INVAS/invas_assembly.yaml at main · deepomicslab/INVAS · GitHub

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name: assembly_env
channels:
  - anaconda
  - conda-forge
  - bioconda
  - defaults
  - r
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - alsa-lib=1.1.5=h516909a_1002
  - amply=0.1.6=pyhd8ed1ab_1
  - argcomplete=1.11.1=py_0
  - argh=0.26.2=py39h06a4308_0
  - bedtools=2.31.1=h13024bc_3
  - biopython=1.78=py39h7f8727e_0
  - blas=1.0=openblas
  - brotli-python=1.0.9=py39h6a678d5_9
  - bwa=0.7.18=he4a0461_1
  - bzip2=1.0.8=h4bc722e_7
  - c-ares=1.34.4=hb9d3cd8_0
  - ca-certificates=2025.8.3=hbd8a1cb_0
  - cffi=1.17.1=py39h15c3d72_0
  - coin-or-cbc=2.10.12=h8b142ea_1
  - coin-or-cgl=0.60.6=he2f9439_0
  - coin-or-clp=1.17.6=h256e9bb_3
  - coin-or-osi=0.108.7=h3b589db_0
  - coin-or-utils=2.11.6=h573740c_0
  - coincbc=2.10.12=2_metapackage
  - cyrus-sasl=2.1.28=h52b45da_1
  - dbus=1.13.18=hb2f20db_0
  - docutils=0.21.2=pyhd8ed1ab_1
  - expat=2.6.4=h6a678d5_0
  - fontconfig=2.14.1=h55d465d_3
  - freebayes=1.0.2=0
  - freetype=2.14.1=ha770c72_0
  - gffutils=0.13=pyh7cba7a3_0
  - giflib=5.2.2=hd590300_0
  - glib=2.78.4=h6a678d5_0
  - glib-tools=2.78.4=h6a678d5_0
  - gst-plugins-base=1.14.1=h6a678d5_1
  - gstreamer=1.14.1=h5eee18b_1
  - hdf5=1.14.3=nompi_h2d575fe_109
  - hisat2=2.2.1=h503566f_8
  - htslib=1.21=h5efdd21_0
  - icu=73.1=h6a678d5_0
  - importlib-metadata=8.6.1=pyha770c72_0
  - isa-l=2.31.1=hb9d3cd8_1
  - jpeg=9e=h5eee18b_3
  - kallisto=0.51.1=h2b92561_2
  - krb5=1.20.1=h143b758_1
  - lcms2=2.12=h3be6417_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libaec=1.1.4=h3f801dc_0
  - libblas=3.9.0=20_linux64_openblas
  - libcblas=3.9.0=20_linux64_openblas
  - libclang=14.0.6=default_hc6dbbc7_2
  - libclang13=14.0.6=default_he11475f_2
  - libcups=2.4.2=h252cb56_2
  - libcurl=8.15.0=hc1efc7f_0
  - libdeflate=1.23=h4ddbbb0_0
  - libedit=3.1.20230828=h5eee18b_0
  - libev=4.33=hd590300_2
  - libffi=3.4.4=h6a678d5_1
  - libfreetype=2.14.1=ha770c72_0
  - libfreetype6=2.14.1=h73754d4_0
  - libgcc=14.2.0=h767d61c_2
  - libgcc-ng=14.2.0=h69a702a_2
  - libgfortran=14.2.0=h69a702a_2
  - libgfortran-ng=14.2.0=h69a702a_2
  - libgfortran5=14.2.0=hf1ad2bd_2
  - libglib=2.78.4=hdc74915_0
  - libgomp=14.2.0=h767d61c_2
  - libiconv=1.16=h5eee18b_3
  - liblapack=3.9.0=20_linux64_openblas
  - liblapacke=3.9.0=20_linux64_openblas
  - libllvm14=14.0.6=hecde1de_4
  - liblzma=5.8.1=hb9d3cd8_2
  - liblzma-devel=5.8.1=hb9d3cd8_2
  - libnghttp2=1.64.0=h161d5f1_0
  - libopenblas=0.3.25=pthreads_h413a1c8_0
  - libpng=1.6.50=h421ea60_1
  - libpq=12.20=hdbd6064_0
  - libssh2=1.11.1=hcf80075_0
  - libstdcxx=14.2.0=h8f9b012_2
  - libstdcxx-ng=11.2.0=h1234567_1
  - libtiff=4.2.0=hecacb30_2
  - libuuid=1.41.5=h5eee18b_0
  - libwebp-base=1.3.2=h5eee18b_1
  - libxcb=1.15=h7f8727e_0
  - libxkbcommon=1.0.1=h097e994_2
  - libxml2=2.13.8=hfdd30dd_0
  - libzlib=1.3.1=hb9d3cd8_2
  - lz4-c=1.9.3=h9c3ff4c_1
  - mysql=5.7.24=h721c034_2
  - ncurses=6.4=h6a678d5_0
  - networkx=3.2.1=py39h06a4308_0
  - numpy=1.26.4=py39heeff2f4_0
  - numpy-base=1.26.4=py39h8a23956_0
  - openjdk=11.0.1=h516909a_1016
  - openjpeg=2.4.0=h9ca470c_2
  - openssl=3.5.3=h26f9b46_0
  - packaging=24.2=pyhd8ed1ab_2
  - parasail-python=1.3.4=py39h746d604_5
  - pbzip2=1.1.13=0
  - pcre2=10.42=hcad00b1_0
  - perl=5.38.2=0_h5eee18b_perl5
  - pigz=2.8=h2797004_0
  - pip=25.0=py39h06a4308_0
  - ply=3.11=py39h06a4308_0
  - pulp=2.8.0=py39hf3d152e_0
  - pycparser=2.22=pyh29332c3_1
  - pyfaidx=0.8.1.3=pyhdfd78af_0
  - pyparsing=3.2.1=pyhd8ed1ab_0
  - pyqt=5.15.10=py39h6a678d5_1
  - pyqt5-sip=12.13.0=py39h5eee18b_1
  - pysam=0.22.1=py39h61809e1_2
  - python=3.9.21=he870216_1
  - python-dateutil=2.9.0post0=py39h06a4308_2
  - python-isal=1.7.2=py39h8cd3c5a_0
  - python-zlib-ng=0.5.1=py39h1635d6b_0
  - python_abi=3.9=2_cp39
  - pyvcf3=1.0.3=pyhdfd78af_0
  - qt-main=5.15.2=h53bd1ea_10
  - readline=8.2=h5eee18b_0
  - scipy=1.8.1=py39he49c0e8_0
  - setuptools=75.8.0=py39h06a4308_0
  - simplejson=3.19.2=py39h5eee18b_1
  - sip=6.7.12=py39h6a678d5_1
  - six=1.17.0=pyhd8ed1ab_0
  - sqlite=3.50.2=hb25bd0a_1
  - stringtie=2.2.1=hecb563c_2
  - tk=8.6.14=h39e8969_0
  - tomli=2.0.1=py39h06a4308_0
  - tornado=6.4.2=py39h5eee18b_0
  - trimmomatic=0.40=hdfd78af_0
  - unicodedata2=15.1.0=py39h5eee18b_1
  - vcflib=1.0.0_rc1=0
  - whatshap=2.4=py39h2de1943_0
  - wheel=0.45.1=py39h06a4308_0
  - xopen=2.0.2=pyh707e725_2
  - xorg-fixesproto=5.0=hb9d3cd8_1003
  - xorg-inputproto=2.3.2=hb9d3cd8_1003
  - xorg-kbproto=1.0.7=hb9d3cd8_1003
  - xorg-libx11=1.8.9=h8ee46fc_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxfixes=5.0.3=h7f98852_1004
  - xorg-libxi=1.7.10=h4bc722e_1
  - xorg-libxrender=0.9.11=hd590300_0
  - xorg-libxtst=1.2.5=h4bc722e_0
  - xorg-recordproto=1.14.2=hb9d3cd8_1003
  - xorg-renderproto=0.11.1=hb9d3cd8_1003
  - xorg-xextproto=7.3.0=hb9d3cd8_1004
  - xorg-xproto=7.0.31=hb9d3cd8_1008
  - xz=5.8.1=hbcc6ac9_2
  - xz-gpl-tools=5.8.1=hbcc6ac9_2
  - xz-tools=5.8.1=hb9d3cd8_2
  - zipp=3.21.0=pyhd8ed1ab_1
  - zlib=1.3.1=hb9d3cd8_2
  - zlib-ng=2.2.5=hde8ca8f_0
  - zstandard=0.23.0=py39h8cd3c5a_1
  - zstd=1.5.7=hb8e6e7a_2
  - pip:
      - contourpy==1.3.0
      - cycler==0.12.1
      - fonttools==4.56.0
      - importlib-resources==6.5.2
      - kiwisolver==1.4.7
      - matplotlib==3.9.4
      - pandas==2.2.3
      - pillow==11.1.0
      - pybedtools==0.11.0
      - pytz==2025.1
      - tzdata==2025.1
      - upsetplot==0.9.0
prefix: /data3/wangxuedong/app/miniconda3/envs/assembly_env