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environment.yml
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environment.yml
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name: base
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- _r-mutex=1.0.1=anacondar_1
- abseil-cpp=20210324.1=h9c3ff4c_0
- alsa-lib=1.2.3=h516909a_0
- ambertools=21.7=py39h58e3450_0
- anyio=3.5.0=py39hf3d152e_0
- aplus=0.11.0=py_1
- aragorn=1.2.38=hec16e2b_5
- argon2-cffi=21.3.0=pyhd8ed1ab_0
- argon2-cffi-bindings=21.2.0=py39h3811e60_1
- argtable2=2.13=h14c3975_1001
- arpack=3.7.0=hdefa2d7_2
- arrow-cpp=4.0.0=py39h6ac3dd5_3_cpu
- astropy=5.0.1=py39hce5d2b2_0
- asttokens=2.0.5=pyhd8ed1ab_0
- atk=2.36.0=ha770c72_4
- atk-1.0=2.36.0=h3371d22_4
- atomicwrites=1.4.0=pyh9f0ad1d_0
- attrs=21.4.0=pyhd8ed1ab_0
- aws-c-cal=0.5.10=h3622835_0
- aws-c-common=0.5.11=h7f98852_0
- aws-c-event-stream=0.2.7=hd2d8ebb_9
- aws-c-io=0.10.2=he6d800f_1
- aws-checksums=0.1.11=hc0e0e8b_6
- aws-sdk-cpp=1.8.186=h9ad65fb_2
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- barrnap=0.9=hdfd78af_4
- bbmap=38.96=h5c4e2a8_1
- bedtools=2.30.0=h7d7f7ad_2
- binutils_impl_linux-64=2.35.1=h27ae35d_9
- binutils_linux-64=2.35=h67ddf6f_30
- blake3=0.2.1=py39h860a657_0
- blast=2.5.0=hc0b0e79_3
- bleach=4.1.0=pyhd8ed1ab_0
- blosc=1.21.0=h9c3ff4c_0
- bokeh=2.4.2=py39hf3d152e_0
- boost=1.74.0=py39h5472131_5
- boost-cpp=1.74.0=hc6e9bd1_3
- bqplot=0.12.33=pyhd8ed1ab_0
- branca=0.4.2=pyhd8ed1ab_0
- brotli=1.0.9=h7f98852_6
- brotli-bin=1.0.9=h7f98852_6
- brotlipy=0.7.0=py39h3811e60_1003
- brunsli=0.1=h9c3ff4c_0
- bwidget=1.9.14=ha770c72_1
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2022.5.18.1=ha878542_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cachetools=5.0.0=pyhd8ed1ab_0
- cairo=1.16.0=h6cf1ce9_1008
- certifi=2022.5.18.1=py39hf3d152e_0
- cffi=1.14.6=py39he32792d_0
- cfitsio=3.470=hb418390_7
- chardet=4.0.0=py39hf3d152e_2
- charls=2.2.0=h9c3ff4c_0
- checkm-genome=1.1.3=py_1
- click=7.1.2=pyh9f0ad1d_0
- click-plugins=1.1.1=py_0
- cligj=0.7.2=pyhd8ed1ab_1
- clipkit=1.2.0=pyhdfd78af_0
- cloudpickle=2.0.0=pyhd8ed1ab_0
- clustalo=1.2.4=h1b792b2_4
- clustalw=2.1=h7d875b9_6
- colorama=0.4.4=pyh9f0ad1d_0
- commonmark=0.9.1=py_0
- conda=4.11.0=py39hf3d152e_0
- conda-package-handling=1.7.3=py39h3811e60_1
- cryptography=36.0.1=py39h95dcef6_0
- curl=7.76.1=h979ede3_1
- cycler=0.11.0=pyhd8ed1ab_0
- cython=0.29.28=py39he80948d_0
- cytoolz=0.11.2=py39h3811e60_1
- cytoscape=3.9.0=hadc2ddb_0
- dask=2022.2.1=pyhd8ed1ab_0
- dask-core=2022.2.1=pyhd8ed1ab_0
- dataclasses=0.8=pyhc8e2a94_3
- dbus=1.13.6=h48d8840_2
- debugpy=1.5.1=py39he80948d_0
- decorator=5.1.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- dendropy=4.5.2=pyh3252c3a_0
- diamond=2.0.13=hdcc8f71_0
- distributed=2022.2.1=pyhd8ed1ab_0
- entrypoints=0.4=pyhd8ed1ab_0
- et_xmlfile=1.1.0=py39h06a4308_0
- ete3=3.1.2=pyh9f0ad1d_0
- executing=0.8.3=pyhd8ed1ab_0
- expat=2.4.6=h27087fc_0
- fastapi=0.74.0=pyhd8ed1ab_0
- fastcluster=1.2.6=py39h1832856_1
- fastqc=0.11.9=hdfd78af_1
- fasttree=2.1.10=h779adbc_5
- fftw=3.3.10=nompi_h77c792f_102
- filelock=3.6.0=pyhd8ed1ab_0
- fiona=1.8.20=py39h494ca2c_0
- flit-core=3.7.1=pyhd8ed1ab_0
- folium=0.12.1.post1=pyhd8ed1ab_1
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- fontconfig=2.13.96=ha180cfb_0
- freetype=2.10.4=h0708190_1
- freexl=1.0.6=h7f98852_0
- fribidi=1.0.10=h36c2ea0_0
- frozendict=2.3.0=py39h3811e60_1
- fsspec=2022.2.0=pyhd8ed1ab_0
- future=0.18.2=py39hf3d152e_4
- gawk=5.1.0=h7f98852_0
- gcc_impl_linux-64=9.3.0=h6df7d76_17
- gcc_linux-64=9.3.0=hf25ea35_30
- gdal=1.9.2=0
- gdk-pixbuf=2.42.6=h04a7f16_0
- geopandas=0.10.2=pyhd8ed1ab_1
- geopandas-base=0.10.2=pyha770c72_1
- geos=3.9.1=h9c3ff4c_2
- geotiff=1.6.0=hcf90da6_5
- gettext=0.19.8.1=h0b5b191_1005
- gflags=2.2.2=he1b5a44_1004
- gfortran_impl_linux-64=9.3.0=hc4a2995_19
- gfortran_linux-64=9.3.0=hdc58fab_30
- ghostscript=9.54.0=h27087fc_2
- giflib=5.2.1=h36c2ea0_2
- glib=2.68.4=h9c3ff4c_0
- glib-tools=2.68.4=h9c3ff4c_0
- glog=0.5.0=h48cff8f_0
- graphite2=1.3.13=h58526e2_1001
- grpc-cpp=1.37.1=h2519f57_2
- gsl=2.6=he838d99_2
- gst-plugins-base=1.18.5=hf529b03_0
- gstreamer=1.18.5=h76c114f_0
- gtk2=2.24.33=hab0c2f8_0
- gxx_impl_linux-64=9.3.0=hbdd7822_17
- gxx_linux-64=9.3.0=h3fbe746_30
- h5py=3.3.0=nompi_py39h98ba4bc_100
- harfbuzz=2.9.1=h83ec7ef_1
- hdf4=4.2.15=h10796ff_3
- hdf5=1.10.6=nompi_h6a2412b_1114
- heapdict=1.0.1=py_0
- hhsuite=3.3.0=py39pl5321h67e14b5_5
- hmmer=3.3.2=h87f3376_2
- htslib=1.12=h9093b5e_1
- icu=68.2=h9c3ff4c_0
- idna=2.10=pyh9f0ad1d_0
- imagecodecs=2021.3.31=py39h559889c_0
- imageio=2.9.0=py_0
- importlib-metadata=4.11.2=py39hf3d152e_0
- importlib_metadata=4.11.2=hd8ed1ab_0
- importlib_resources=5.4.0=pyhd8ed1ab_0
- infernal=1.1.4=pl5321hec16e2b_1
- ipydatawidgets=4.2.0=pyhd3deb0d_0
- ipykernel=6.9.1=py39hef51801_0
- ipyleaflet=0.15.0=pyhd8ed1ab_3
- ipympl=0.8.8=pyhd8ed1ab_0
- ipython=8.1.1=py39hf3d152e_0
- ipython_genutils=0.2.0=py_1
- ipyvolume=0.6.0a8=pyhd8ed1ab_0
- ipyvue=1.7.0=pyhd8ed1ab_0
- ipyvuetify=1.8.2=pyhd8ed1ab_0
- ipywebrtc=0.6.0=pyhd8ed1ab_0
- ipywidgets=7.6.5=pyhd8ed1ab_0
- jalview=2.11.1.4=hdfd78af_2
- javafx-sdk=12.0.2=h19c363d_2
- jedi=0.18.1=py39hf3d152e_0
- jinja2=3.0.3=pyhd8ed1ab_0
- joblib=1.1.0=pyhd8ed1ab_0
- jpeg=9e=h7f98852_0
- json-c=0.15=h98cffda_0
- jsonschema=4.4.0=pyhd8ed1ab_0
- jupyter_client=7.1.2=pyhd8ed1ab_0
- jupyter_core=4.9.2=py39hf3d152e_0
- jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
- jupyterlab_widgets=1.0.2=pyhd8ed1ab_0
- jxrlib=1.1=h7f98852_2
- kealib=1.4.14=hcc255d8_2
- keras=2.7.0=pyhd8ed1ab_0
- kernel-headers_linux-64=2.6.32=he073ed8_15
- kiwisolver=1.3.2=py39h1a9c180_1
- krb5=1.17.2=h926e7f8_0
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.35.1=h7274673_9
- lerc=2.2.1=h9c3ff4c_0
- libaec=1.0.6=h9c3ff4c_0
- libarchive=3.5.1=h3f442fb_1
- libblas=3.9.0=13_linux64_openblas
- libbrotlicommon=1.0.9=h7f98852_6
- libbrotlidec=1.0.9=h7f98852_6
- libbrotlienc=1.0.9=h7f98852_6
- libcblas=3.9.0=13_linux64_openblas
- libcurl=7.76.1=hc4aaa36_1
- libdap4=3.20.6=hd7c4107_2
- libdeflate=1.7=h7f98852_5
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libevent=2.1.10=h9b69904_4
- libffi=3.3=h58526e2_2
- libgcc=7.2.0=h69d50b8_2
- libgcc-devel_linux-64=9.3.0=hb95220a_17
- libgcc-ng=11.2.0=h1d223b6_13
- libgdal=3.2.2=hbf32332_3
- libgfortran-ng=9.4.0=h69a702a_10
- libgfortran5=9.4.0=h62347ff_10
- libglib=2.68.4=h3e27bee_0
- libgomp=11.2.0=h1d223b6_13
- libiconv=1.16=h516909a_0
- libidn11=1.34=h1cef754_0
- libidn2=2.3.2=h7f98852_0
- libkml=1.3.0=h238a007_1014
- liblapack=3.9.0=13_linux64_openblas
- libllvm11=11.1.0=hf817b99_3
- libnetcdf=4.8.0=nompi_hcd642e3_103
- libnghttp2=1.47.0=h727a467_0
- libnsl=2.0.0=h7f98852_0
- libogg=1.3.4=h7f98852_1
- libopenblas=0.3.18=pthreads_h8fe5266_0
- libopus=1.3.1=h7f98852_1
- libpng=1.6.37=h21135ba_2
- libpq=13.2=hfd2b0eb_2
- libprotobuf=3.16.0=h780b84a_0
- librttopo=1.1.0=h1185371_6
- libsodium=1.0.18=h36c2ea0_1
- libsolv=0.7.19=h780b84a_5
- libspatialindex=1.9.3=h9c3ff4c_4
- libspatialite=5.0.1=h20cb978_4
- libssh2=1.10.0=ha56f1ee_2
- libstdcxx-devel_linux-64=9.3.0=hf0c5c8d_17
- libstdcxx-ng=11.2.0=he4da1e4_13
- libthrift=0.14.1=he6d91bd_2
- libtiff=4.2.0=hbd63e13_2
- libunistring=0.9.10=h7f98852_0
- libutf8proc=2.7.0=h7f98852_0
- libuuid=2.32.1=h7f98852_1000
- libvorbis=1.3.7=h9c3ff4c_0
- libwebp-base=1.2.2=h7f98852_1
- libxcb=1.13=h7f98852_1004
- libxkbcommon=1.0.3=he3ba5ed_0
- libxml2=2.9.12=h72842e0_0
- libxslt=1.1.33=h15afd5d_2
- libzip=1.8.0=h4de3113_1
- libzlib=1.2.11=h36c2ea0_1013
- libzopfli=1.0.3=h9c3ff4c_0
- llvmlite=0.38.0=py39h1bbdace_0
- locket=0.2.0=py_2
- lz4-c=1.9.3=h9c3ff4c_1
- lzo=2.10=h516909a_1000
- macrel=1.2.0=pyh5e36f6f_0
- make=4.3=hd18ef5c_1
- mamba=0.13.0=py39h951de11_0
- mapclassify=2.4.3=pyhd8ed1ab_0
- markupsafe=2.1.0=py39hb9d737c_0
- matplotlib=3.4.3=py39hf3d152e_1
- matplotlib-base=3.4.3=py39h2fa2bec_2
- matplotlib-inline=0.1.3=pyhd8ed1ab_0
- megahit=1.2.9=h2e03b76_1
- minced=0.4.2=hdfd78af_1
- mistune=0.8.4=py39h3811e60_1005
- mmseqs2=13.45111=pl5321hf1761c0_2
- msgpack-python=1.0.3=py39h1a9c180_0
- munch=2.5.0=py_0
- mysql-common=8.0.25=ha770c72_0
- mysql-libs=8.0.25=h935591d_0
- nbclient=0.5.11=pyhd8ed1ab_0
- nbconvert=6.4.2=py39hf3d152e_0
- nbformat=5.1.3=pyhd8ed1ab_0
- ncurses=6.2=h58526e2_4
- nest-asyncio=1.5.4=pyhd8ed1ab_0
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- sortedcontainers=2.4.0=pyhd8ed1ab_0
- sqlite=3.37.0=h9cd32fc_0
- stack_data=0.2.0=pyhd8ed1ab_0
- starlette=0.17.1=pyhd8ed1ab_0
- statsmodels=0.13.2=py39hce5d2b2_0
- sysroot_linux-64=2.12=he073ed8_15
- tabulate=0.8.9=pyhd8ed1ab_0
- tbb=2021.5.0=h4bd325d_0
- tbl2asn=25.7=h9ee0642_1
- tblib=1.7.0=pyhd8ed1ab_0
- tenacity=8.0.1=pyhd8ed1ab_0
- terminado=0.13.2=py39hf3d152e_0
- testpath=0.6.0=pyhd8ed1ab_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- tifffile=2021.4.8=pyhd8ed1ab_0
- tiledb=2.2.9=h91fcb0e_0
- tk=8.6.12=h27826a3_0
- tktable=2.10=hb7b940f_3
- toolz=0.11.2=pyhd8ed1ab_0
- tornado=6.1=py39h3811e60_2
- tqdm=4.55.1=pyhd8ed1ab_0
- traitlets=5.1.1=pyhd8ed1ab_0
- traittypes=0.2.1=pyh9f0ad1d_2
- typing-extensions=4.1.1=hd8ed1ab_0
- typing_extensions=4.1.1=pyha770c72_0
- tzcode=2021e=h7f98852_0
- tzdata=2021e=he74cb21_0
- tzlocal=3.0=py39hf3d152e_2
- umap-learn=0.5.2=py39hf3d152e_1
- upsetplot=0.6.0=pyhd8ed1ab_0
- urllib3=1.26.8=pyhd8ed1ab_1
- vaex=4.5.0=pyhd8ed1ab_0
- vaex-astro=0.8.3=pyhd8ed1ab_0
- vaex-core=4.8.0=py39h50574b8_0
- vaex-hdf5=0.10.0=pyhd8ed1ab_0
- vaex-jupyter=0.6.0=pyhd8ed1ab_0
- vaex-ml=0.14.0=pyhd8ed1ab_0
- vaex-server=0.6.1=pyhd8ed1ab_0
- vaex-viz=0.5.1=pyhd8ed1ab_0
- vsearch=2.18.0=h95f258a_0
- wcwidth=0.2.5=pyh9f0ad1d_2
- webencodings=0.5.1=py_1
- weblogo=3.7.9=pyhdfd78af_0
- wget=1.20.3=ha56f1ee_1
- wheel=0.37.1=pyhd8ed1ab_0
- widgetsnbextension=3.5.2=py39hf3d152e_1
- xarray=2022.3.0=pyhd8ed1ab_0
- xerces-c=3.2.3=h9d8b166_3
- xmltodict=0.12.0=py_0
- xorg-fixesproto=5.0=h7f98852_1002
- xorg-inputproto=2.3.2=h7f98852_1002
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.2=h7f98852_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- xorg-libxfixes=5.0.3=h7f98852_1004
- xorg-libxi=1.7.10=h7f98852_0
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
- xorg-libxtst=1.2.3=h7f98852_1002
- xorg-recordproto=1.14.2=h7f98852_1002
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xyzservices=2022.2.0=pyhd8ed1ab_0
- xz=5.2.5=h516909a_1
- yaml=0.2.5=h7f98852_2
- zeromq=4.3.4=h9c3ff4c_1
- zfp=0.5.5=h9c3ff4c_8
- zict=2.1.0=pyhd8ed1ab_0
- zipp=3.7.0=pyhd8ed1ab_1
- zlib=1.2.11=h36c2ea0_1013
- zstd=1.4.9=ha95c52a_0
- pip:
- absl-py==1.0.0
- amberlite==16.0
- amberutils==21.0
- astunparse==1.6.3
- biopython==1.76
- build==0.7.0
- cachecontrol==0.12.10
- cairocffi==1.3.0
- cairosvg==2.5.2
- carveme==1.5.1
- chart-studio==1.1.0
- colorcet==3.0.0
- cssselect2==0.5.0
- eggnog-mapper==2.1.7
- entrezpy==2.1.3
- flatbuffers==2.0
- gast==0.4.0
- gensim==4.1.2
- google-auth==2.3.3
- google-auth-oauthlib==0.4.6
- google-pasta==0.2.0
- gor4==1.0.2
- grpcio==1.43.0
- hdmedians==0.14.2
- holoviews==1.14.9
- jsonpickle==2.2.0
- keras-preprocessing==1.1.2
- libclang==12.0.0
- littleutils==0.2.2
- lockfile==0.12.2
- logomaker==0.8
- lxml==4.7.1
- markdown==3.3.6
- mictools==1.1.4
- minepy==1.2.5
- mmpbsa-py==16.0
- mmseqs==1.0.0
- modlamp==4.3.0
- mpmath==1.2.1
- mysql-connector-python==8.0.17
- natsort==8.0.2
- ncbi-taxonomist==1.2.1
- nose==1.3.7
- oauthlib==3.1.1
- opencv-python==4.5.5.64
- opt-einsum==3.3.0
- outdated==0.2.1
- packmol-memgen==1.2.1rc0
- pandas==1.3.4
- pandas-flavor==0.2.0
- panel==0.13.0
- param==1.12.1
- pdb4amber==20.1
- pep517==0.12.0
- peptidebuilder==1.1.0
- pingouin==0.5.0
- protobuf==3.19.1
- psutil==5.7.0
- pyasn1==0.4.8
- pyasn1-modules==0.2.8
- pyct==0.4.8
- pyopa==0.8.0
- pyproject-toml==0.0.10
- pyreadr==0.4.4
- pyrodigal==0.7.3
- pysankey==0.0.1
- python-levenshtein==0.12.2
- python-libsbml==5.19.0
- python-xz==0.4.0
- pytraj==2.0.6
- pyvis==0.2.1
- pyviz-comms==2.2.0
- quantumrandom==1.9.0
- reframed==1.2.1
- requests-oauthlib==1.3.0
- retrying==1.3.3
- rpsg-cdias==0.0.1
- rsa==4.8
- sander==16.0
- scikit-bio==0.5.6
- sklearn==0.0
- smart-open==5.2.1
- sqlitedict==1.7.0
- svgutils==0.3.4
- sympy==1.9
- tensorboard==2.7.0
- tensorboard-data-server==0.6.1
- tensorboard-plugin-wit==1.8.0
- tensorflow==2.7.0
- tensorflow-estimator==2.7.0
- tensorflow-io-gcs-filesystem==0.23.1
- termcolor==1.1.0
- tinycss2==1.1.1
- tmhmm-py==1.2.1
- toml==0.10.2
- tomli==2.0.0
- torch==1.10.1
- umap==0.1.1
- verstack==0.5.1
- werkzeug==2.0.2
- wrapt==1.13.3
- xgboost==1.5.0
- xlsxwriter==1.4.3