environment.yml

name: BIOS424
channels:
  - hcc
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.1=anacondar_1
  - alsa-lib=1.2.11=hd590300_1
  - augustus=3.5.0=pl5321heb9362c_5
  - bamtools=2.5.2=hdcf5f25_5
  - bbmap=39.17=he5f24ec_0
  - bcftools=1.21=h8b25389_0
  - binutils_impl_linux-64=2.43=h4bf12b8_4
  - biopython=1.85=py39h8cd3c5a_1
  - blast=2.16.0=hc155240_3
  - boost-cpp=1.85.0=h44aadfe_2
  - brotli=1.1.0=hb9d3cd8_2
  - brotli-bin=1.1.0=hb9d3cd8_2
  - brotli-python=1.1.0=py39hf88036b_2
  - busco=5.8.2=pyhdfd78af_0
  - bwidget=1.10.1=ha770c72_0
  - 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
  - cairo=1.18.0=h3faef2a_0
  - cdbtools=0.99=hdcf5f25_10
  - certifi=2025.1.31=pyhd8ed1ab_0
  - cffi=1.17.1=py39h15c3d72_0
  - charset-normalizer=3.4.1=pyhd8ed1ab_0
  - colorama=0.4.6=pyhd8ed1ab_1
  - compleasm=0.2.6=pyh7cba7a3_0
  - contourpy=1.3.0=py39h74842e3_2
  - curl=8.8.0=he654da7_1
  - cycler=0.12.1=pyhd8ed1ab_1
  - dendropy=4.5.2=pyh3252c3a_0
  - diamond=2.1.10=h43eeafb_2
  - dorado=0.7.2=h5e1937b_0
  - entrez-direct=22.4=he881be0_0
  - expat=2.6.4=h5888daf_0
  - filelock=3.17.0=pyhd8ed1ab_0
  - flye=2.9.5=py39hdf45acc_1
  - 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=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.56.0=py39h9399b63_0
  - freetype=2.12.1=h267a509_2
  - fribidi=1.0.10=h36c2ea0_0
  - fsspec=2025.2.0=pyhd8ed1ab_0
  - gawk=5.3.1=hcd3d067_0
  - gcc_impl_linux-64=14.2.0=hdb7739f_2
  - genometools-genometools=1.6.5=py39h33ebc56_3
  - gettext=0.23.1=h5888daf_0
  - gettext-tools=0.23.1=h5888daf_0
  - gfortran_impl_linux-64=14.2.0=h0ee6e4a_2
  - giflib=5.2.2=hd590300_0
  - gmp=6.3.0=hac33072_2
  - gmpy2=2.1.5=py39h7196dd7_3
  - graphite2=1.3.13=h59595ed_1003
  - grpcio=1.62.2=py39h174d805_0
  - gsl=2.7=he838d99_0
  - gxx_impl_linux-64=14.2.0=h2ead766_2
  - h2=4.2.0=pyhd8ed1ab_0
  - h5py=3.13.0=nompi_py39h30a5a8d_100
  - harfbuzz=8.5.0=hfac3d4d_0
  - hdf5=1.14.3=nompi_hdf9ad27_105
  - hmmer=3.1b2=3
  - hpack=4.1.0=pyhd8ed1ab_0
  - htslib=1.21=h5efdd21_0
  - hyperframe=6.1.0=pyhd8ed1ab_0
  - icu=73.2=h59595ed_0
  - idna=3.10=pyhd8ed1ab_1
  - importlib-resources=6.5.2=pyhd8ed1ab_0
  - importlib_resources=6.5.2=pyhd8ed1ab_0
  - intervaltree=3.1.0=pyhd8ed1ab_1
  - irissv=1.0.5=hdfd78af_0
  - jasminesv=1.1.5=hdfd78af_0
  - jinja2=3.1.5=pyhd8ed1ab_0
  - k8=0.2.5=hdcf5f25_4
  - kernel-headers_linux-64=3.10.0=he073ed8_18
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.7=py39h74842e3_0
  - kmc=3.2.4=h6dccd9a_2
  - krb5=1.21.3=h659f571_0
  - lcms2=2.16=hb7c19ff_0
  - ld_impl_linux-64=2.43=h712a8e2_4
  - lerc=4.0.0=h27087fc_0
  - libabseil=20240116.2=cxx17_he02047a_1
  - libaec=1.1.3=h59595ed_0
  - libasprintf=0.23.1=h8e693c7_0
  - libasprintf-devel=0.23.1=h8e693c7_0
  - libblas=3.9.0=31_h59b9bed_openblas
  - libboost=1.85.0=hba137d9_2
  - libboost-devel=1.85.0=h00ab1b0_2
  - libboost-headers=1.85.0=ha770c72_2
  - 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
  - libcups=2.3.3=h4637d8d_4
  - libcurl=8.8.0=hca28451_1
  - libdeflate=1.20=hd590300_0
  - libedit=3.1.20250104=pl5321h7949ede_0
  - libev=4.33=hd590300_2
  - libexpat=2.6.4=h5888daf_0
  - libffi=3.4.6=h2dba641_0
  - libgcc=14.2.0=h767d61c_2
  - libgcc-devel_linux-64=14.2.0=h9c4974d_102
  - libgcc-ng=14.2.0=h69a702a_2
  - libgettextpo=0.23.1=h5888daf_0
  - libgettextpo-devel=0.23.1=h5888daf_0
  - libgfortran=14.2.0=h69a702a_2
  - libgfortran-ng=14.2.0=h69a702a_2
  - libgfortran5=14.2.0=hf1ad2bd_2
  - libglib=2.80.2=hf974151_0
  - libgomp=14.2.0=h767d61c_2
  - libgrpc=1.62.2=h15f2491_0
  - libhwloc=2.11.2=default_h0d58e46_1001
  - libiconv=1.18=h4ce23a2_1
  - libidn2=2.3.7=hd590300_0
  - libjpeg-turbo=3.0.0=hd590300_1
  - liblapack=3.9.0=31_h7ac8fdf_openblas
  - liblzma=5.6.4=hb9d3cd8_0
  - liblzma-devel=5.6.4=hb9d3cd8_0
  - libnghttp2=1.58.0=h47da74e_1
  - libnsl=2.0.1=hd590300_0
  - libopenblas=0.3.29=pthreads_h94d23a6_0
  - libopenssl-static=3.4.1=hb9d3cd8_0
  - libpng=1.6.43=h2797004_0
  - libprotobuf=4.25.3=h08a7969_0
  - libre2-11=2023.09.01=h5a48ba9_2
  - libsanitizer=14.2.0=hed042b8_2
  - libsqlite=3.46.0=hde9e2c9_0
  - libssh2=1.11.0=h0841786_0
  - libstdcxx=14.2.0=h8f9b012_2
  - libstdcxx-devel_linux-64=14.2.0=h9c4974d_102
  - libstdcxx-ng=14.2.0=h4852527_2
  - libtiff=4.6.0=h1dd3fc0_3
  - libtorch=2.3.1=cpu_generic_h970db74_0
  - libunistring=0.9.10=h7f98852_0
  - libuuid=2.38.1=h0b41bf4_0
  - libuv=1.50.0=hb9d3cd8_0
  - libwebp-base=1.5.0=h851e524_0
  - libxcb=1.15=h0b41bf4_0
  - libxcrypt=4.4.36=hd590300_1
  - libxml2=2.13.5=hfdd30dd_0
  - libzlib=1.2.13=h4ab18f5_6
  - lp_solve=5.5.2.11=hd590300_0
  - make=4.4.1=hb9d3cd8_2
  - mappy=2.28=py39he47c912_2
  - markupsafe=3.0.2=py39h9399b63_1
  - matplotlib-base=3.9.4=py39h16632d1_0
  - medaka=2.0.1=py39hf77f13f_0
  - metaeuk=7.bba0d80=pl5321h6a68c12_1
  - metis=5.1.0=hd0bcaf9_1007
  - minimap2=2.28=he4a0461_3
  - miniprot=0.13=he4a0461_1
  - mpc=1.3.1=h24ddda3_1
  - mpfr=4.2.1=h90cbb55_3
  - mpmath=1.3.0=pyhd8ed1ab_1
  - mummer=3.23=pl5321h503566f_21
  - munkres=1.1.4=pyh9f0ad1d_0
  - mysql-connector-c=6.1.11=h659d440_1008
  - ncbi-vdb=3.2.0=h9948957_0
  - ncurses=6.5=h2d0b736_3
  - networkx=3.2.1=pyhd8ed1ab_0
  - nomkl=1.0=h5ca1d4c_0
  - numpy=1.26.4=py39h474f0d3_0
  - ont-fast5-api=4.1.3=pyhdfd78af_0
  - openjdk=22.0.1=hb622114_0
  - openjpeg=2.5.2=h488ebb8_0
  - openssl=3.4.1=h7b32b05_0
  - packaging=24.2=pyhd8ed1ab_2
  - pandas=2.2.3=py39h3b40f6f_2
  - pango=1.54.0=h84a9a3c_0
  - parasail-python=1.3.4=py39heaaa4ec_2
  - pcre2=10.43=hcad00b1_0
  - perl=5.32.1=7_hd590300_perl5
  - perl-app-cpanminus=1.7048=pl5321hd8ed1ab_0
  - perl-archive-tar=2.40=pl5321hdfd78af_0
  - perl-carp=1.50=pl5321hd8ed1ab_0
  - perl-class-method-modifiers=2.13=pl5321ha770c72_0
  - perl-common-sense=3.75=pl5321hd8ed1ab_0
  - perl-compress-raw-bzip2=2.201=pl5321hbf60520_0
  - perl-compress-raw-zlib=2.202=pl5321hadc24fc_0
  - perl-constant=1.33=pl5321hd8ed1ab_0
  - perl-dbi=1.643=pl5321hb9d3cd8_1
  - perl-encode=3.21=pl5321hb9d3cd8_1
  - perl-exporter=5.74=pl5321hd8ed1ab_0
  - perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0
  - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
  - perl-file-path=2.18=pl5321hd8ed1ab_0
  - perl-file-temp=0.2304=pl5321hd8ed1ab_0
  - perl-file-which=1.24=pl5321hd8ed1ab_0
  - perl-inc-latest=0.500=pl5321ha770c72_0
  - perl-io-compress=2.201=pl5321h503566f_4
  - perl-io-zlib=1.14=pl5321hdfd78af_0
  - perl-json=4.10=pl5321hdfd78af_1
  - perl-json-xs=4.03=pl5321h9948957_4
  - perl-list-moreutils=0.430=pl5321hdfd78af_0
  - perl-list-moreutils-xs=0.430=pl5321h7b50bb2_4
  - perl-module-build=0.4234=pl5321ha770c72_1
  - perl-moo=2.005004=pl5321ha770c72_0
  - perl-parallel-forkmanager=2.03=pl5321hdfd78af_0
  - perl-parent=0.243=pl5321hd8ed1ab_0
  - perl-pathtools=3.75=pl5321hb9d3cd8_1
  - perl-role-tiny=2.002004=pl5321ha770c72_0
  - perl-scalar-list-utils=1.68=pl5321hb9d3cd8_0
  - perl-storable=3.15=pl5321hb9d3cd8_0
  - perl-sub-quote=2.006006=pl5321ha770c72_0
  - perl-test-fatal=0.016=pl5321ha770c72_0
  - perl-try-tiny=0.31=pl5321ha770c72_0
  - perl-types-serialiser=1.01=pl5321hdfd78af_0
  - perl-yaml=1.30=pl5321hdfd78af_0
  - pillow=10.3.0=py39h90c7501_0
  - pip=25.0.1=pyh8b19718_0
  - pixman=0.44.2=h29eaf8c_0
  - prodigal=2.6.3=h7b50bb2_10
  - progressbar33=2.4=pyhd8ed1ab_1
  - pthread-stubs=0.4=hb9d3cd8_1002
  - purge-dups-runner=2019.12.20=pyhdfd78af_0
  - purge_dups=1.2.6=py39h7132678_1
  - pyabpoa=1.5.3=py39he47c912_0
  - pycparser=2.22=pyh29332c3_1
  - pyparsing=3.2.1=pyhd8ed1ab_0
  - pysam=0.22.1=py39h61809e1_2
  - pysocks=1.7.1=pyha55dd90_7
  - pyspoa=0.2.1=py39hdf45acc_3
  - python=3.9.19=h0755675_0_cpython
  - python-dateutil=2.9.0.post0=pyhff2d567_1
  - python-edlib=1.3.9.post1=py39h2de1943_1
  - python-tzdata=2025.1=pyhd8ed1ab_0
  - python_abi=3.9=5_cp39
  - pytorch=2.3.1=cpu_generic_py39he75b87c_0
  - pytz=2024.1=pyhd8ed1ab_0
  - qhull=2020.2=h434a139_5
  - r-base=4.4.0=h019f4a6_1
  - r-cli=3.6.4=r44h93ab643_1
  - r-colorspace=2.1_1=r44hdb488b9_0
  - r-crayon=1.5.3=r44hc72bb7e_1
  - r-ellipsis=0.3.2=r44hb1dbf0f_3
  - r-fansi=1.0.6=r44hb1dbf0f_1
  - r-farver=2.1.2=r44ha18555a_1
  - r-ggplot2=3.5.1=r44hc72bb7e_1
  - r-glue=1.8.0=r44h2b5f3a1_0
  - r-gtable=0.3.6=r44hc72bb7e_0
  - r-isoband=0.2.7=r44ha18555a_3
  - r-labeling=0.4.3=r44hc72bb7e_1
  - r-lattice=0.22_6=r44hb1dbf0f_1
  - r-lifecycle=1.0.4=r44hc72bb7e_1
  - r-magrittr=2.0.3=r44hb1dbf0f_3
  - r-mass=7.3_64=r44h2b5f3a1_0
  - r-matrix=1.7_2=r44h2ae2be5_0
  - r-mgcv=1.9_1=r44h0d28552_1
  - r-munsell=0.5.1=r44hc72bb7e_1
  - r-nlme=3.1_167=r44hb67ce94_0
  - r-pillar=1.10.1=r44hc72bb7e_0
  - r-pkgconfig=2.0.3=r44hc72bb7e_4
  - r-r6=2.6.1=r44hc72bb7e_0
  - r-rcolorbrewer=1.1_3=r44h785f33e_3
  - r-rlang=1.1.5=r44h93ab643_0
  - r-scales=1.3.0=r44hc72bb7e_1
  - r-tibble=3.2.1=r44hdb488b9_3
  - r-utf8=1.2.4=r44hb1dbf0f_1
  - r-vctrs=0.6.5=r44h0d4f4ea_1
  - r-viridislite=0.4.2=r44hc72bb7e_2
  - r-withr=3.0.2=r44hc72bb7e_0
  - racon=1.5.0=hdcf5f25_5
  - ragtag=2.1.0=pyhb7b1952_0
  - re2=2023.09.01=h7f4b329_2
  - readline=8.2=h8c095d6_2
  - requests=2.32.3=pyhd8ed1ab_1
  - rpsbproc=0.5.0=h6a68c12_1
  - samtools=1.21=h50ea8bc_0
  - scipy=1.13.1=py39haf93ffa_0
  - sed=4.8=he412f7d_0
  - sepp=4.4.0=py39_0
  - seqkit=2.9.0=h9ee0642_0
  - setuptools=75.8.0=pyhff2d567_0
  - six=1.17.0=pyhd8ed1ab_0
  - sleef=3.8=h1b44611_0
  - sniffles=2.2=pyhdfd78af_0
  - sortedcontainers=2.4.0=pyhd8ed1ab_1
  - sqlite=3.46.0=h6d4b2fc_0
  - suitesparse=5.10.1=h5a4f163_3
  - svim-asm=1.0.3=pyhdfd78af_0
  - sympy=1.13.3=pypyh2585a3b_103
  - sysroot_linux-64=2.17=h0157908_18
  - tar=1.34=hb2e2bae_1
  - tbb=2022.0.0=hceb3a55_0
  - tk=8.6.13=noxft_h4845f30_101
  - tktable=2.10=h8bc8fbc_6
  - tqdm=4.67.1=pyhd8ed1ab_1
  - typing_extensions=4.12.2=pyha770c72_1
  - tzdata=2025a=h78e105d_0
  - ucsc-fatotwobit=472=he8037a5_0
  - ucsc-twobitinfo=472=h9b8f530_0
  - unicodedata2=16.0.0=py39h8cd3c5a_0
  - urllib3=2.3.0=pyhd8ed1ab_0
  - wget=1.21.4=hda4d442_0
  - wheel=0.45.1=pyhd8ed1ab_1
  - wurlitzer=3.1.1=pyhd8ed1ab_1
  - xorg-fixesproto=5.0=hb9d3cd8_1003
  - xorg-inputproto=2.3.2=hb9d3cd8_1003
  - xorg-kbproto=1.0.7=hb9d3cd8_1003
  - xorg-libice=1.1.2=hb9d3cd8_0
  - xorg-libsm=1.2.5=he73a12e_0
  - xorg-libx11=1.8.9=h8ee46fc_0
  - xorg-libxau=1.0.12=hb9d3cd8_0
  - xorg-libxdmcp=1.1.5=hb9d3cd8_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-libxt=1.3.0=hd590300_1
  - 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=5.6.4=hbcc6ac9_0
  - xz-gpl-tools=5.6.4=hbcc6ac9_0
  - xz-tools=5.6.4=hb9d3cd8_0
  - zipp=3.21.0=pyhd8ed1ab_1
  - zlib=1.2.13=h4ab18f5_6
  - zstandard=0.23.0=py39h08a7858_1
  - zstd=1.5.6=ha6fb4c9_0
prefix: /home/groups/dpetrov/jahemker/miniconda3/envs/BIOS424