name: pathogen_detection
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1
  - _openmp_mutex=4.5
  - abritamr=1.0.20
  - annotated-types=0.7.0
  - attrs=25.3.0
  - aws-c-auth=0.7.22
  - aws-c-cal=0.6.15
  - aws-c-common=0.9.23
  - aws-c-compression=0.2.18
  - aws-c-event-stream=0.4.2
  - aws-c-http=0.8.2
  - aws-c-io=0.14.9
  - aws-c-mqtt=0.10.4
  - aws-c-s3=0.5.10
  - aws-c-sdkutils=0.1.16
  - aws-checksums=0.1.18
  - aws-crt-cpp=0.26.12
  - aws-sdk-cpp=1.11.329
  - bcftools=1.23
  - bedtools=2.31.1
  - biopython=1.85
  - blast=2.16.0
  - brotli=1.1.0
  - brotli-bin=1.1.0
  - brotli-python=1.0.9
  - bwa=0.7.19
  - bzip2=1.0.8
  - c-ares=1.34.6
  - ca-certificates=2026.1.4
  - cached-property=1.5.2
  - cached_property=1.5.2
  - certifi=2025.8.3
  - cffi=1.17.1
  - charset-normalizer=3.4.3
  - circos=0.69.9
  - click=8.1.8
  - colorama=0.4.6
  - coloredlogs=15.0.1
  - colormath=3.0.0
  - contourpy=1.3.0
  - cpython=3.9.23
  - csvtk=0.36.0
  - curl=8.18.0
  - cycler=0.12.1
  - entrez-direct=22.4
  - expat=2.7.3
  - fastp=1.1.0
  - fastqc=0.12.1
  - filelock=3.19.1
  - flye=2.9.6
  - 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=2.15.0
  - fonts-conda-forge=1
  - fonttools=4.59.1
  - freetype=2.14.1
  - fsspec=2025.7.0
  - gflags=2.2.2
  - giflib=5.2.2
  - git=2.51.0
  - glimmerhmm=3.0.4
  - glog=0.7.1
  - gmp=6.3.0
  - gmpy2=2.2.1
  - gperftools=2.17.2
  - grpcio=1.62.2
  - gsl=2.7
  - h2=4.2.0
  - h5py=3.14.0
  - hdf5=1.14.6
  - hmmer=3.4
  - hpack=4.1.0
  - htslib=1.23
  - humanfriendly=10.0
  - humanize=4.12.3
  - hyperframe=6.1.0
  - icu=78.2
  - idna=3.10
  - importlib-metadata=8.7.0
  - importlib-resources=6.5.2
  - importlib_resources=6.5.2
  - intervaltree=3.1.0
  - isa-l=2.31.1
  - jinja2=3.1.6
  - joblib=1.5.1
  - jpeg=9e
  - jsonschema=4.25.1
  - jsonschema-specifications=2025.4.1
  - k8=1.2
  - kaleido-core=0.2.1
  - kernel-headers_linux-64=6.12.0
  - keyutils=1.6.3
  - kiwisolver=1.4.7
  - kraken2=2.17.1
  - krb5=1.21.3
  - krona=2.8.1
  - lcms2=2.17
  - ld_impl_linux-64=2.45
  - lerc=4.0.0
  - libabseil=20240116.2
  - libaec=1.1.5
  - libarrow=16.1.0
  - libarrow-acero=16.1.0
  - libarrow-dataset=16.1.0
  - libarrow-substrait=16.1.0
  - libblas=3.11.0
  - libbrotlicommon=1.1.0
  - libbrotlidec=1.1.0
  - libbrotlienc=1.1.0
  - libcblas=3.11.0
  - libcrc32c=1.1.2
  - libcurl=8.18.0
  - libdeflate=1.22
  - libedit=3.1.20250104
  - libev=4.33
  - libevent=2.1.12
  - libexpat=2.7.3
  - libffi=3.5.2
  - libfreetype=2.14.1
  - libfreetype6=2.14.1
  - libgcc=15.2.0
  - libgcc-ng=15.2.0
  - libgd=2.3.3
  - libgfortran=15.2.0
  - libgfortran-ng=15.2.0
  - libgfortran5=15.2.0
  - libgomp=15.2.0
  - libgoogle-cloud=2.25.0
  - libgoogle-cloud-storage=2.25.0
  - libgrpc=1.62.2
  - libiconv=1.18
  - libidn2=2.3.8
  - liblapack=3.11.0
  - liblzma=5.8.2
  - liblzma-devel=5.8.2
  - libnghttp2=1.67.0
  - libnsl=2.0.1
  - libopenblas=0.3.30
  - libparquet=16.1.0
  - libpng=1.6.54
  - libprotobuf=4.25.3
  - libre2-11=2023.09.01
  - libsqlite=3.51.2
  - libssh2=1.11.1
  - libstdcxx=15.2.0
  - libstdcxx-ng=15.2.0
  - libthrift=0.19.0
  - libtiff=4.7.1
  - libtorch=2.3.1
  - libunistring=0.9.10
  - libunwind=1.8.3
  - libutf8proc=2.8.0
  - libuuid=2.41.3
  - libuv=1.51.0
  - libwebp=1.6.0
  - libwebp-base=1.6.0
  - libxcrypt=4.4.36
  - libzlib=1.3.1
  - lz4-c=1.9.4
  - mappy=2.30
  - markdown=3.8.2
  - markdown-it-py=3.0.0
  - markupsafe=3.0.2
  - mathjax=2.7.7
  - matplotlib-base=3.9.4
  - mdurl=0.1.2
  - medaka=2.1.1
  - minimap2=2.30
  - mpc=1.3.1
  - mpfr=4.2.1
  - mpi=1.0
  - mpmath=1.3.0
  - multiqc=1.33
  - munkres=1.0.7
  - nanoget=1.19.4
  - nanoplot=1.46.2
  - narwhals=2.1.2
  - natsort=8.4.0
  - ncbi-amrfinderplus=3.12.8
  - ncbi-vdb=3.3.0
  - ncurses=6.5
  - networkx=3.2.1
  - nomkl=1.0
  - nspr=4.38
  - nss=3.118
  - numpy=1.26.4
  - ont-fast5-api=4.1.3
  - openjdk=11.0.1
  - openjpeg=2.5.4
  - openmpi=4.1.6
  - openssl=3.6.1
  - orc=2.0.1
  - packaging=26.0
  - pandas=2.3.1
  - parallel=20160622
  - parasail-python=1.3.4
  - pcre2=10.45
  - perl=5.32.1
  - perl-archive-tar=3.04
  - perl-b-cow=0.007
  - perl-carp=1.38
  - perl-clone=0.46
  - perl-common-sense=3.75
  - perl-compress-raw-bzip2=2.214
  - perl-compress-raw-zlib=2.214
  - perl-config-general=2.67
  - perl-digest-perl-md5=1.91
  - perl-encode=3.19
  - perl-exporter=5.72
  - perl-exporter-tiny=1.002002
  - perl-extutils-makemaker=7.70
  - perl-font-ttf=1.06
  - perl-gd=2.84
  - perl-inc-latest=0.500
  - perl-io-compress=2.216
  - perl-io-string=1.08
  - perl-io-zlib=1.15
  - perl-json=4.10
  - perl-json-xs=4.04
  - 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-implementation=0.09
  - perl-module-runtime=0.016
  - perl-number-format=1.76
  - perl-params-validate=1.31
  - perl-parent=0.236
  - perl-pathtools=3.75
  - perl-readonly=2.05
  - perl-regexp-common=2017060201
  - perl-scalar-list-utils=1.62
  - perl-set-intspan=1.19
  - perl-statistics-basic=1.6611
  - perl-svg=2.87
  - perl-test-fatal=0.016
  - perl-test-nowarnings=1.06
  - perl-text-format=0.63
  - perl-threaded=5.32.1
  - perl-time-hires=1.9764
  - perl-try-tiny=0.31
  - perl-types-serialiser=1.01
  - perl-xml-parser=2.44_01
  - pillow=11.1.0
  - pip=25.2
  - plotly=6.3.0
  - polars=1.34.0
  - polars-lts-cpu=1.34.0.deprecated
  - polars-runtime-32=1.34.0
  - polars-runtime-compat=1.34.0
  - popt=1.16
  - porechop=0.2.4
  - progressbar33=2.4
  - pyabpoa=1.5.5
  - pyaml-env=1.2.2
  - pyarrow=16.1.0
  - pyarrow-core=16.1.0
  - pycparser=2.22
  - pydantic=2.11.7
  - pydantic-core=2.33.2
  - pygments=2.19.2
  - pyparsing=3.2.3
  - pysam=0.23.3
  - pysocks=1.7.1
  - pyspoa=0.3.2
  - python=3.9.23
  - python-dateutil=2.9.0.post0
  - python-dotenv=1.1.1
  - python-edlib=1.3.9.post1
  - python-kaleido=0.2.1
  - python-tzdata=2025.2
  - python_abi=3.9
  - pytorch=2.3.1
  - pytz=2025.2
  - pyyaml=6.0.2
  - qhull=2020.2
  - quast=5.3.0
  - re2=2023.09.01
  - readline=8.3
  - referencing=0.36.2
  - regex=2025.7.34
  - requests=2.32.5
  - rich=14.1.0
  - rich-click=1.8.9
  - rpds-py=0.27.0
  - rpsbproc=0.5.1
  - rsync=3.3.0
  - s2n=1.4.16
  - samtools=1.23
  - scipy=1.13.1
  - setuptools=80.9.0
  - simplejson=3.20.1
  - six=1.17.0
  - sleef=3.9.0
  - snappy=1.2.2
  - sortedcontainers=2.4.0
  - spectra=0.0.11
  - sqlite=3.51.2
  - sympy=1.14.0
  - sysroot_linux-64=2.39
  - tar=1.35
  - tiktoken=0.11.0
  - tk=8.6.13
  - toml=0.10.2
  - tqdm=4.67.1
  - typeguard=4.4.4
  - typing-extensions=4.14.1
  - typing-inspection=0.4.1
  - typing_extensions=4.14.1
  - tzdata=2025c
  - unicodedata2=16.0.0
  - urllib3=2.5.0
  - wget=1.25.0
  - wheel=0.45.1
  - wurlitzer=3.1.1
  - xlsxwriter=3.2.5
  - xxhash=0.8.2
  - xz=5.8.2
  - xz-gpl-tools=5.8.2
  - xz-tools=5.8.2
  - yaml=0.2.5
  - zipp=3.23.0
  - zlib=1.3.1
  - zstandard=0.23.0
  - zstd=1.5.7