yml create mode 100644 2025.4/pathogenome/staged/seed-environment-conda.yml diff --git a/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml b/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml new file mode 100644 index 00000000..4eebd6a2 --- /dev/null +++ b/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml @@ -0,0 +1,591 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed +- conda-forge +- bioconda +dependencies: +- _r-mutex=1.0.1 +- anyio=4.6.2.post1 +- appdirs=1.4.4 +- appnope=0.1.4 +- argcomplete=3.5.1 +- argh=0.31.3 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- arrow=1.3.0 +- asttokens=2.4.1 +- atpublic=5.0 +- attrs=24.2.0 +- bcrypt=4.2.0 +- beautifulsoup4=4.12.3 +- bedtools=2.31.1 +- bibtexparser=1.4.2 +- bioconductor-annotationdbi=1.64.1 +- bioconductor-biobase=2.62.0 +- bioconductor-biocfilecache=2.10.1 +- bioconductor-biocgenerics=0.48.1 +- bioconductor-biocio=1.12.0 +- bioconductor-biocparallel=1.36.0 +- bioconductor-biomart=2.58.0 +- bioconductor-biostrings=2.70.1 +- bioconductor-bsgenome=1.70.1 +- bioconductor-data-packages=20231203 +- bioconductor-decontam=1.22.0 +- bioconductor-delayedarray=0.28.0 +- bioconductor-genomeinfodb=1.38.1 +- bioconductor-genomeinfodbdata=1.2.11 +- bioconductor-genomicalignments=1.38.0 +- bioconductor-genomicfeatures=1.54.1 +- bioconductor-genomicranges=1.54.1 +- bioconductor-iranges=2.36.0 +- bioconductor-keggrest=1.42.0 +- bioconductor-matrixgenerics=1.14.0 +- bioconductor-rhtslib=2.4.0 +- bioconductor-rsamtools=2.18.0 +- bioconductor-rtracklayer=1.62.0 +- bioconductor-s4arrays=1.2.0 +- bioconductor-s4vectors=0.40.2 +- bioconductor-sparsearray=1.2.2 +- bioconductor-structuralvariantannotation=1.18.0 +- bioconductor-summarizedexperiment=1.32.0 +- bioconductor-variantannotation=1.48.1 +- bioconductor-xvector=0.42.0 +- bioconductor-zlibbioc=1.48.0 +- biom-format=2.1.15 +- biopython=1.84 +- blast=2.16.0 +- bleach=6.1.0 +- bowtie2=2.5.1 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- bwa=0.7.18 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.34.2 +- ca-certificates=2024.8.30 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.18.0 +- cctools_osx-64=986 +- certifi=2024.8.30 +- cffi=1.17.1 +- charset-normalizer=3.4.0 +- checkv=1.0.3 +- circos=0.69.9 +- 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 +- colorama=0.4.6 +- comm=0.2.2 +- 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 +- curl=8.8.0 +- cycler=0.12.1 +- debugpy=1.8.7 +- decorator=4.4.2 +- defusedxml=0.7.1 +- diamond=2.1.8 +- dill=0.3.9 +- entrez-direct=22.4 +- entrypoints=0.4 +- exceptiongroup=1.2.2 +- executing=2.1.0 +- expat=2.6.3 +- fastcluster=1.2.6 +- filelock=3.16.1 +- flufl.lock=8.1.0 +- 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=4.54.1 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- future=1.0.0 +- gettext=0.22.5 +- gettext-tools=0.22.5 +- gffutils=0.10.1 +- gfortran_impl_osx-64=12.3.0 +- gfortran_osx-64=12.3.0 +- giflib=5.2.2 +- glimmerhmm=3.0.4 +- globus-sdk=3.46.0 +- gmp=6.3.0 +- graphite2=1.3.13 +- gridss=2.11.1 +- h5py=3.11.0 +- harfbuzz=8.5.0 +- hdf5=1.14.3 +- hdmedians=0.14.2 +- hmmer=3.4 +- htslib=1.21 +- icu=73.2 +- idna=3.10 +- ijson=3.3.0 +- importlib-metadata=8.5.0 +- importlib_resources=6.4.5 +- iniconfig=2.0.0 +- insilicoseq=2.0.1 +- iow=1.0.5 +- ipykernel=6.29.5 +- ipython=8.21.0 +- ipython_genutils=0.2.0 +- ipywidgets=8.1.5 +- isl=0.26 +- isoduration=20.11.0 +- jedi=0.19.1 +- jinja2=3.1.4 +- joblib=1.4.2 +- jq=1.7.1 +- jsonlines=3.0.0 +- jsonpointer=3.0.0 +- jsonschema=4.23.0 +- jsonschema-specifications=2024.10.1 +- jsonschema-with-format-nongpl=4.23.0 +- jupyter_client=7.4.9 +- jupyter_core=5.7.2 +- jupyter_events=0.10.0 +- jupyter_server=2.14.2 +- jupyter_server_terminals=0.5.3 +- jupyterlab_pygments=0.3.0 +- jupyterlab_widgets=3.0.13 +- k8=0.2.5 +- kcounter=0.1.1 +- kiwisolver=1.4.7 +- kraken2=2.1.3 +- krb5=1.21.3 +- lcms2=2.16 +- ld64_osx-64=711 +- lerc=4.0.0 +- libaec=1.1.3 +- libasprintf=0.22.5 +- libasprintf-devel=0.22.5 +- libblas=3.9.0 +- libbrotlicommon=1.1.0 +- libbrotlidec=1.1.0 +- libbrotlienc=1.1.0 +- libcblas=3.9.0 +- libclang-cpp18.1=18.1.7 +- libcurl=8.8.0 +- libcxx=19.1.2 +- libdeflate=1.20 +- libedit=3.1.20191231 +- libev=4.33 +- libexpat=2.6.3 +- libffi=3.4.2 +- libgd=2.3.3 +- libgettextpo=0.22.5 +- libgettextpo-devel=0.22.5 +- libgfortran=5.0.0 +- libgfortran-devel_osx-64=12.3.0 +- libgfortran5=13.2.0 +- libglib=2.80.2 +- libhwloc=2.11.1 +- libiconv=1.17 +- libidn2=2.3.7 +- libintl=0.22.5 +- libintl-devel=0.22.5 +- libjpeg-turbo=3.0.0 +- liblapack=3.9.0 +- liblapacke=3.9.0 +- libllvm18=18.1.7 +- libnghttp2=1.58.0 +- libopenblas=0.3.28 +- libpng=1.6.43 +- libprotobuf=3.20.3 +- libsodium=1.0.18 +- libsqlite=3.46.0 +- libssh2=1.11.0 +- libtiff=4.6.0 +- libunistring=0.9.10 +- libwebp=1.4.0 +- libwebp-base=1.4.0 +- libxcb=1.15 +- libxml2=2.12.7 +- libxslt=1.1.39 +- 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perl-compress-raw-bzip2=2.201 +- perl-compress-raw-zlib=2.202 +- perl-config-general=2.65 +- perl-digest-perl-md5=1.9 +- perl-encode=3.21 +- 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-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=4.03 +- 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=0.4234 +- perl-module-build-tiny=0.039 +- perl-module-implementation=0.09 +- perl-module-runtime=0.016 +- perl-number-format=1.76 +- perl-params-validate=1.31 +- perl-parent=0.242 +- perl-pathtools=3.75 +- perl-readonly=2.05 +- perl-regexp-common=2017060201 +- perl-scalar-list-utils=1.63 +- perl-set-intspan=1.19 +- perl-statistics-basic=1.6611 +- perl-storable=3.15 +- 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 +- pexpect=4.9.0 +- pickleshare=0.7.5 +- pillow=10.3.0 +- pip=24.3.1 +- pixman=0.43.4 +- pkgutil-resolve-name=1.3.10 +- platformdirs=4.3.6 +- pluggy=1.5.0 +- popt=1.16 +- prodigal-gv=2.11.0 +- prometheus_client=0.21.0 +- prompt-toolkit=3.0.48 +- protobuf=3.20.3 +- psutil=6.1.0 +- pthread-stubs=0.4 +- ptyprocess=0.7.0 +- pure_eval=0.2.3 +- pycparser=2.22 +- pyfaidx=0.8.1.3 +- pygments=2.18.0 +- pyhmmer=0.10.15 +- pyjwt=2.9.0 +- pynacl=1.5.0 +- pyobjc-core=10.3.1 +- pyobjc-framework-cocoa=10.3.1 +- pyparsing=3.2.0 +- pysam=0.22.1 +- pysocks=1.7.1 +- pytest=8.3.3 +- python=3.10.14 +- python-dateutil=2.8.2 +- python-fastjsonschema=2.20.0 +- python-json-logger=2.0.7 +- python-tzdata=2024.2 +- python_abi=3.10 +- pytz=2024.2 +- pyvcf3=1.0.3 +- pyyaml=6.0.2 +- pyzmq=24.0.1 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-metadata=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.1 +- q2templates=2024.10.0 +- qiime2=2024.10.1 +- quast=5.2.0 +- r-abind=1.4_5 +- r-argparser=0.7.2 +- r-askpass=1.2.1 +- r-assertthat=0.2.1 +- r-backports=1.5.0 +- r-base=4.3.3 +- r-base64enc=0.1_3 +- r-bh=1.84.0_0 +- r-bit=4.5.0 +- r-bit64=4.5.2 +- r-bitops=1.0_9 +- r-blob=1.2.4 +- r-brio=1.1.5 +- r-broom=1.0.7 +- r-bslib=0.8.0 +- r-cachem=1.1.0 +- r-callr=3.7.6 +- r-cellranger=1.1.0 +- r-cli=3.6.3 +- r-clipr=0.8.0 +- r-codetools=0.2_20 +- r-colorspace=2.1_1 +- r-conflicted=1.2.0 +- r-cpp11=0.5.0 +- r-crayon=1.5.3 +- r-curl=5.2.1 +- r-data.table=1.15.2 +- r-dbi=1.2.3 +- r-dbplyr=2.5.0 +- 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typeguard=4.4.0 +- types-python-dateutil=2.9.0.20241003 +- typing-extensions=4.12.2 +- typing_extensions=4.12.2 +- typing_utils=0.1.0 +- tzdata=2024b +- tzlocal=2.1 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.4 +- uri-template=1.3.0 +- urllib3=1.26.19 +- vsearch=2.22.1 +- wcwidth=0.2.13 +- webcolors=24.8.0 +- webencodings=0.5.1 +- websocket-client=1.8.0 +- wget=1.21.4 +- wheel=0.44.0 +- widgetsnbextension=4.0.13 +- xmltodict=0.14.2 +- xorg-libxau=1.0.11 +- xorg-libxdmcp=1.1.5 +- xxhash=0.8.2 +- xz=5.2.6 +- yaml=0.2.5 +- yq=3.4.3 +- zeromq=4.3.5 +- zipp=3.20.2 +- zlib=1.2.13 +- zstd=1.5.6 diff --git a/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml b/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml new file mode 100644 index 00000000..f7a2afa9 --- /dev/null +++ b/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml @@ -0,0 +1,652 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed +- conda-forge +- bioconda +dependencies: +- _libgcc_mutex=0.1 +- _openmp_mutex=4.5 +- _r-mutex=1.0.1 +- alsa-lib=1.2.11 +- anyio=4.6.2.post1 +- appdirs=1.4.4 +- argcomplete=3.5.1 +- argh=0.31.3 +- argon2-cffi=23.1.0 +- argon2-cffi-bindings=21.2.0 +- arrow=1.3.0 +- asttokens=2.4.1 +- atpublic=5.0 +- attr=2.5.1 +- attrs=24.2.0 +- bc=1.07.1 +- bcftools=1.21 +- bcrypt=4.2.0 +- beautifulsoup4=4.12.3 +- bedtools=2.31.1 +- bibtexparser=1.4.2 +- binutils_impl_linux-64=2.43 +- bioconductor-annotationdbi=1.64.1 +- bioconductor-biobase=2.62.0 +- bioconductor-biocfilecache=2.10.1 +- bioconductor-biocgenerics=0.48.1 +- bioconductor-biocio=1.12.0 +- bioconductor-biocparallel=1.36.0 +- bioconductor-biomart=2.58.0 +- bioconductor-biostrings=2.70.1 +- bioconductor-bsgenome=1.70.1 +- bioconductor-data-packages=20231203 +- bioconductor-decontam=1.22.0 +- bioconductor-delayedarray=0.28.0 +- bioconductor-genomeinfodb=1.38.1 +- bioconductor-genomeinfodbdata=1.2.11 +- bioconductor-genomicalignments=1.38.0 +- bioconductor-genomicfeatures=1.54.1 +- bioconductor-genomicranges=1.54.1 +- bioconductor-iranges=2.36.0 +- bioconductor-keggrest=1.42.0 +- bioconductor-matrixgenerics=1.14.0 +- bioconductor-rhtslib=2.4.0 +- bioconductor-rsamtools=2.18.0 +- bioconductor-rtracklayer=1.62.0 +- bioconductor-s4arrays=1.2.0 +- bioconductor-s4vectors=0.40.2 +- bioconductor-sparsearray=1.2.2 +- bioconductor-structuralvariantannotation=1.18.0 +- bioconductor-summarizedexperiment=1.32.0 +- bioconductor-variantannotation=1.48.1 +- bioconductor-xvector=0.42.0 +- bioconductor-zlibbioc=1.48.0 +- biom-format=2.1.15 +- biopython=1.84 +- blast=2.16.0 +- bleach=6.1.0 +- bowtie2=2.5.1 +- brotli=1.1.0 +- brotli-bin=1.1.0 +- brotli-python=1.1.0 +- bwa=0.7.18 +- bwidget=1.9.14 +- bzip2=1.0.8 +- c-ares=1.34.2 +- ca-certificates=2024.8.30 +- cached-property=1.5.2 +- cached_property=1.5.2 +- cairo=1.18.0 +- certifi=2024.8.30 +- cffi=1.17.1 +- charset-normalizer=3.4.0 +- checkv=1.0.3 +- circos=0.69.9 +- click=8.1.7 +- colorama=0.4.6 +- comm=0.2.2 +- conda-pack=0.7.0 +- contourpy=1.3.0 +- cryptography=43.0.3 +- curl=8.8.0 +- cycler=0.12.1 +- dbus=1.13.6 +- debugpy=1.8.7 +- decorator=4.4.2 +- defusedxml=0.7.1 +- diamond=2.1.8 +- dill=0.3.9 +- entrez-direct=22.4 +- entrypoints=0.4 +- exceptiongroup=1.2.2 +- executing=2.1.0 +- expat=2.6.3 +- fastcluster=1.2.6 +- filelock=3.16.1 +- flufl.lock=8.1.0 +- 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=4.54.1 +- fqdn=1.5.1 +- freetype=2.12.1 +- fribidi=1.0.10 +- future=1.0.0 +- gcc_impl_linux-64=14.2.0 +- gettext=0.22.5 +- gettext-tools=0.22.5 +- gffutils=0.10.1 +- gfortran_impl_linux-64=14.2.0 +- giflib=5.2.2 +- glib=2.80.2 +- glib-tools=2.80.2 +- glimmerhmm=3.0.4 +- globus-sdk=3.46.0 +- graphite2=1.3.13 +- gridss=2.13.2 +- gsl=2.7 +- gst-plugins-base=1.24.4 +- gstreamer=1.24.4 +- gxx_impl_linux-64=14.2.0 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libsqlite=3.46.0 +- libssh2=1.11.0 +- libstdcxx=14.2.0 +- libstdcxx-devel_linux-64=14.2.0 +- libstdcxx-ng=14.2.0 +- libsystemd0=256.7 +- libtiff=4.6.0 +- libunistring=0.9.10 +- libuuid=2.38.1 +- libvorbis=1.3.7 +- libwebp=1.4.0 +- libwebp-base=1.4.0 +- libxcb=1.15 +- libxcrypt=4.4.36 +- libxkbcommon=1.7.0 +- libxml2=2.12.7 +- libxslt=1.1.39 +- libzlib=1.2.13 +- llvm-openmp=8.0.1 +- lxml=5.2.2 +- lz4=4.3.3 +- lz4-c=1.9.4 +- make=4.4.1 +- markupsafe=3.0.2 +- matplotlib=3.8.4 +- matplotlib-base=3.8.4 +- matplotlib-inline=0.1.7 +- megahit=1.2.9 +- minimap2=2.28 +- mistune=3.0.2 +- mpg123=1.32.8 +- mpi=1.0.1 +- munkres=1.1.4 +- mysql-common=8.3.0 +- mysql-libs=8.3.0 +- natsort=8.4.0 +- nbclassic=1.1.0 +- nbclient=0.10.0 +- nbconvert-core=7.16.4 +- nbformat=5.10.4 +- ncbi-amrfinderplus=3.12.8 +- ncbi-datasets-pylib=16.6.1 +- ncbi-vdb=3.1.1 +- ncurses=6.5 +- nest-asyncio=1.6.0 +- networkx=3.1 +- notebook=6.5.5 +- notebook-shim=0.2.4 +- nspr=4.36 +- nss=3.100 +- numpy=1.26.4 +- oniguruma=6.9.9 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r-backports=1.5.0 +- r-base=4.3.3 +- r-base64enc=0.1_3 +- r-bh=1.84.0_0 +- r-bit=4.5.0 +- r-bit64=4.5.2 +- r-bitops=1.0_9 +- r-blob=1.2.4 +- r-brio=1.1.5 +- r-broom=1.0.7 +- r-bslib=0.8.0 +- r-cachem=1.1.0 +- r-callr=3.7.6 +- r-cellranger=1.1.0 +- r-cli=3.6.3 +- r-clipr=0.8.0 +- r-codetools=0.2_20 +- r-colorspace=2.1_1 +- r-conflicted=1.2.0 +- r-cpp11=0.5.0 +- r-crayon=1.5.3 +- r-curl=5.2.1 +- r-data.table=1.15.2 +- r-dbi=1.2.3 +- r-dbplyr=2.5.0 +- r-desc=1.4.3 +- r-diffobj=0.3.5 +- r-digest=0.6.37 +- r-dplyr=1.1.4 +- r-dtplyr=1.3.1 +- r-ellipsis=0.3.2 +- r-evaluate=1.0.1 +- r-fansi=1.0.6 +- r-farver=2.1.2 +- r-fastmap=1.2.0 +- r-filelock=1.0.3 +- r-fontawesome=0.5.2 +- r-forcats=1.0.0 +- r-formatr=1.14 +- r-fs=1.6.4 +- r-futile.logger=1.4.3 +- r-futile.options=1.0.1 +- r-gargle=1.5.2 +- r-generics=0.1.3 +- r-getopt=1.20.4 +- r-ggplot2=3.5.1 +- r-glue=1.8.0 +- r-googledrive=2.1.1 +- r-googlesheets4=1.1.1 +- r-gtable=0.3.6 +- r-haven=2.5.4 +- r-here=1.0.1 +- r-highr=0.11 +- r-hms=1.1.3 +- r-htmltools=0.5.8.1 +- r-httr=1.4.7 +- r-ids=1.0.1 +- r-isoband=0.2.7 +- r-jquerylib=0.1.4 +- r-jsonlite=1.8.9 +- r-knitr=1.48 +- r-labeling=0.4.3 +- r-lambda.r=1.2.4 +- r-lattice=0.22_6 +- r-lifecycle=1.0.4 +- r-lubridate=1.9.3 +- r-magrittr=2.0.3 +- r-mass=7.3_60.0.1 +- r-matrix=1.6_5 +- r-matrixstats=1.4.1 +- r-memoise=2.0.1 +- r-mgcv=1.9_1 +- r-mime=0.12 +- r-modelr=0.1.11 +- r-munsell=0.5.1 +- r-nlme=3.1_165 +- r-openssl=2.2.2 +- r-optparse=1.7.5 +- r-pillar=1.9.0 +- r-pkgbuild=1.4.5 +- r-pkgconfig=2.0.3 +- r-pkgload=1.4.0 +- 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=3.8.4 +- r-progress=1.2.3 +- r-ps=1.8.1 +- r-purrr=1.0.2 +- r-r6=2.5.1 +- r-ragg=1.3.3 +- r-rappdirs=0.3.3 +- r-rcolorbrewer=1.1_3 +- r-rcpp=1.0.13 +- r-rcpptoml=0.2.2 +- r-rcurl=1.98_1.16 +- r-readr=2.1.5 +- r-readxl=1.4.3 +- r-rematch=2.0.0 +- r-rematch2=2.1.2 +- r-reprex=2.1.1 +- r-reshape2=1.4.4 +- r-restfulr=0.0.15 +- r-reticulate=1.36.0 +- r-rjson=0.2.23 +- r-rlang=1.1.4 +- r-rmarkdown=2.28 +- r-rprojroot=2.0.4 +- r-rsqlite=2.3.7 +- r-rstudioapi=0.17.1 +- r-rvest=1.0.4 +- r-sass=0.4.9 +- r-scales=1.3.0 +- r-selectr=0.4_2 +- r-snow=0.4_4 +- r-stringdist=0.9.12 +- r-stringi=1.8.4 +- r-stringr=1.5.1 +- r-sys=3.4.3 +- r-systemfonts=1.1.0 +- r-testthat=3.2.1.1 +- r-textshaping=0.4.0 +- r-tibble=3.2.1 +- r-tidyr=1.3.1 +- r-tidyselect=1.2.1 +- r-tidyverse=2.0.0 +- r-timechange=0.3.0 +- r-tinytex=0.53 +- r-tzdb=0.4.0 +- r-utf8=1.2.4 +- r-uuid=1.2_1 +- r-vctrs=0.6.5 +- r-viridislite=0.4.2 +- r-vroom=1.6.5 +- r-waldo=0.5.3 +- r-withr=3.0.2 +- r-xfun=0.48 +- r-xml=3.99_0.17 +- r-xml2=1.3.6 +- r-yaml=2.3.10 +- readline=8.2 +- referencing=0.35.1 +- repeatmasker=4.1.7p1 +- requests=2.32.3 +- rescript=2024.10.0 +- rfc3339-validator=0.1.4 +- rfc3986-validator=0.1.1 +- rmblast=2.14.1 +- rpds-py=0.20.0 +- rpsbproc=0.5.0 +- rsync=3.3.0 +- samtools=1.21 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 +- seaborn=0.12.2 +- seaborn-base=0.12.2 +- sed=4.8 +- send2trash=1.8.3 +- setproctitle=1.3.3 +- setuptools=75.1.0 +- shortuuid=1.0.13 +- simplejson=3.19.3 +- sip=6.7.12 +- six=1.16.0 +- sniffio=1.3.1 +- soupsieve=2.5 +- spades=3.15.2 +- stack_data=0.6.2 +- statsmodels=0.14.4 +- sysroot_linux-64=2.17 +- tar=1.34 +- tbb=2021.13.0 +- tblib=3.0.0 +- terminado=0.18.1 +- threadpoolctl=3.5.0 +- tinycss2=1.4.0 +- tk=8.6.13 +- tktable=2.10 +- toml=0.10.2 +- tomli=2.0.2 +- tomlkit=0.13.2 +- tornado=6.4.1 +- traitlets=5.9.0 +- trf=4.09.1 +- typeguard=4.4.0 +- types-python-dateutil=2.9.0.20241003 +- typing-extensions=4.12.2 +- typing_extensions=4.12.2 +- typing_utils=0.1.0 +- tzdata=2024b +- tzlocal=2.1 +- unicodedata2=15.1.0 +- unifrac=1.3 +- unifrac-binaries=1.4 +- uri-template=1.3.0 +- urllib3=1.26.19 +- vsearch=2.22.1 +- wcwidth=0.2.13 +- webcolors=24.8.0 +- webencodings=0.5.1 +- websocket-client=1.8.0 +- wget=1.21.4 +- wheel=0.44.0 +- widgetsnbextension=4.0.13 +- 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=2.42 +- xmltodict=0.14.2 +- xorg-fixesproto=5.0 +- xorg-inputproto=2.3.2 +- xorg-kbproto=1.0.7 +- xorg-libice=1.1.1 +- xorg-libsm=1.2.4 +- xorg-libx11=1.8.9 +- xorg-libxau=1.0.11 +- xorg-libxdmcp=1.1.5 +- xorg-libxext=1.3.4 +- xorg-libxfixes=5.0.3 +- xorg-libxi=1.7.10 +- xorg-libxrender=0.9.11 +- xorg-libxt=1.3.0 +- xorg-libxtst=1.2.5 +- xorg-recordproto=1.14.2 +- xorg-renderproto=0.11.1 +- xorg-xextproto=7.3.0 +- xorg-xf86vidmodeproto=2.3.1 +- xorg-xproto=7.0.31 +- xxhash=0.8.2 +- xz=5.2.6 +- yaml=0.2.5 +- yq=3.4.3 +- zeromq=4.3.5 +- zipp=3.20.2 +- zlib=1.2.13 +- zstd=1.5.6 diff --git a/2025.4/pathogenome/passed/seed-environment-conda.yml b/2025.4/pathogenome/passed/seed-environment-conda.yml new file mode 100644 index 00000000..8ce428d2 --- /dev/null +++ b/2025.4/pathogenome/passed/seed-environment-conda.yml @@ -0,0 +1,47 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released +- conda-forge +- bioconda +dependencies: +- biom-format=2.1.15 +- bowtie2=2.5.1 +- h5py=3.11.0 +- hdf5=1.14.3 +- matplotlib=3.8.4 +- notebook=6.5.5 +- numpy=1.26.4 +- pandas=2.2.2 +- parsl=2024.4.15 +- patsy=0.5.6 +- pysam=0.22.1 +- python=3.10 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-metadata=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.1 +- q2templates=2024.10.0 +- qiime2=2024.10.1 +- r-base=4.3.3 +- r-reticulate=1.36.0 +- rescript=2024.10.0 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 +- seaborn=0.12.2 +- unifrac-binaries=1.4 +- unifrac=1.3 +- vsearch=2.22.1 +extras: + variant_override: + qiime2_epoch: '2025.4' diff --git a/2025.4/pathogenome/staged/seed-environment-conda.yml b/2025.4/pathogenome/staged/seed-environment-conda.yml new file mode 100644 index 00000000..eb4a6112 --- /dev/null +++ b/2025.4/pathogenome/staged/seed-environment-conda.yml @@ -0,0 +1,48 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released +- conda-forge +- bioconda +dependencies: +- biom-format=2.1.15 +- bowtie2=2.5.1 +- h5py=3.11.0 +- hdf5=1.14.3 +- matplotlib=3.8.4 +- notebook=6.5.5 +- numpy=1.26.4 +- pandas=2.2.2 +- parsl=2024.4.15 +- patsy=0.5.6 +- pysam=0.22.1 +- python=3.10 +- python_abi=3.9 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-metadata=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.1 +- q2templates=2024.10.0 +- qiime2=2024.10.1 +- r-base=4.3.3 +- r-reticulate=1.36.0 +- rescript=2024.10.0 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 +- seaborn=0.12.2 +- unifrac-binaries=1.4 +- unifrac=1.3 +- vsearch=2.22.1 +extras: + variant_override: + qiime2_epoch: '2025.4' From 0145cc4f246dfbe4829a35796ab867f5536b662a Mon Sep 17 00:00:00 2001 From: q2d2 Date: Fri, 1 Nov 2024 19:57:11 +0000 Subject: [PATCH 2/2] Update conda environments (Prepare-2025.4-pathogenome) --- .../qiime2-pathogenome-macos-latest-conda.yml | 54 +++++++++---------- ...qiime2-pathogenome-ubuntu-latest-conda.yml | 50 ++++++++--------- .../passed/seed-environment-conda.yml | 38 ++++++------- .../staged/seed-environment-conda.yml | 38 ++++++------- 4 files changed, 90 insertions(+), 90 deletions(-) diff --git a/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml b/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml index 4eebd6a2..7034e852 100644 --- a/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml +++ b/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed +- https://packages.qiime2.org/qiime2/2025.4/pathogenome/passed - conda-forge - bioconda dependencies: @@ -53,7 +53,7 @@ dependencies: - biom-format=2.1.15 - biopython=1.84 - blast=2.16.0 -- bleach=6.1.0 +- bleach=6.2.0 - bowtie2=2.5.1 - brotli=1.1.0 - brotli-bin=1.1.0 @@ -179,7 +179,7 @@ dependencies: - libcblas=3.9.0 - libclang-cpp18.1=18.1.7 - libcurl=8.8.0 -- libcxx=19.1.2 +- libcxx=19.1.3 - libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 @@ -192,7 +192,7 @@ 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 @@ -216,7 +216,7 @@ dependencies: - libxml2=2.12.7 - libxslt=1.1.39 - libzlib=1.2.13 -- llvm-openmp=19.1.2 +- llvm-openmp=19.1.3 - llvm-tools=18.1.7 - lxml=5.2.2 - lz4=4.3.3 @@ -353,23 +353,23 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- q2-amrfinderplus=2024.10.0 -- q2-assembly=2024.10.0 -- q2-demux=2024.10.0 -- q2-feature-classifier=2024.10.0 -- q2-feature-table=2024.10.0 -- q2-longitudinal=2024.10.0 -- q2-metadata=2024.10.0 -- q2-mystery-stew=2024.10.0 -- q2-quality-control=2024.10.0 -- q2-sample-classifier=2024.10.0 -- q2-taxa=2024.10.0 -- q2-types=2024.10.0 -- q2-viromics=2024.10.0 -- q2-vizard=2024.10.0 -- q2cli=2024.10.1 -- q2templates=2024.10.0 -- qiime2=2024.10.1 +- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede +- q2-assembly=2025.4.0.dev0 +- q2-demux=2025.4.0.dev0 +- q2-feature-classifier=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0 +- q2-longitudinal=2025.4.0.dev0 +- q2-metadata=2025.4.0.dev0 +- q2-mystery-stew=2025.4.0.dev0 +- q2-quality-control=2025.4.0.dev0 +- q2-sample-classifier=2025.4.0.dev0 +- q2-taxa=2025.4.0.dev0 +- q2-types=2025.4.0.dev0 +- q2-viromics=2025.4.0.dev0+2.g48e387f +- q2-vizard=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 - r-abind=1.4_5 - r-argparser=0.7.2 @@ -414,7 +414,7 @@ dependencies: - r-fontawesome=0.5.2 - r-forcats=1.0.0 - r-formatr=1.14 -- r-fs=1.6.4 +- r-fs=1.6.5 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 - r-gargle=1.5.2 @@ -520,10 +520,10 @@ dependencies: - readline=8.2 - referencing=0.35.1 - requests=2.32.3 -- rescript=2024.10.0 +- rescript=2025.4.0.dev0 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 -- rpds-py=0.20.0 +- rpds-py=0.20.1 - rpsbproc=0.5.0 - rsync=3.3.0 - samtools=1.21 @@ -534,7 +534,7 @@ dependencies: - seaborn-base=0.12.2 - send2trash=1.8.3 - setproctitle=1.3.3 -- setuptools=75.1.0 +- setuptools=75.3.0 - shortuuid=1.0.13 - sigtool=0.1.3 - simplejson=3.19.3 @@ -546,7 +546,7 @@ dependencies: - statsmodels=0.14.4 - 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 diff --git a/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml b/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml index f7a2afa9..14b8eb84 100644 --- a/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml +++ b/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed +- https://packages.qiime2.org/qiime2/2025.4/pathogenome/passed - conda-forge - bioconda dependencies: @@ -59,7 +59,7 @@ dependencies: - biom-format=2.1.15 - biopython=1.84 - blast=2.16.0 -- bleach=6.1.0 +- bleach=6.2.0 - bowtie2=2.5.1 - brotli=1.1.0 - brotli-bin=1.1.0 @@ -206,7 +206,7 @@ dependencies: - libglib=2.80.2 - libgomp=14.2.0 - libgpg-error=1.50 -- libhwloc=2.11.1 +- libhwloc=2.11.2 - libiconv=1.17 - libidn2=2.3.7 - libjpeg-turbo=3.0.0 @@ -386,23 +386,23 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- q2-amrfinderplus=2024.10.0 -- q2-assembly=2024.10.0 -- q2-demux=2024.10.0 -- q2-feature-classifier=2024.10.0 -- q2-feature-table=2024.10.0 -- q2-longitudinal=2024.10.0 -- q2-metadata=2024.10.0 -- q2-mystery-stew=2024.10.0 -- q2-quality-control=2024.10.0 -- q2-sample-classifier=2024.10.0 -- q2-taxa=2024.10.0 -- q2-types=2024.10.0 -- q2-viromics=2024.10.0 -- q2-vizard=2024.10.0 -- q2cli=2024.10.1 -- q2templates=2024.10.0 -- qiime2=2024.10.1 +- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede +- q2-assembly=2025.4.0.dev0 +- q2-demux=2025.4.0.dev0 +- q2-feature-classifier=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0 +- q2-longitudinal=2025.4.0.dev0 +- q2-metadata=2025.4.0.dev0 +- q2-mystery-stew=2025.4.0.dev0 +- q2-quality-control=2025.4.0.dev0 +- q2-sample-classifier=2025.4.0.dev0 +- q2-taxa=2025.4.0.dev0 +- q2-types=2025.4.0.dev0 +- q2-viromics=2025.4.0.dev0+2.g48e387f +- q2-vizard=2025.4.0.dev0 +- q2cli=2025.4.0.dev0+1.g0ac7869 +- q2templates=2025.4.0.dev0 +- qiime2=2025.4.0.dev0+1.gab00603 - qt-main=5.15.8 - quast=5.2.0 - r-abind=1.4_5 @@ -448,7 +448,7 @@ dependencies: - r-fontawesome=0.5.2 - r-forcats=1.0.0 - r-formatr=1.14 -- r-fs=1.6.4 +- r-fs=1.6.5 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 - r-gargle=1.5.2 @@ -555,11 +555,11 @@ dependencies: - referencing=0.35.1 - repeatmasker=4.1.7p1 - requests=2.32.3 -- rescript=2024.10.0 +- rescript=2025.4.0.dev0 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rmblast=2.14.1 -- rpds-py=0.20.0 +- rpds-py=0.20.1 - rpsbproc=0.5.0 - rsync=3.3.0 - samtools=1.21 @@ -571,7 +571,7 @@ dependencies: - sed=4.8 - send2trash=1.8.3 - setproctitle=1.3.3 -- setuptools=75.1.0 +- setuptools=75.3.0 - shortuuid=1.0.13 - simplejson=3.19.3 - sip=6.7.12 @@ -583,7 +583,7 @@ dependencies: - statsmodels=0.14.4 - sysroot_linux-64=2.17 - tar=1.34 -- tbb=2021.13.0 +- tbb=2022.0.0 - tblib=3.0.0 - terminado=0.18.1 - threadpoolctl=3.5.0 diff --git a/2025.4/pathogenome/passed/seed-environment-conda.yml b/2025.4/pathogenome/passed/seed-environment-conda.yml index 8ce428d2..16e77086 100644 --- a/2025.4/pathogenome/passed/seed-environment-conda.yml +++ b/2025.4/pathogenome/passed/seed-environment-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released +- https://packages.qiime2.org/qiime2/2025.4/pathogenome/passed - conda-forge - bioconda dependencies: @@ -15,26 +15,26 @@ dependencies: - patsy=0.5.6 - pysam=0.22.1 - python=3.10 -- q2-amrfinderplus=2024.10.0 -- q2-assembly=2024.10.0 -- q2-demux=2024.10.0 -- q2-feature-classifier=2024.10.0 -- q2-feature-table=2024.10.0 -- q2-longitudinal=2024.10.0 -- q2-metadata=2024.10.0 -- q2-mystery-stew=2024.10.0 -- q2-quality-control=2024.10.0 -- q2-sample-classifier=2024.10.0 -- q2-taxa=2024.10.0 -- q2-types=2024.10.0 -- q2-viromics=2024.10.0 -- q2-vizard=2024.10.0 -- q2cli=2024.10.1 -- q2templates=2024.10.0 -- qiime2=2024.10.1 +- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede +- q2-assembly=2025.4.0.dev0 +- q2-demux=2025.4.0.dev0 +- q2-feature-classifier=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0 +- q2-longitudinal=2025.4.0.dev0 +- q2-metadata=2025.4.0.dev0 +- q2-mystery-stew=2025.4.0.dev0 +- q2-quality-control=2025.4.0.dev0 +- q2-sample-classifier=2025.4.0.dev0 +- q2-taxa=2025.4.0.dev0 +- q2-types=2025.4.0.dev0 +- q2-viromics=2025.4.0.dev0+2.g48e387f +- q2-vizard=2025.4.0.dev0 +- q2cli=2025.4.0.dev0+1.g0ac7869 +- q2templates=2025.4.0.dev0 +- qiime2=2025.4.0.dev0+1.gab00603 - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2024.10.0 +- rescript=2025.4.0.dev0 - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0 diff --git a/2025.4/pathogenome/staged/seed-environment-conda.yml b/2025.4/pathogenome/staged/seed-environment-conda.yml index eb4a6112..d60f2af7 100644 --- a/2025.4/pathogenome/staged/seed-environment-conda.yml +++ b/2025.4/pathogenome/staged/seed-environment-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released +- https://packages.qiime2.org/qiime2/2025.4/pathogenome/staged - conda-forge - bioconda dependencies: @@ -16,26 +16,26 @@ dependencies: - pysam=0.22.1 - python=3.10 - python_abi=3.9 -- q2-amrfinderplus=2024.10.0 -- q2-assembly=2024.10.0 -- q2-demux=2024.10.0 -- q2-feature-classifier=2024.10.0 -- q2-feature-table=2024.10.0 -- q2-longitudinal=2024.10.0 -- q2-metadata=2024.10.0 -- q2-mystery-stew=2024.10.0 -- q2-quality-control=2024.10.0 -- q2-sample-classifier=2024.10.0 -- q2-taxa=2024.10.0 -- q2-types=2024.10.0 -- q2-viromics=2024.10.0 -- q2-vizard=2024.10.0 -- q2cli=2024.10.1 -- q2templates=2024.10.0 -- qiime2=2024.10.1 +- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede +- q2-assembly=2025.4.0.dev0 +- q2-demux=2025.4.0.dev0 +- q2-feature-classifier=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0 +- q2-longitudinal=2025.4.0.dev0 +- q2-metadata=2025.4.0.dev0 +- q2-mystery-stew=2025.4.0.dev0 +- q2-quality-control=2025.4.0.dev0 +- q2-sample-classifier=2025.4.0.dev0 +- q2-taxa=2025.4.0.dev0 +- q2-types=2025.4.0.dev0 +- q2-viromics=2025.4.0.dev0+2.g48e387f +- q2-vizard=2025.4.0.dev0 +- q2cli=2025.4.0.dev0+1.g0ac7869 +- q2templates=2025.4.0.dev0 +- qiime2=2025.4.0.dev0+1.gab00603 - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2024.10.0 +- rescript=2025.4.0.dev0 - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0