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environment.yml
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environment.yml
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name: atac_rna_processing
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- alsa-lib=1.2.8=h166bdaf_0
- anyio=3.6.2=pyhd8ed1ab_0
- appdirs=1.4.4=pyh9f0ad1d_0
- argon2-cffi=21.3.0=pyhd8ed1ab_0
- argon2-cffi-bindings=21.2.0=py310h5764c6d_3
- arrow-cpp=12.0.0=ha770c72_1_cpu
- asttokens=2.2.1=pyhd8ed1ab_0
- attr=2.5.1=h166bdaf_1
- attrs=22.2.0=pyh71513ae_0
- autopep8=2.0.1=pyhd8ed1ab_0
- aws-c-auth=0.6.26=h2c7c9e7_6
- aws-c-cal=0.5.26=h71eb795_0
- aws-c-common=0.8.17=hd590300_0
- aws-c-compression=0.2.16=h4f47f36_6
- aws-c-event-stream=0.2.20=h69ce273_6
- aws-c-http=0.7.7=h7b8353a_3
- aws-c-io=0.13.21=h2c99d58_4
- aws-c-mqtt=0.8.6=h3a1964a_15
- aws-c-s3=0.2.8=h0933b68_4
- aws-c-sdkutils=0.1.9=h4f47f36_1
- aws-checksums=0.1.14=h4f47f36_6
- aws-crt-cpp=0.19.9=h85076f6_5
- aws-sdk-cpp=1.10.57=hf40e4db_10
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=pyhd8ed1ab_3
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- beautifulsoup4=4.11.1=pyha770c72_0
- bedtools=2.30.0=h468198e_3
- biopython=1.80=py310h5764c6d_0
- bleach=5.0.1=pyhd8ed1ab_0
- boto3=1.26.64=pyhd8ed1ab_0
- botocore=1.29.64=pyhd8ed1ab_0
- brotli=1.0.9=h166bdaf_8
- brotli-bin=1.0.9=h166bdaf_8
- brotlipy=0.7.0=py310h5764c6d_1005
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2023.7.22=hbcca054_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- certifi=2023.7.22=pyhd8ed1ab_0
- cffi=1.15.1=py310h255011f_3
- cftime=1.6.2=py310hde88566_1
- charset-normalizer=2.1.1=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_0
- comm=0.1.2=pyhd8ed1ab_0
- contourpy=1.0.7=py310hdf3cbec_0
- cryptography=39.0.2=py310h34c0648_0
- curl=8.1.2=h409715c_0
- cycler=0.11.0=pyhd8ed1ab_0
- dbus=1.13.18=hb2f20db_0
- debugpy=1.6.5=py310heca2aa9_0
- decorator=5.1.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- elementpath=3.0.2=pyhd8ed1ab_0
- entrypoints=0.4=pyhd8ed1ab_0
- et_xmlfile=1.0.1=py_1001
- exceptiongroup=1.1.2=pyhd8ed1ab_0
- executing=1.2.0=pyhd8ed1ab_0
- expat=2.5.0=h27087fc_0
- fasteners=0.17.3=pyhd8ed1ab_0
- fftw=3.3.10=nompi_hf0379b8_106
- flit-core=3.8.0=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=hab24e00_0
- fontconfig=2.14.1=hc2a2eb6_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.38.0=py310h5764c6d_1
- freetype=2.12.1=hca18f0e_1
- gettext=0.21.1=h27087fc_0
- gflags=2.2.2=he1b5a44_1004
- ghostscript=9.54.0=h27087fc_2
- giflib=5.2.1=h0b41bf4_3
- glib=2.74.1=h6239696_1
- glib-tools=2.74.1=h6239696_1
- glog=0.6.0=h6f12383_0
- griddataformats=1.0.1=pyhd8ed1ab_0
- gsd=3.1.1=py310h278f3c1_0
- gst-plugins-base=1.14.1=h6a678d5_1
- gstreamer=1.14.1=h5eee18b_1
- gstreamer-orc=0.4.33=h166bdaf_0
- h5py=3.8.0=nompi_py310h0311031_100
- hdf4=4.2.15=h9772cbc_5
- hdf5=1.12.2=nompi_h4df4325_101
- icu=58.2=hf484d3e_1000
- idna=3.4=pyhd8ed1ab_0
- importlib-metadata=6.0.0=pyha770c72_0
- importlib_resources=5.10.2=pyhd8ed1ab_0
- iniconfig=2.0.0=pyhd8ed1ab_0
- ipykernel=6.20.1=pyh210e3f2_0
- ipyparallel=8.4.1=pyhd8ed1ab_0
- ipython=8.8.0=pyh41d4057_0
- ipython_genutils=0.2.0=py_1
- ipywidgets=8.0.4=pyhd8ed1ab_0
- jack=1.9.22=h11f4161_0
- jedi=0.18.2=pyhd8ed1ab_0
- jinja2=3.1.2=pyhd8ed1ab_1
- jmespath=1.0.1=pyhd8ed1ab_0
- joblib=1.2.0=pyhd8ed1ab_0
- jpeg=9e=h166bdaf_2
- jsonschema=4.17.3=pyhd8ed1ab_0
- jupyter=1.0.0=py310hff52083_8
- jupyter_client=7.4.8=pyhd8ed1ab_0
- jupyter_console=6.4.4=pyhd8ed1ab_0
- jupyter_core=5.1.3=py310hff52083_0
- jupyter_events=0.6.2=pyhd8ed1ab_0
- jupyter_server=2.0.6=pyhd8ed1ab_0
- jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
- jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
- jupyterlab_widgets=3.0.5=pyhd8ed1ab_0
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.4=py310hbf28c38_1
- krb5=1.20.1=h81ceb04_0
- lame=3.100=h166bdaf_1003
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.39=hcc3a1bd_1
- lerc=4.0.0=h27087fc_0
- libabseil=20230125.0=cxx17_hcb278e6_1
- libaec=1.0.6=hcb278e6_1
- libarrow=12.0.0=h1cdf7b0_1_cpu
- libblas=3.9.0=16_linux64_openblas
- libbrotlicommon=1.0.9=h166bdaf_8
- libbrotlidec=1.0.9=h166bdaf_8
- libbrotlienc=1.0.9=h166bdaf_8
- libcap=2.67=he9d0100_0
- libcblas=3.9.0=16_linux64_openblas
- libclang=10.0.1=default_hde54327_1
- libclang13=15.0.3=default_h3a83d3e_0
- libcrc32c=1.1.2=h9c3ff4c_0
- libcups=2.3.3=h36d4200_3
- libcurl=8.1.2=h409715c_0
- libdb=6.2.32=h9c3ff4c_0
- libdeflate=1.18=h0b41bf4_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libevent=2.1.12=hf998b51_1
- libffi=3.4.2=h7f98852_5
- libflac=1.4.2=h27087fc_0
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=12.2.0=h65d4601_19
- libgcrypt=1.10.1=h166bdaf_0
- libgfortran-ng=12.2.0=h69a702a_19
- libgfortran5=12.2.0=h337968e_19
- libglib=2.74.1=h606061b_1
- libgomp=12.2.0=h65d4601_19
- libgoogle-cloud=2.10.0=hac9eb74_0
- libgpg-error=1.46=h620e276_0
- libgrpc=1.54.2=hcf146ea_0
- libiconv=1.17=h166bdaf_0
- libjpeg-turbo=2.1.4=h166bdaf_0
- liblapack=3.9.0=16_linux64_openblas
- libllvm10=10.0.1=he513fc3_3
- libllvm15=15.0.3=h503ea73_0
- libnetcdf=4.8.1=nompi_h21705cb_104
- libnghttp2=1.52.0=h61bc06f_0
- libnsl=2.0.0=h7f98852_0
- libnuma=2.0.16=h0b41bf4_1
- libogg=1.3.4=h7f98852_1
- libopenblas=0.3.21=pthreads_h78a6416_3
- libopus=1.3.1=h7f98852_1
- libpng=1.6.39=h753d276_0
- libpq=12.15=hdbd6064_1
- libprotobuf=3.21.12=h3eb15da_0
- libsndfile=1.2.0=hb75c966_0
- libsodium=1.0.18=h36c2ea0_1
- libsqlite=3.40.0=h753d276_0
- libssh2=1.11.0=h0841786_0
- libstdcxx-ng=12.2.0=h46fd767_19
- libsystemd0=253=h8c4010b_1
- libthrift=0.18.1=h8fd135c_2
- libtiff=4.2.0=hf544144_3
- libtool=2.4.7=h27087fc_0
- libudev1=253=h0b41bf4_1
- libutf8proc=2.8.0=h166bdaf_0
- libuuid=2.32.1=h7f98852_1000
- libvorbis=1.3.7=h9c3ff4c_0
- libwebp=1.2.4=h11a3e52_1
- libwebp-base=1.2.4=h166bdaf_0
- libxcb=1.15=h0b41bf4_0
- libxkbcommon=1.0.3=he3ba5ed_0
- libxml2=2.9.14=h74e7548_0
- libzip=1.10.1=h2629f0a_0
- libzlib=1.2.13=h166bdaf_4
- lz4-c=1.9.3=h9c3ff4c_1
- markupsafe=2.1.1=py310h5764c6d_2
- matplotlib-base=3.6.2=py310h8d5ebf3_0
- matplotlib-inline=0.1.6=pyhd8ed1ab_0
- mdanalysis=2.6.1=py310hf4b3c1f_0
- mistune=2.0.4=pyhd8ed1ab_0
- mmtf-python=1.1.3=pyhd8ed1ab_0
- mpg123=1.31.1=h27087fc_0
- mrcfile=1.4.3=pyhd8ed1ab_0
- msgpack-python=1.0.5=py310hdf3cbec_0
- munkres=1.1.4=pyh9f0ad1d_0
- mysql-common=8.0.33=hf1915f5_2
- mysql-connector-c=6.1.6=0
- mysql-libs=8.0.33=hca2cd23_2
- natsort=8.2.0=pyhd8ed1ab_0
- nbclassic=0.4.8=pyhd8ed1ab_0
- nbclient=0.7.2=pyhd8ed1ab_0
- nbconvert=7.2.7=pyhd8ed1ab_0
- nbconvert-core=7.2.7=pyhd8ed1ab_0
- nbconvert-pandoc=7.2.7=pyhd8ed1ab_0
- nbformat=5.7.1=pyhd8ed1ab_0
- ncls=0.0.65=py310h1425a21_1
- ncurses=6.3=h27087fc_1
- nest-asyncio=1.5.6=pyhd8ed1ab_0
- netcdf4=1.6.2=nompi_py310h55e1e36_100
- networkx=3.1=pyhd8ed1ab_0
- nglview=3.0.6=pyhba93850_0
- notebook=6.5.2=pyha770c72_1
- notebook-shim=0.2.2=pyhd8ed1ab_0
- nspr=4.35=h27087fc_0
- nss=3.82=he02c5a1_0
- numpy=1.23.1=py310h53a5b5f_0
- openjpeg=2.4.0=hb52868f_1
- openpyxl=3.0.10=py310h5764c6d_2
- openssl=3.1.2=hd590300_0
- orc=1.8.3=h2f23424_1
- packaging=23.0=pyhd8ed1ab_0
- pandas=1.5.2=py310h9b08913_2
- pandoc=2.19.2=h32600fe_1
- pandocfilters=1.5.0=pyhd8ed1ab_0
- parallel=20221122=ha770c72_0
- parquet-cpp=1.5.1=2
- parso=0.8.3=pyhd8ed1ab_0
- patsy=0.5.3=pyhd8ed1ab_0
- pbr=5.11.1=pyhd8ed1ab_0
- pcre2=10.40=hc3806b6_0
- perl=5.32.1=2_h7f98852_perl5
- pexpect=4.8.0=pyh1a96a4e_2
- pickleshare=0.7.5=py_1003
- pillow=9.4.0=py310h6a678d5_0
- pip=22.3.1=pyhd8ed1ab_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
- platformdirs=2.6.2=pyhd8ed1ab_0
- pluggy=1.2.0=pyhd8ed1ab_0
- ply=3.11=py_1
- pooch=1.6.0=pyhd8ed1ab_0
- prometheus_client=0.15.0=pyhd8ed1ab_0
- prompt-toolkit=3.0.36=pyha770c72_0
- prompt_toolkit=3.0.36=hd8ed1ab_0
- psutil=5.9.4=py310h5764c6d_0
- pthread-stubs=0.4=h36c2ea0_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pulseaudio=16.1=hcb278e6_3
- pulseaudio-client=16.1=h5195f5e_3
- pulseaudio-daemon=16.1=ha8d29e2_3
- pure_eval=0.2.2=pyhd8ed1ab_0
- pyarrow=12.0.0=py310he6bfd7f_1_cpu
- pycodestyle=2.10.0=pyhd8ed1ab_0
- pycparser=2.21=pyhd8ed1ab_0
- pyedr=0.7.1=pyhd8ed1ab_0
- pyfaidx=0.7.1=pyh5e36f6f_0
- pygments=2.14.0=pyhd8ed1ab_0
- pyliftover=0.4=py_0
- pyopenssl=23.0.0=pyhd8ed1ab_0
- pyparsing=3.0.9=pyhd8ed1ab_0
- pyqt=5.15.4=py310hd8f1fbe_0
- pyqt5-sip=12.9.0=py310hd8f1fbe_0
- pyranges=0.0.120=pyh7cba7a3_0
- pyrle=0.0.35=py310h1425a21_1
- pyrsistent=0.19.3=py310h1fa729e_0
- pysam=0.21.0=py310h41dec4a_1
- pysocks=1.7.1=pyha2e5f31_6
- pytabix=0.1=py310hc8f18ef_2
- pytest=7.4.0=pyhd8ed1ab_0
- python=3.10.10=he550d4f_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-fastjsonschema=2.16.2=pyhd8ed1ab_0
- python-json-logger=2.0.4=pyhd8ed1ab_0
- python_abi=3.10=3_cp310
- pytng=0.3.0=py310hc908c09_0
- pytz=2022.7=pyhd8ed1ab_0
- pyvcf3=1.0.3=pyhdfd78af_0
- pyyaml=6.0=py310h5764c6d_5
- pyzmq=24.0.1=py310h330234f_1
- qt-main=5.15.2=h327a75a_7
- qtconsole=5.4.0=pyhd8ed1ab_0
- qtconsole-base=5.4.0=pyha770c72_0
- qtpy=2.3.0=pyhd8ed1ab_0
- rdma-core=28.9=h59595ed_1
- re2=2023.02.02=hcb278e6_0
- readline=8.2=h8228510_1
- requests=2.28.1=pyhd8ed1ab_1
- rfc3339-validator=0.1.4=pyhd8ed1ab_0
- rfc3986-validator=0.1.1=pyh9f0ad1d_0
- s2n=1.3.44=h06160fa_0
- s3transfer=0.6.0=pyhd8ed1ab_0
- scikit-learn=1.2.1=py310h209a8ca_0
- scipy=1.10.0=py310h8deb116_0
- seaborn=0.12.2=hd8ed1ab_0
- seaborn-base=0.12.2=pyhd8ed1ab_0
- send2trash=1.8.0=pyhd8ed1ab_0
- seqlogo=5.29.8=py_0
- setuptools=65.6.3=pyhd8ed1ab_0
- sip=6.5.1=py310h122e73d_2
- six=1.16.0=pyh6c4a22f_0
- snakeviz=2.2.0=pyhd8ed1ab_0
- snappy=1.1.10=h9fff704_0
- sniffio=1.3.0=pyhd8ed1ab_0
- sorted_nearest=0.0.37=py310h1425a21_0
- soupsieve=2.3.2.post1=pyhd8ed1ab_0
- sqlite=3.40.0=h4ff8645_0
- stack_data=0.6.2=pyhd8ed1ab_0
- statsmodels=0.13.5=py310hde88566_2
- tabulate=0.9.0=pyhd8ed1ab_1
- terminado=0.17.1=pyh41d4057_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- tidynamics=1.1.2=pyhd8ed1ab_0
- tinycss2=1.2.1=pyhd8ed1ab_0
- tk=8.6.12=h27826a3_0
- toml=0.10.2=pyhd8ed1ab_0
- tomli=2.0.1=pyhd8ed1ab_0
- tornado=6.2=py310h5764c6d_1
- tqdm=4.64.1=pyhd8ed1ab_0
- traitlets=5.8.1=pyhd8ed1ab_0
- typing-extensions=4.4.0=hd8ed1ab_0
- typing_extensions=4.4.0=pyha770c72_0
- tzdata=2022g=h191b570_0
- ucsc-liftover=357=0
- ucx=1.14.1=hf587318_2
- unicodedata2=15.0.0=py310h5764c6d_0
- urllib3=1.26.14=pyhd8ed1ab_0
- wcwidth=0.2.5=pyh9f0ad1d_2
- webencodings=0.5.1=py_1
- weblogo=3.7.12=pyhd8ed1ab_0
- websocket-client=1.4.2=pyhd8ed1ab_0
- wheel=0.38.4=pyhd8ed1ab_0
- widgetsnbextension=4.0.5=pyhd8ed1ab_0
- xcb-util=0.4.0=h516909a_0
- xcb-util-image=0.4.0=h8ee46fc_1
- xcb-util-keysyms=0.4.0=h516909a_0
- xcb-util-renderutil=0.3.9=hd590300_1
- xcb-util-wm=0.4.1=h516909a_0
- xmlschema=2.2.1=pyhd8ed1ab_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xz=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- zeromq=4.3.4=h9c3ff4c_1
- zipp=3.11.0=pyhd8ed1ab_0
- zlib=1.2.13=h166bdaf_4
- zstd=1.5.2=h6239696_4
- pip:
- atac-rna-data-processing==0.1
- gprofiler-official==1.0.0
- hic-straw==1.3.1
- pybind11==2.10.3
- python-box==7.0.1
- ruamel-yaml==0.17.24
- ruamel-yaml-clib==0.2.7
prefix: /home/xf2217/mambaforge-pypy3/envs/atac_rna_processing