Configuration#
This page provides technical information about the configuration of the software and workflows used to generate this report.
MalariaGEN Python API#
Markdown(f"""
* Software version: {malariagen_data.__version__}
* API: {setup.malariagen_api.__class__.__name__}
* Storage URL: {setup.malariagen_api._url}
* Cohorts analysis version: {setup.malariagen_api._cohorts_analysis}
* Site filters analysis version: {setup.malariagen_api._site_filters_analysis}
""")
Software version: 15.0.1
API: Ag3
Storage URL: gs://vo_agam_release_master_us_central1/
Cohorts analysis version: 20240924
Site filters analysis version: dt_20200416
Workflow configuration#
# Declare an identifier for this atlas. Will also be used as a URL slug.
atlas_id: "agam"
# Atlas title describing the taxon or taxonomic group covered.
atlas_title: "Malaria Vector Selection Atlas — *Anopheles gambiae* complex"
# Set the analysis version identifier. This will be used to identify
# the outputs from a particular run of the analysis workflow. If you
# change any of the parameters in this configuration file then please
# also update the analysis version.
analysis_version: "2025.03.05"
# Set minimum and maximum cohort size parameters.
min_cohort_size: 15
max_cohort_size: 100 # If larger, will be randomly downsampled.
# Select the sample sets to include in the analysis.
sample_sets:
- "3.0" # All of Ag1000G phase 3, unrestricted
- "1237-VO-BJ-DJOGBENOU-VMF00050" # GAARD Benin, unrestricted
- "1237-VO-BJ-DJOGBENOU-VMF00067" # GAARD Benin, unrestricted
- "1244-VO-GH-YAWSON-VMF00051" # GAARD Ghana, unrestricted
- "1245-VO-CI-CONSTANT-VMF00054" # GAARD Cote d'Ivoire, unrestricted
- "1253-VO-TG-DJOGBENOU-VMF00052" # GAARD Togo, unrestricted
- "1178-VO-UG-LAWNICZAK-VMF00025" # Ugandan samples via Mara, unrestricted
- "1244-VO-GH-YAWSON-VMF00149" # GAARDIAN Ghana, with Martin Donnelly's permission
- "barron-2019" # unrestricted
- "crawford-2016" # unrestricted
- "tennessen-2021" # unrestricted
- "bergey-2019" # unrestricted
- "campos-2021" # unrestricted
- "fontaine-2015-rebuild" # unrestricted
# Filter samples to include in the analysis.
sample_query: "taxon in ['gambiae', 'coluzzii', 'arabiensis', 'bissau']"
# Declare which taxa to analyse.
taxa: ['gambiae', 'coluzzii', 'arabiensis', 'bissau']
# Map taxa to phasing analysis.
taxon_phasing_analysis:
gambiae: "gamb_colu"
coluzzii: "gamb_colu"
bissau: "gamb_colu"
arabiensis: "arab"
# Map taxa to site mask.
taxon_site_mask:
gambiae: "gamb_colu"
coluzzii: "gamb_colu"
bissau: "gamb_colu"
arabiensis: "arab"
# Select the contigs to analyse.
contigs:
- "2RL"
- "3RL"
- "X"
# Pin the cohorts analysis version in order to get reproducible results.
cohorts_analysis: "20240924"
# Window size calibration parameters.
h12_calibration_contig: "3RL"
h12_calibration_window_sizes: [100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1200, 1400, 1600, 1800, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 6000, 7000, 8000, 9000, 10000]
h12_calibration_threshold: 0.08
g123_calibration_contig: "3RL"
g123_calibration_window_sizes: [100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1200, 1400, 1600, 1800, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 6000, 7000, 8000, 9000, 10000]
g123_calibration_threshold: 0.08
# IHS configuration.
ihs_window_size: 100
# Configuration for H12 signal detection.
h12_signal_detection_min_delta_aic: 1000
h12_signal_detection_min_stat_max: 0.1
h12_signal_detection_gflanks: [6]
# Set this value to "single-threaded" when running snakemake with
# more than 1 CPU to avoid thrashing. Otherwise, both dask and
# snakemake will be trying to use multiple CPUs, and so CPU
# resources are likely to be oversubscribed.
dask_scheduler: "single-threaded"
# Insecticide resistance alerts.
ir_alerts:
- 'SA-AGAM-01'
- 'SA-AGAM-02'
- 'SA-AGAM-03'
- 'SA-AGAM-04'
- 'SA-AGAM-05'
- 'SA-AGAM-06'
- 'SA-AGAM-07'
- 'SA-AGAM-08'
- 'SA-AGAM-09'
Software versions#
name: selection-atlas
channels:
- conda-forge
- bioconda
- nodefaults
- conda-forge/label/broken
dependencies:
- _openmp_mutex=4.5=3_kmp_llvm
- accessible-pygments=0.0.5=pyhd8ed1ab_1
- aiohttp=3.9.5=py312h98912ed_0
- aiosignal=1.3.2=pyhd8ed1ab_0
- alabaster=0.7.16=pyhd8ed1ab_0
- alsa-lib=1.2.13=hb9d3cd8_0
- amply=0.1.6=pyhd8ed1ab_1
- annotated-types=0.7.0=pyhd8ed1ab_1
- ansicolors=1.1.8=pyhd8ed1ab_0
- anyio=4.9.0=pyh29332c3_0
- aom=3.9.1=hac33072_0
- appdirs=1.4.4=pyhd8ed1ab_1
- archspec=0.2.5=pyhd8ed1ab_0
- argon2-cffi=23.1.0=pyhd8ed1ab_1
- argon2-cffi-bindings=21.2.0=py312h66e93f0_5
- argparse-dataclass=2.0.0=pyhd8ed1ab_0
- arrow=1.3.0=pyhd8ed1ab_1
- asteval=1.0.6=pyhd8ed1ab_0
- asttokens=3.0.0=pyhd8ed1ab_1
- async-lru=2.0.5=pyh29332c3_0
- attrs=25.3.0=pyh71513ae_0
- aws-c-auth=0.8.6=hd08a7f5_4
- aws-c-cal=0.8.7=h043a21b_0
- aws-c-common=0.12.0=hb9d3cd8_0
- aws-c-compression=0.3.1=h3870646_2
- aws-c-event-stream=0.5.4=h04a3f94_2
- aws-c-http=0.9.4=hb9b18c6_4
- aws-c-io=0.17.0=h3dad3f2_6
- aws-c-mqtt=0.12.2=h108da3e_2
- aws-c-s3=0.7.13=h822ba82_2
- aws-c-sdkutils=0.2.3=h3870646_2
- aws-checksums=0.2.3=h3870646_2
- aws-crt-cpp=0.31.0=h55f77e1_4
- aws-sdk-cpp=1.11.510=h37a5c72_3
- azure-core-cpp=1.14.0=h5cfcd09_0
- azure-identity-cpp=1.10.0=h113e628_0
- azure-storage-blobs-cpp=12.13.0=h3cf044e_1
- azure-storage-common-cpp=12.8.0=h736e048_1
- azure-storage-files-datalake-cpp=12.12.0=ha633028_1
- babel=2.17.0=pyhd8ed1ab_0
- beautifulsoup4=4.13.3=pyha770c72_0
- biopython=1.85=py312h66e93f0_1
- black=24.10.0=py312h7900ff3_0
- bleach=6.2.0=pyh29332c3_4
- bleach-with-css=6.2.0=h82add2a_4
- blinker=1.9.0=pyhff2d567_0
- blosc=1.21.6=he440d0b_1
- bokeh=3.7.0=pyhd8ed1ab_0
- boltons=24.0.0=pyhd8ed1ab_1
- branca=0.8.1=pyhd8ed1ab_0
- brotli=1.1.0=hb9d3cd8_2
- brotli-bin=1.1.0=hb9d3cd8_2
- brotli-python=1.1.0=py312h2ec8cdc_2
- bzip2=1.0.8=h4bc722e_7
- c-ares=1.34.4=hb9d3cd8_0
- ca-certificates=2025.1.31=hbcca054_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cachetools=5.5.2=pyhd8ed1ab_0
- cairo=1.18.4=h3394656_0
- certifi=2025.1.31=pyhd8ed1ab_0
- cffi=1.17.1=py312h06ac9bb_0
- cfgv=3.3.1=pyhd8ed1ab_1
- charset-normalizer=3.4.1=pyhd8ed1ab_0
- click=8.1.8=pyh707e725_0
- cloudpickle=3.1.1=pyhd8ed1ab_0
- coin-or-cbc=2.10.12=h00e76a6_2
- coin-or-cgl=0.60.9=h82e2f02_4
- coin-or-clp=1.17.10=h8a7a1e7_1
- coin-or-osi=0.108.11=h96cc833_4
- coin-or-utils=2.11.12=h3a12e53_2
- coincbc=2.10.12=2_metapackage
- colorama=0.4.6=pyhd8ed1ab_1
- coloredlogs=15.0.1=pyhd8ed1ab_4
- comm=0.2.2=pyhd8ed1ab_1
- conda=25.3.0=py312h7900ff3_0
- conda-inject=1.3.2=pyhd8ed1ab_0
- conda-libmamba-solver=25.3.0=pyhd8ed1ab_0
- conda-package-handling=2.4.0=pyh7900ff3_2
- conda-package-streaming=0.11.0=pyhd8ed1ab_1
- configargparse=1.7=pyhd8ed1ab_1
- connection_pool=0.0.3=pyhd3deb0d_0
- contourpy=1.3.1=py312h68727a3_0
- cpp-expected=1.1.0=hf52228f_0
- cpython=3.12.9=py312hd8ed1ab_1
- crc32c=2.7.1=py312h66e93f0_1
- cryptography=44.0.2=py312hda17c39_0
- cycler=0.12.1=pyhd8ed1ab_1
- cyrus-sasl=2.1.27=h54b06d7_7
- cytoolz=1.0.1=py312h66e93f0_0
- dask=2025.3.0=pyhd8ed1ab_0
- dask-core=2025.3.0=pyhd8ed1ab_0
- dav1d=1.2.1=hd590300_0
- dbus=1.13.6=h5008d03_3
- debugpy=1.8.13=py312h2ec8cdc_0
- decorator=5.2.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- deprecated=1.2.18=pyhd8ed1ab_0
- dill=0.3.9=pyhd8ed1ab_1
- distlib=0.3.9=pyhd8ed1ab_1
- distributed=2025.3.0=pyhd8ed1ab_0
- distro=1.9.0=pyhd8ed1ab_1
- docutils=0.21.2=pyhd8ed1ab_1
- donfig=0.8.1.post1=pyhd8ed1ab_1
- double-conversion=3.3.1=h5888daf_0
- dpath=2.2.0=pyha770c72_0
- eido=0.2.4=pyhd8ed1ab_0
- entrypoints=0.4=pyhd8ed1ab_1
- exceptiongroup=1.2.2=pyhd8ed1ab_1
- executing=2.1.0=pyhd8ed1ab_1
- expat=2.6.4=h5888daf_0
- filelock=3.18.0=pyhd8ed1ab_0
- fmt=11.1.4=h07f6e7f_1
- folium=0.19.5=pyhd8ed1ab_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_3
- fontconfig=2.15.0=h7e30c49_1
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.56.0=py312h178313f_0
- fqdn=1.5.1=pyhd8ed1ab_1
- freetype=2.13.3=h48d6fc4_0
- freexl=2.0.0=h9dce30a_2
- frozendict=2.4.6=py312h66e93f0_0
- frozenlist=1.5.0=py312h178313f_1
- fsspec=2025.3.0=pyhd8ed1ab_0
- future=1.0.0=pyhd8ed1ab_2
- gcsfs=2025.3.0=pyhd8ed1ab_0
- geopandas=1.0.1=pyhd8ed1ab_3
- geopandas-base=1.0.1=pyha770c72_3
- geos=3.13.1=h97f6797_0
- geotiff=1.7.4=h239500f_2
- gflags=2.2.2=h5888daf_1005
- giflib=5.2.2=hd590300_0
- gitdb=4.0.12=pyhd8ed1ab_0
- gitpython=3.1.44=pyhff2d567_0
- glog=0.7.1=hbabe93e_0
- gmp=6.3.0=hac33072_2
- gmpy2=2.1.5=py312h7201bc8_3
- google-api-core=2.24.2=pyhd8ed1ab_0
- google-auth=2.38.0=pyhd8ed1ab_0
- google-auth-oauthlib=1.2.1=pyhd8ed1ab_1
- google-cloud-core=2.4.3=pyhd8ed1ab_0
- google-cloud-sdk=516.0.0=py312h7900ff3_0
- google-cloud-storage=3.1.0=pyhd8ed1ab_0
- google-crc32c=1.7.1=py312hb42adb9_0
- google-resumable-media=2.7.2=pyhd8ed1ab_2
- googleapis-common-protos=1.69.2=pyhd8ed1ab_0
- graphite2=1.3.13=h59595ed_1003
- greenlet=3.1.1=py312h2ec8cdc_1
- grpcio=1.71.0=py312h9c3ccc5_0
- gtest=1.16.0=h84d6215_0
- h11=0.14.0=pyhd8ed1ab_1
- h2=4.2.0=pyhd8ed1ab_0
- harfbuzz=10.4.0=h76408a6_0
- hpack=4.1.0=pyhd8ed1ab_0
- httpcore=1.0.7=pyh29332c3_1
- httpx=0.28.1=pyhd8ed1ab_0
- humanfriendly=10.0=pyh707e725_8
- hyperframe=6.1.0=pyhd8ed1ab_0
- icu=75.1=he02047a_0
- identify=2.6.9=pyhd8ed1ab_0
- idna=3.10=pyhd8ed1ab_1
- imagesize=1.4.1=pyhd8ed1ab_0
- immutables=0.21=py312h66e93f0_0
- importlib-metadata=8.6.1=pyha770c72_0
- importlib_resources=6.5.2=pyhd8ed1ab_0
- iniconfig=2.0.0=pyhd8ed1ab_1
- ipykernel=6.29.5=pyh3099207_0
- ipyleaflet=0.19.2=pyhd8ed1ab_1
- ipython=9.0.2=pyhfb0248b_0
- ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
- ipywidgets=8.1.5=pyhd8ed1ab_1
- iso3166=2.1.1=pyhd8ed1ab_1
- isoduration=20.11.0=pyhd8ed1ab_1
- jedi=0.19.2=pyhd8ed1ab_1
- jinja2=3.1.6=pyhd8ed1ab_0
- joblib=1.4.2=pyhd8ed1ab_1
- json-c=0.18=h6688a6e_0
- json5=0.10.0=pyhd8ed1ab_1
- jsonpatch=1.33=pyhd8ed1ab_1
- jsonpointer=3.0.0=py312h7900ff3_1
- jsonschema=4.23.0=pyhd8ed1ab_1
- jsonschema-specifications=2024.10.1=pyhd8ed1ab_1
- jsonschema-with-format-nongpl=4.23.0=hd8ed1ab_1
- jupyter-book=1.0.4=pyh29332c3_0
- jupyter-cache=1.0.1=pyhff2d567_0
- jupyter-lsp=2.2.5=pyhd8ed1ab_1
- jupyter_client=8.6.3=pyhd8ed1ab_1
- jupyter_core=5.7.2=pyh31011fe_1
- jupyter_events=0.12.0=pyh29332c3_0
- jupyter_leaflet=0.19.2=pyhd8ed1ab_1
- jupyter_server=2.15.0=pyhd8ed1ab_0
- jupyter_server_terminals=0.5.3=pyhd8ed1ab_1
- jupyterlab=4.3.6=pyhd8ed1ab_0
- jupyterlab_pygments=0.3.0=pyhd8ed1ab_2
- jupyterlab_server=2.27.3=pyhd8ed1ab_1
- jupyterlab_widgets=3.0.13=pyhd8ed1ab_1
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.8=py312h84d6215_0
- krb5=1.21.3=h659f571_0
- latexcodec=2.0.1=pyh9f0ad1d_0
- lcms2=2.17=h717163a_0
- ld_impl_linux-64=2.43=h712a8e2_4
- lerc=4.0.0=h27087fc_0
- libabseil=20250127.1=cxx17_hbbce691_0
- libarchive=3.7.7=h4585015_3
- libarrow=19.0.1=h120c447_5_cpu
- libarrow-acero=19.0.1=hcb10f89_5_cpu
- libarrow-dataset=19.0.1=hcb10f89_5_cpu
- libarrow-substrait=19.0.1=h1bed206_5_cpu
- libavif16=1.2.1=h63b8bd6_0
- libblas=3.9.0=31_h59b9bed_openblas
- libbrotlicommon=1.1.0=hb9d3cd8_2
- libbrotlidec=1.1.0=hb9d3cd8_2
- libbrotlienc=1.1.0=hb9d3cd8_2
- libcblas=3.9.0=31_he106b2a_openblas
- libclang-cpp19.1=19.1.7=default_hb5137d0_2
- libclang13=20.1.1=default_h9c6a7e4_0
- libcrc32c=1.1.2=h9c3ff4c_0
- libcups=2.3.3=h4637d8d_4
- libcurl=8.12.1=h332b0f4_0
- libde265=1.0.15=h00ab1b0_0
- libdeflate=1.23=h4ddbbb0_0
- libdrm=2.4.124=hb9d3cd8_0
- libedit=3.1.20250104=pl5321h7949ede_0
- libegl=1.7.0=ha4b6fd6_2
- libev=4.33=hd590300_2
- libevent=2.1.12=hf998b51_1
- libexpat=2.6.4=h5888daf_0
- libffi=3.4.6=h2dba641_0
- libgcc=14.2.0=h767d61c_2
- libgcc-ng=14.2.0=h69a702a_2
- libgdal-core=3.10.2=hae73b24_5
- libgfortran=14.2.0=h69a702a_2
- libgfortran5=14.2.0=hf1ad2bd_2
- libgl=1.7.0=ha4b6fd6_2
- libglib=2.84.0=h2ff4ddf_0
- libglvnd=1.7.0=ha4b6fd6_2
- libglx=1.7.0=ha4b6fd6_2
- libgoogle-cloud=2.36.0=hc4361e1_1
- libgoogle-cloud-storage=2.36.0=h0121fbd_1
- libgrpc=1.71.0=he753a82_0
- libheif=1.19.7=gpl_hc18d805_100
- libiconv=1.18=h4ce23a2_1
- libjpeg-turbo=3.0.0=hd590300_1
- libkml=1.3.0=hf539b9f_1021
- liblapack=3.9.0=31_h7ac8fdf_openblas
- liblapacke=3.9.0=31_he2f377e_openblas
- libllvm19=19.1.7=ha7bfdaf_1
- libllvm20=20.1.1=ha7bfdaf_0
- liblzma=5.6.4=hb9d3cd8_0
- libmamba=2.0.8=hf3fef5c_1
- libmambapy=2.0.8=py312h1aa6db5_1
- libnghttp2=1.64.0=h161d5f1_0
- libnsl=2.0.1=hd590300_0
- libntlm=1.8=hb9d3cd8_0
- libopenblas=0.3.29=pthreads_h94d23a6_0
- libopengl=1.7.0=ha4b6fd6_2
- libopentelemetry-cpp=1.19.0=hd1b1c89_0
- libopentelemetry-cpp-headers=1.19.0=ha770c72_0
- libparquet=19.0.1=h081d1f1_5_cpu
- libpciaccess=0.18=hd590300_0
- libpng=1.6.47=h943b412_0
- libpq=17.4=h27ae623_0
- libprotobuf=5.29.3=h501fc15_0
- libre2-11=2024.07.02=hba17884_3
- librttopo=1.1.0=hd718a1a_18
- libsodium=1.0.20=h4ab18f5_0
- libsolv=0.7.30=h3509ff9_0
- libspatialite=5.1.0=he17ca71_14
- libsqlite=3.49.1=hee588c1_2
- libssh2=1.11.1=hf672d98_0
- libstdcxx=14.2.0=h8f9b012_2
- libstdcxx-ng=14.2.0=h4852527_2
- libthrift=0.21.0=h0e7cc3e_0
- libtiff=4.7.0=hd9ff511_3
- libtorch=2.6.0=cpu_generic_hde16104_3
- libutf8proc=2.10.0=h4c51ac1_0
- libuuid=2.38.1=h0b41bf4_0
- libuv=1.50.0=hb9d3cd8_0
- libwebp-base=1.5.0=h851e524_0
- libxcb=1.17.0=h8a09558_0
- libxcrypt=4.4.36=hd590300_1
- libxkbcommon=1.8.1=hc4a0caf_0
- libxml2=2.13.6=h8d12d68_0
- libxslt=1.1.39=h76b75d6_0
- libzlib=1.3.1=hb9d3cd8_2
- linkify-it-py=2.0.3=pyhd8ed1ab_1
- llvm-openmp=20.1.1=h024ca30_1
- llvmlite=0.44.0=py312h374181b_1
- lmfit=1.3.3=pyhd8ed1ab_0
- locket=1.0.0=pyhd8ed1ab_0
- logmuse=0.2.8=pyhd8ed1ab_1
- lz4=4.3.3=py312hf0f0c11_2
- lz4-c=1.10.0=h5888daf_1
- lzo=2.10=hd590300_1001
- mapclassify=2.8.1=pyhd8ed1ab_1
- markdown-it-py=3.0.0=pyhd8ed1ab_1
- markupsafe=3.0.2=py312h178313f_1
- matplotlib=3.10.1=py312h7900ff3_0
- matplotlib-base=3.10.1=py312hd3ec401_0
- matplotlib-inline=0.1.7=pyhd8ed1ab_1
- mdit-py-plugins=0.4.2=pyhd8ed1ab_1
- mdurl=0.1.2=pyhd8ed1ab_1
- menuinst=2.2.0=py312h7900ff3_0
- minizip=4.0.7=h05a5f5f_3
- mistune=3.1.3=pyh29332c3_0
- mpc=1.3.1=h24ddda3_1
- mpfr=4.2.1=h90cbb55_3
- mpmath=1.3.0=pyhd8ed1ab_1
- msgpack-python=1.1.0=py312h68727a3_0
- multidict=6.2.0=py312h178313f_0
- munkres=1.1.4=pyh9f0ad1d_0
- mypy_extensions=1.0.0=pyha770c72_1
- mysql-common=9.0.1=h266115a_5
- mysql-libs=9.0.1=he0572af_5
- myst-nb=1.2.0=pyh29332c3_0
- myst-parser=3.0.1=pyhd8ed1ab_0
- narwhals=1.32.0=pyhd8ed1ab_0
- nbclient=0.10.2=pyhd8ed1ab_0
- nbconvert-core=7.16.6=pyh29332c3_0
- nbformat=5.10.4=pyhd8ed1ab_1
- ncurses=6.5=h2d0b736_3
- nest-asyncio=1.6.0=pyhd8ed1ab_1
- networkx=3.4.2=pyh267e887_2
- nlohmann_json=3.11.3=he02047a_1
- nodeenv=1.9.1=pyhd8ed1ab_1
- nomkl=1.0=h5ca1d4c_0
- notebook-shim=0.2.4=pyhd8ed1ab_1
- numba=0.61.0=py312h2e6246c_1
- numcodecs=0.15.1=py312hf9745cd_0
- numpy=2.1.3=py312h58c1407_0
- oauthlib=3.2.2=pyhd8ed1ab_1
- openjpeg=2.5.3=h5fbd93e_0
- openldap=2.6.9=he970967_0
- openssl=3.4.1=h7b32b05_0
- optree=0.14.1=py312h68727a3_1
- orc=2.1.1=h17f744e_1
- overrides=7.7.0=pyhd8ed1ab_1
- packaging=24.2=pyhd8ed1ab_2
- pandas=2.2.3=py312hf9745cd_1
- pandocfilters=1.5.0=pyhd8ed1ab_0
- papermill=2.6.0=pyhd8ed1ab_1
- parso=0.8.4=pyhd8ed1ab_1
- partd=1.4.2=pyhd8ed1ab_0
- pathspec=0.12.1=pyhd8ed1ab_1
- patsy=1.0.1=pyhd8ed1ab_1
- pcre2=10.44=hba22ea6_2
- pephubclient=0.4.4=pyhd8ed1ab_1
- peppy=0.40.7=pyhd8ed1ab_2
- pexpect=4.9.0=pyhd8ed1ab_1
- pickleshare=0.7.5=pyhd8ed1ab_1004
- pillow=11.1.0=py312h80c1187_0
- pip=25.0.1=pyh8b19718_0
- pixman=0.44.2=h29eaf8c_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_2
- plac=1.4.3=pyhd8ed1ab_1
- platformdirs=4.3.7=pyh29332c3_0
- plotly=5.24.1=pyhd8ed1ab_1
- pluggy=1.5.0=pyhd8ed1ab_1
- pre-commit=4.2.0=pyha770c72_0
- proj=9.6.0=h0054346_0
- prometheus-cpp=1.3.0=ha5d0236_0
- prometheus_client=0.21.1=pyhd8ed1ab_0
- prompt-toolkit=3.0.50=pyha770c72_0
- propcache=0.2.1=py312h178313f_1
- proto-plus=1.26.1=pyhd8ed1ab_0
- protobuf=5.29.3=py312h0f4f066_0
- psutil=7.0.0=py312h66e93f0_0
- pthread-stubs=0.4=hb9d3cd8_1002
- ptyprocess=0.7.0=pyhd8ed1ab_1
- pulp=2.8.0=py312h7900ff3_0
- pure_eval=0.2.3=pyhd8ed1ab_1
- pyarrow=19.0.1=py312h7900ff3_0
- pyarrow-core=19.0.1=py312h01725c0_0_cpu
- pyasn1=0.6.1=pyhd8ed1ab_2
- pyasn1-modules=0.4.1=pyhd8ed1ab_1
- pybind11=2.13.6=pyh1ec8472_2
- pybind11-abi=4=hd8ed1ab_3
- pybind11-global=2.13.6=pyh415d2e4_2
- pybtex=0.24.0=pyhd8ed1ab_3
- pybtex-docutils=1.0.3=py312h7900ff3_2
- pycosat=0.6.6=py312h66e93f0_2
- pycparser=2.22=pyh29332c3_1
- pydantic=2.10.6=pyh3cfb1c2_0
- pydantic-core=2.27.2=py312h12e396e_0
- pydata-sphinx-theme=0.15.4=pyhd8ed1ab_0
- pygments=2.19.1=pyhd8ed1ab_0
- pyjwt=2.10.1=pyhd8ed1ab_0
- pyogrio=0.10.0=py312h02b19dd_1
- pyopenssl=25.0.0=pyhd8ed1ab_0
- pyparsing=3.2.2=pyhd8ed1ab_0
- pyproj=3.7.1=py312h03c6e1f_1
- pyprojroot=0.3.0=pyhd8ed1ab_2
- pyside6=6.8.2=py312h91f0f75_1
- pysocks=1.7.1=pyha55dd90_7
- pytest=8.3.5=pyhd8ed1ab_0
- python=3.12.9=h9e4cc4f_1_cpython
- python-dateutil=2.9.0.post0=pyhff2d567_1
- python-fastjsonschema=2.21.1=pyhd8ed1ab_0
- python-json-logger=2.0.7=pyhd8ed1ab_0
- python-tzdata=2025.2=pyhd8ed1ab_0
- python_abi=3.12=5_cp312
- pytorch=2.6.0=cpu_generic_py312_hbe15e8c_3
- pytorch-cpu=2.6.0=cpu_generic_hd752803_3
- pytz=2024.1=pyhd8ed1ab_0
- pyu2f=0.1.5=pyhd8ed1ab_1
- pyyaml=6.0.2=py312h178313f_2
- pyzmq=26.3.0=py312hbf22597_0
- qhull=2020.2=h434a139_5
- qt6-main=6.8.2=h588cce1_0
- rav1e=0.6.6=he8a937b_2
- re2=2024.07.02=h9925aae_3
- readline=8.2=h8c095d6_2
- referencing=0.36.2=pyh29332c3_0
- reproc=14.2.5.post0=hb9d3cd8_0
- reproc-cpp=14.2.5.post0=h5888daf_0
- requests=2.32.3=pyhd8ed1ab_1
- requests-oauthlib=2.0.0=pyhd8ed1ab_1
- reretry=0.11.8=pyhd8ed1ab_1
- rfc3339-validator=0.1.4=pyhd8ed1ab_1
- rfc3986-validator=0.1.1=pyh9f0ad1d_0
- rich=13.9.4=pyhd8ed1ab_1
- rpds-py=0.24.0=py312h3b7be25_0
- rsa=4.9=pyhd8ed1ab_1
- ruamel.yaml=0.18.10=py312h66e93f0_0
- ruamel.yaml.clib=0.2.8=py312h66e93f0_1
- ruff=0.11.2=py312hf79aa60_0
- s2n=1.5.14=h6c98b2b_0
- scikit-learn=1.6.1=py312h7a48858_0
- scipy=1.15.2=py312ha707e6e_0
- send2trash=1.8.3=pyh0d859eb_1
- setuptools=75.8.2=pyhff2d567_0
- setuptools-scm=8.2.1=pyhd8ed1ab_0
- shapely=2.0.7=py312h21f5128_1
- shellingham=1.5.4=pyhd8ed1ab_1
- simdjson=3.12.2=h84d6215_0
- six=1.17.0=pyhd8ed1ab_0
- slack-sdk=3.35.0=pyhd8ed1ab_0
- slack_sdk=3.35.0=hd8ed1ab_0
- sleef=3.8=h1b44611_0
- smart_open=7.1.0=pyhd8ed1ab_0
- smmap=5.0.2=pyhd8ed1ab_0
- snakefmt=0.11.0=pyhdfd78af_0
- snakemake=9.1.2=hdfd78af_0
- snakemake-interface-common=1.17.4=pyhdfd78af_0
- snakemake-interface-executor-plugins=9.3.3=pyhdfd78af_0
- snakemake-interface-logger-plugins=1.2.3=pyhdfd78af_0
- snakemake-interface-report-plugins=1.1.0=pyhdfd78af_0
- snakemake-interface-storage-plugins=4.2.1=pyhdfd78af_0
- snakemake-minimal=9.1.2=pyhdfd78af_0
- snappy=1.2.1=h8bd8927_1
- sniffio=1.3.1=pyhd8ed1ab_1
- snowballstemmer=2.2.0=pyhd8ed1ab_0
- sortedcontainers=2.4.0=pyhd8ed1ab_1
- soupsieve=2.5=pyhd8ed1ab_1
- spdlog=1.15.1=hb29a8c4_0
- sphinx=7.4.7=pyhd8ed1ab_0
- sphinx-book-theme=1.1.4=pyh29332c3_0
- sphinx-comments=0.0.3=pyhd8ed1ab_1
- sphinx-copybutton=0.5.2=pyhd8ed1ab_1
- sphinx-design=0.6.1=pyhd8ed1ab_2
- sphinx-external-toc=1.0.1=pyhd8ed1ab_1
- sphinx-jupyterbook-latex=1.0.0=pyhd8ed1ab_1
- sphinx-multitoc-numbering=0.1.3=pyhd8ed1ab_1
- sphinx-thebe=0.3.1=pyhd8ed1ab_1
- sphinx-togglebutton=0.3.2=pyhd8ed1ab_0
- sphinxcontrib-applehelp=2.0.0=pyhd8ed1ab_1
- sphinxcontrib-bibtex=2.6.3=pyhd8ed1ab_1
- sphinxcontrib-devhelp=2.0.0=pyhd8ed1ab_1
- sphinxcontrib-htmlhelp=2.1.0=pyhd8ed1ab_1
- sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_1
- sphinxcontrib-qthelp=2.0.0=pyhd8ed1ab_1
- sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_1
- sqlalchemy=2.0.39=py312h66e93f0_1
- sqlite=3.49.1=h9eae976_2
- stack_data=0.6.3=pyhd8ed1ab_1
- statsmodels=0.14.4=py312hc0a28a1_0
- svt-av1=3.0.1=h5888daf_0
- sympy=1.13.3=pyh2585a3b_105
- tabulate=0.9.0=pyhd8ed1ab_2
- tblib=3.0.0=pyhd8ed1ab_1
- tenacity=9.0.0=pyhd8ed1ab_1
- terminado=0.18.1=pyh0d859eb_0
- threadpoolctl=3.6.0=pyhecae5ae_0
- throttler=1.2.2=pyhd8ed1ab_0
- tinycss2=1.4.0=pyhd8ed1ab_0
- tk=8.6.13=noxft_h4845f30_101
- toml=0.10.2=pyhd8ed1ab_1
- tomli=2.2.1=pyhd8ed1ab_1
- toolz=1.0.0=pyhd8ed1ab_1
- tornado=6.4.2=py312h66e93f0_0
- tqdm=4.67.1=pyhd8ed1ab_1
- traitlets=5.14.3=pyhd8ed1ab_1
- traittypes=0.2.1=pyh9f0ad1d_2
- truststore=0.10.1=pyh29332c3_0
- typer=0.15.2=pyhff008b6_0
- typer-slim=0.15.2=pyh29332c3_0
- typer-slim-standard=0.15.2=h801b22e_0
- types-python-dateutil=2.9.0.20241206=pyhd8ed1ab_0
- typing-extensions=4.12.2=hd8ed1ab_1
- typing_extensions=4.12.2=pyha770c72_1
- typing_utils=0.1.0=pyhd8ed1ab_1
- tzdata=2025b=h78e105d_0
- ubiquerg=0.8.0=pyhd8ed1ab_0
- uc-micro-py=1.0.3=pyhd8ed1ab_1
- ukkonen=1.0.1=py312h68727a3_5
- uncertainties=3.2.2=pyhd8ed1ab_2
- unicodedata2=16.0.0=py312h66e93f0_0
- uri-template=1.3.0=pyhd8ed1ab_1
- uriparser=0.9.8=hac33072_0
- urllib3=2.3.0=pyhd8ed1ab_0
- veracitools=0.1.3=py_0
- virtualenv=20.29.3=pyhd8ed1ab_0
- wayland=1.23.1=h3e06ad9_0
- wcwidth=0.2.13=pyhd8ed1ab_1
- webcolors=24.11.1=pyhd8ed1ab_0
- webencodings=0.5.1=pyhd8ed1ab_3
- websocket-client=1.8.0=pyhd8ed1ab_1
- wheel=0.45.1=pyhd8ed1ab_1
- widgetsnbextension=4.0.13=pyhd8ed1ab_1
- wrapt=1.17.2=py312h66e93f0_0
- x265=3.5=h924138e_3
- xarray=2025.3.0=pyhd8ed1ab_0
- xcb-util=0.4.1=hb711507_2
- xcb-util-cursor=0.1.5=hb9d3cd8_0
- xcb-util-image=0.4.0=hb711507_2
- xcb-util-keysyms=0.4.1=hb711507_0
- xcb-util-renderutil=0.3.10=hb711507_0
- xcb-util-wm=0.4.2=hb711507_0
- xerces-c=3.2.5=h988505b_2
- xkeyboard-config=2.43=hb9d3cd8_0
- xorg-libice=1.1.2=hb9d3cd8_0
- xorg-libsm=1.2.6=he73a12e_0
- xorg-libx11=1.8.12=h4f16b4b_0
- xorg-libxau=1.0.12=hb9d3cd8_0
- xorg-libxcomposite=0.4.6=hb9d3cd8_2
- xorg-libxcursor=1.2.3=hb9d3cd8_0
- xorg-libxdamage=1.1.6=hb9d3cd8_0
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
- xorg-libxext=1.3.6=hb9d3cd8_0
- xorg-libxfixes=6.0.1=hb9d3cd8_0
- xorg-libxi=1.8.2=hb9d3cd8_0
- xorg-libxrandr=1.5.4=hb9d3cd8_0
- xorg-libxrender=0.9.12=hb9d3cd8_0
- xorg-libxtst=1.2.5=hb9d3cd8_3
- xorg-libxxf86vm=1.1.6=hb9d3cd8_0
- xyzservices=2025.1.0=pyhd8ed1ab_0
- yaml=0.2.5=h7f98852_2
- yaml-cpp=0.8.0=h59595ed_0
- yarl=1.18.3=py312h178313f_1
- yte=1.7.0=pyha770c72_1
- zeromq=4.3.5=h3b0a872_7
- zict=3.0.0=pyhd8ed1ab_1
- zipp=3.21.0=pyhd8ed1ab_1
- zlib=1.3.1=hb9d3cd8_2
- zstandard=0.23.0=py312h66e93f0_1
- zstd=1.5.7=hb8e6e7a_2
- pip:
- aiobotocore==2.21.1
- aioitertools==0.12.0
- anjl==1.4.0
- asciitree==0.3.3
- bed-reader==1.0.6
- botocore==1.37.1
- dash==3.0.1
- dash-cytoscape==1.0.2
- fasteners==0.19
- flask==3.0.3
- igv-notebook==0.6.2
- ipinfo==5.1.1
- itsdangerous==2.2.0
- jmespath==1.0.1
- malariagen-data==15.0.1
- numpydoc-decorator==2.2.1
- orjson==3.10.16
- protopunica==0.14.8.post2
- retrying==1.3.4
- s3fs==2025.3.0
- scikit-allel==1.3.13
- termcolor==2.3.0
- typeguard==4.4.2
- werkzeug==3.0.6
- yaspin==3.1.0
- zarr==2.18.4
prefix: /opt/conda/envs/selection-atlas