diff --git a/environment.yaml b/environment.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d51ff33ddb3de58cb91472a29fcf585601906c7d --- /dev/null +++ b/environment.yaml @@ -0,0 +1,200 @@ +name: PoreC-env +channels: + - nanoporetech + - conda-forge + - bioconda + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - amply=0.1.6=pyhd8ed1ab_0 + - asciitree=0.3.3=py_2 + - aws-c-auth=0.7.20=h5f1c8d9_0 + - aws-c-cal=0.6.12=h2ba76a8_0 + - aws-c-common=0.9.17=h4ab18f5_0 + - aws-c-compression=0.2.18=h36a0aea_4 + - aws-c-event-stream=0.4.2=h161de36_10 + - aws-c-http=0.8.1=h63f54a0_13 + - aws-c-io=0.14.8=h96d4d28_0 + - aws-c-mqtt=0.10.4=hcc7299c_2 + - aws-c-s3=0.5.8=h10bd90f_3 + - aws-c-sdkutils=0.1.16=h36a0aea_0 + - aws-checksums=0.1.18=h36a0aea_4 + - aws-crt-cpp=0.26.8=h02fd9b4_10 + - aws-sdk-cpp=1.11.267=h51dfee4_8 + - bioframe=0.6.4=pyhdfd78af_0 + - biopython=1.83=py38h01eb140_0 + - blas=1.1=openblas + - bokeh=3.1.1=pyhd8ed1ab_0 + - brotli=1.1.0=hd590300_1 + - brotli-bin=1.1.0=hd590300_1 + - brotli-python=1.1.0=py38h17151c0_1 + - bzip2=1.0.8=hd590300_5 + - c-ares=1.28.1=hd590300_0 + - ca-certificates=2024.2.2=hbcca054_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - certifi=2024.2.2=pyhd8ed1ab_0 + - cffi=1.16.0=py38h6d47a40_0 + - charset-normalizer=3.3.2=pyhd8ed1ab_0 + - click=8.1.7=unix_pyh707e725_0 + - cloudpickle=3.0.0=pyhd8ed1ab_0 + - coin-or-cbc=2.10.10=h9002f0b_0 + - coin-or-cgl=0.60.7=h516709c_0 + - coin-or-clp=1.17.8=h1ee7a9c_0 + - coin-or-osi=0.108.10=haf5fa05_0 + - coin-or-utils=2.11.11=hee58242_0 + - coincbc=2.10.10=0_metapackage + - contourpy=1.1.1=py38h7f3f72f_1 + - cooler=0.9.3=pyhdfd78af_0 + - coreutils=9.5=hd590300_0 + - cycler=0.12.1=pyhd8ed1ab_0 + - cytoolz=0.12.3=py38h01eb140_0 + - dask=2023.5.0=pyhd8ed1ab_0 + - dask-core=2023.5.0=pyhd8ed1ab_0 + - dill=0.3.8=pyhd8ed1ab_0 + - distributed=2023.5.0=pyhd8ed1ab_0 + - docutils=0.20.1=py38h578d9bd_3 + - fonttools=4.51.0=py38h01eb140_0 + - freetype=2.12.1=h267a509_2 + - fsspec=2024.3.1=pyhca7485f_0 + - gflags=2.2.2=he1b5a44_1004 + - glog=0.7.0=hed5481d_0 + - h5py=3.11.0=nompi_py38h2c1edd7_100 + - hdf5=1.14.3=nompi_h4f84152_101 + - hic2cool=1.0.1=pyh7cba7a3_0 + - htslib=1.20=h81da01d_0 + - idna=3.7=pyhd8ed1ab_0 + - importlib-metadata=7.1.0=pyha770c72_0 + - importlib_metadata=7.1.0=hd8ed1ab_0 + - isa-l=2.31.0=hd590300_1 + - jinja2=3.1.4=pyhd8ed1ab_0 + - keyutils=1.6.1=h166bdaf_0 + - kiwisolver=1.4.5=py38h7f3f72f_1 + - krb5=1.21.2=h659d440_0 + - lcms2=2.16=hb7c19ff_0 + - ld_impl_linux-64=2.40=h55db66e_0 + - lerc=4.0.0=h27087fc_0 + - libabseil=20240116.2=cxx17_h59595ed_0 + - libaec=1.1.3=h59595ed_0 + - libarrow=13.0.0=ha811a96_37_cpu + - libblas=3.9.0=22_linux64_openblas + - libbrotlicommon=1.1.0=hd590300_1 + - libbrotlidec=1.1.0=hd590300_1 + - libbrotlienc=1.1.0=hd590300_1 + - libcblas=3.9.0=22_linux64_openblas + - libcrc32c=1.1.2=h9c3ff4c_0 + - libcurl=8.7.1=hca28451_0 + - libdeflate=1.19=hd590300_0 + - libedit=3.1.20191231=he28a2e2_2 + - libev=4.33=hd590300_2 + - libevent=2.1.12=hf998b51_1 + - libffi=3.4.2=h7f98852_5 + - libgcc-ng=13.2.0=h77fa898_7 + - libgfortran-ng=13.2.0=h69a702a_7 + - libgfortran5=13.2.0=hca663fb_7 + - libgomp=13.2.0=h77fa898_7 + - libgoogle-cloud=2.23.0=h9be4e54_1 + - libgoogle-cloud-storage=2.23.0=hc7a4891_1 + - libgrpc=1.62.2=h15f2491_0 + - libjpeg-turbo=3.0.0=hd590300_1 + - liblapack=3.9.0=22_linux64_openblas + - liblapacke=3.9.0=22_linux64_openblas + - libnghttp2=1.58.0=h47da74e_1 + - libnl=3.9.0=hd590300_0 + - libnsl=2.0.1=hd590300_0 + - libopenblas=0.3.27=pthreads_h413a1c8_0 + - libpng=1.6.43=h2797004_0 + - libprotobuf=4.25.3=h08a7969_0 + - libre2-11=2023.09.01=h5a48ba9_2 + - libsqlite=3.45.3=h2797004_0 + - libssh2=1.11.0=h0841786_0 + - libstdcxx-ng=13.2.0=hc0a3c3a_7 + - libthrift=0.19.0=hb90f79a_1 + - libtiff=4.6.0=ha9c0a0a_2 + - libutf8proc=2.8.0=h166bdaf_0 + - libuuid=2.38.1=h0b41bf4_0 + - libwebp-base=1.4.0=hd590300_0 + - libxcb=1.15=h0b41bf4_0 + - libxcrypt=4.4.36=hd590300_1 + - libzlib=1.2.13=hd590300_5 + - locket=1.0.0=pyhd8ed1ab_0 + - lz4=4.3.3=py38hdcd8cb4_0 + - lz4-c=1.9.4=hcb278e6_0 + - markupsafe=2.1.5=py38h01eb140_0 + - matplotlib-base=3.5.3=py38h38b5ce0_2 + - msgpack-python=1.0.8=py38hea7755e_0 + - multiprocess=0.70.16=py38h01eb140_0 + - munkres=1.1.4=pyh9f0ad1d_0 + - ncurses=6.5=h59595ed_0 + - networkx=2.8.8=pyhd8ed1ab_0 + - numpy=1.24.4=py38h59b608b_0 + - openblas=0.3.27=pthreads_h7a3da1a_0 + - openjpeg=2.5.2=h488ebb8_0 + - openssl=3.3.0=hd590300_0 + - orc=2.0.0=h17fec99_1 + - packaging=24.0=pyhd8ed1ab_0 + - pairix=0.3.8=py38h7cf9df2_1 + - pairtools=1.1.0=py38hd5d73cc_0 + - pandas=2.0.3=py38h01efb38_1 + - partd=1.4.1=pyhd8ed1ab_0 + - pbgzip=2016.08.04=h9d449c0_5 + - pbzip2=1.1.13=h1fcc475_2 + - perl=5.32.1=7_hd590300_perl5 + - pigz=2.8=h2797004_0 + - pillow=10.3.0=py38h9e66945_0 + - pip=24.0=pyhd8ed1ab_0 + - platformdirs=4.2.1=pyhd8ed1ab_0 + - pooch=1.8.1=pyhd8ed1ab_0 + - pore-c-py=2.1.2=py_0 + - psutil=5.9.8=py38h01eb140_0 + - pthread-stubs=0.4=h36c2ea0_1001 + - pulp=2.8.0=py38h578d9bd_0 + - pyarrow=13.0.0=py38hc396e17_37_cpu + - pycparser=2.22=pyhd8ed1ab_0 + - pyfaidx=0.8.1.1=pyhdfd78af_0 + - pyparsing=3.1.2=pyhd8ed1ab_0 + - pysam=0.22.0=py38h9bf148f_1 + - pysocks=1.7.1=pyha2e5f31_6 + - python=3.8.19=hd12c33a_0_cpython + - python-dateutil=2.9.0=pyhd8ed1ab_0 + - python-isal=1.6.1=py38h01eb140_0 + - python-tzdata=2024.1=pyhd8ed1ab_0 + - python-zlib-ng=0.4.3=py38hd7de54c_0 + - python_abi=3.8=4_cp38 + - pytz=2024.1=pyhd8ed1ab_0 + - pyvcf3=1.0.3=pyhdfd78af_0 + - pyyaml=6.0.1=py38h01eb140_1 + - rdma-core=51.0=hd3aeb46_0 + - re2=2023.09.01=h7f4b329_2 + - readline=8.2=h8228510_1 + - requests=2.31.0=pyhd8ed1ab_0 + - s2n=1.4.13=he19d79f_0 + - samtools=1.20=h50ea8bc_0 + - scipy=1.10.1=py38h32ae08f_1 + - setuptools=69.5.1=pyhd8ed1ab_0 + - simplejson=3.19.2=py38h01eb140_0 + - six=1.16.0=pyh6c4a22f_0 + - snappy=1.2.0=hdb0a2a9_1 + - sortedcontainers=2.4.0=pyhd8ed1ab_0 + - tblib=3.0.0=pyhd8ed1ab_0 + - tk=8.6.13=noxft_h4845f30_101 + - toolz=0.12.1=pyhd8ed1ab_0 + - tornado=6.4=py38h01eb140_0 + - ucx=1.15.0=ha691c75_8 + - unicodedata2=15.1.0=py38h01eb140_0 + - urllib3=2.2.1=pyhd8ed1ab_0 + - whatshap=2.3=py38h2494328_0 + - wheel=0.43.0=pyhd8ed1ab_1 + - xopen=2.0.1=py38h578d9bd_0 + - xorg-libxau=1.0.11=hd590300_0 + - xorg-libxdmcp=1.1.3=h7f98852_0 + - xyzservices=2024.4.0=pyhd8ed1ab_0 + - xz=5.2.6=h166bdaf_0 + - yaml=0.2.5=h7f98852_2 + - zict=3.0.0=pyhd8ed1ab_0 + - zipp=3.17.0=pyhd8ed1ab_0 + - zlib=1.2.13=hd590300_5 + - zlib-ng=2.0.7=h0b41bf4_0 + - zstandard=0.22.0=py38ha98ab4e_0 + - zstd=1.5.5=hfc55251_0 \ No newline at end of file