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environment.yml
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name: malvirus-repro-exp
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- agate=1.6.0=py_3
- agate-dbf=0.2.1=py_0
- agate-excel=0.2.3=py_0
- agate-sql=0.5.4=py_0
- aiohttp=3.7.4=py38h497a2fe_0
- amply=0.1.4=py_0
- appdirs=1.4.4=pyh9f0ad1d_0
- async-timeout=3.0.1=py_1000
- attrs=20.3.0=pyhd3deb0d_0
- babel=2.9.0=pyhd3deb0d_0
- bcftools=1.10.2=h4f4756c_3
- binutils_impl_linux-64=2.35.1=h193b22a_2
- binutils_linux-64=2.35=h67ddf6f_30
- biopython=1.78=py38h7b6447c_0
- blas=1.1=openblas
- boto=2.49.0=py_0
- boto3=1.17.21=pyhd8ed1ab_0
- botocore=1.20.21=pyhd8ed1ab_0
- brotlipy=0.7.0=py38h497a2fe_1001
- bwa=0.7.17=hed695b0_7
- bz2file=0.98=py_0
- bzip2=1.0.8=h7f98852_4
- c-ares=1.17.1=h7f98852_1
- ca-certificates=2020.12.5=ha878542_0
- cachetools=4.2.1=pyhd8ed1ab_0
- certifi=2020.12.5=py38h578d9bd_1
- cffi=1.14.4=py38ha312104_0
- chardet=4.0.0=py38h578d9bd_1
- coincbc=2.10.5=hab63836_1
- conda=4.9.2=py38h578d9bd_0
- conda-package-handling=1.7.2=py38h8df0ef7_0
- configargparse=1.3=pyhd8ed1ab_0
- cryptography=3.4.4=py38h3e25421_0
- csvkit=1.0.4=py_0
- curl=7.71.1=he644dc0_8
- cycler=0.10.0=py_2
- datrie=0.8.2=py38h1e0a361_1
- dbfread=2.0.7=py_0
- docutils=0.16=py38h578d9bd_3
- et_xmlfile=1.0.1=py_1001
- filelock=3.0.12=pyh9f0ad1d_0
- freetype=2.10.4=h0708190_1
- gcc_impl_linux-64=7.5.0=habd7529_19
- gcc_linux-64=7.5.0=h47867f9_30
- gitdb=4.0.5=pyhd8ed1ab_1
- gitpython=3.1.14=pyhd8ed1ab_0
- gofasta=0.0.3=0
- google-api-core=1.25.1=pyh44b312d_0
- google-auth=1.27.1=pyhd3eb1b0_0
- google-cloud-core=1.6.0=pyhd3eb1b0_0
- google-cloud-storage=1.36.1=pyhd3eb1b0_0
- google-crc32c=1.1.2=py38h8838a9a_0
- google-resumable-media=1.2.0=pyhd3deb0d_0
- googleapis-common-protos=1.52.0=py38h578d9bd_1
- greenlet=1.0.0=py38h709712a_0
- gsl=2.6=he838d99_2
- gxx_impl_linux-64=7.5.0=hd0bb8aa_19
- gxx_linux-64=7.5.0=h555fc39_30
- hdf5=1.10.5=nompi_h7c3c948_1111
- htslib=1.10.2=hd3b49d5_1
- icu=68.1=h58526e2_0
- idna=2.10=pyh9f0ad1d_0
- importlib-metadata=3.7.0=py38h578d9bd_0
- importlib_metadata=3.7.0=hd8ed1ab_0
- ipython_genutils=0.2.0=py_1
- isodate=0.6.0=py_1
- jdcal=1.4.1=py_0
- jmespath=0.10.0=pyh9f0ad1d_0
- joblib=1.0.1=pyhd8ed1ab_0
- jpeg=9d=h516909a_0
- jsonschema=3.2.0=py38h32f6830_1
- jupyter_core=4.7.1=py38h578d9bd_0
- k8=0.2.5=he513fc3_0
- kernel-headers_linux-64=2.6.32=h77966d4_13
- kiwisolver=1.3.1=py38h1fd1430_1
- kmc=3.1.2rc1=h2d02072_0
- krb5=1.17.2=h926e7f8_0
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.35.1=hea4e1c9_2
- leather=0.3.3=py_0
- libarchive=3.5.1=h3f442fb_1
- libblas=3.9.0=8_openblas
- libcblas=3.9.0=8_openblas
- libcrc32c=1.1.1=he1b5a44_2
- libcurl=7.71.1=hcdd3856_8
- libdeflate=1.6=h516909a_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libffi=3.2.1=he1b5a44_1007
- libgcc-devel_linux-64=7.5.0=hda03d7c_19
- libgcc-ng=9.3.0=h2828fa1_18
- libgfortran-ng=7.5.0=h14aa051_18
- libgfortran4=7.5.0=h14aa051_18
- libgomp=9.3.0=h2828fa1_18
- libiconv=1.16=h516909a_0
- liblapack=3.9.0=8_openblas
- libnghttp2=1.43.0=h812cca2_0
- libopenblas=0.3.12=pthreads_hb3c22a3_1
- libpng=1.6.37=hed695b0_2
- libprotobuf=3.15.5=h780b84a_0
- libsolv=0.7.17=h780b84a_0
- libssh2=1.9.0=hab1572f_5
- libstdcxx-devel_linux-64=7.5.0=hb016644_19
- libstdcxx-ng=9.3.0=h6de172a_18
- libtiff=4.2.0=hdc55705_0
- libwebp-base=1.2.0=h7f98852_2
- libxml2=2.9.10=h72842e0_3
- lofreq=2.1.5=py38h1bd3507_3
- lz4-c=1.9.3=h9c3ff4c_0
- lzo=2.10=h516909a_1000
- mafft=7.475=h779adbc_1
- malva=1.3.1=h8e334b0_1
- mamba=0.7.14=py38h2aa5da1_0
- matplotlib-base=3.3.4=py38h0efea84_0
- matplotlib-venn=0.11.6=pyh9f0ad1d_0
- minimap2=2.17=hed695b0_3
- multidict=5.1.0=py38h497a2fe_1
- nbformat=5.1.2=pyhd8ed1ab_1
- ncbi-ngs-sdk=2.11.0=hff44eed_0
- ncurses=6.2=h58526e2_4
- numpy=1.20.1=py38h18fd61f_0
- olefile=0.46=pyh9f0ad1d_1
- openblas=0.3.12=pthreads_h43bd3aa_1
- openpyxl=3.0.7=pyhd8ed1ab_0
- openssl=1.1.1k=h7f98852_0
- ossuuid=1.6.2=hf484d3e_1000
- pandas=1.2.3=py38h51da96c_0
- parallel=20210222=ha770c72_0
- parsedatetime=2.6=pyh9f0ad1d_0
- perl=5.26.2=h36c2ea0_1008
- perl-app-cpanminus=1.7044=pl526_1
- perl-business-isbn=3.004=pl526_0
- perl-business-isbn-data=20140910.003=pl526_0
- perl-carp=1.38=pl526_3
- perl-constant=1.33=pl526_1
- perl-data-dumper=2.173=pl526_0
- perl-encode=2.88=pl526_1
- perl-exporter=5.72=pl526_1
- perl-extutils-makemaker=7.36=pl526_1
- perl-file-path=2.16=pl526_0
- perl-file-temp=0.2304=pl526_2
- perl-mime-base64=3.15=pl526_1
- perl-parent=0.236=pl526_1
- perl-uri=1.76=pl526_0
- perl-xml-libxml=2.0132=pl526h7ec2d77_1
- perl-xml-namespacesupport=1.12=pl526_0
- perl-xml-sax=1.02=pl526_0
- perl-xml-sax-base=1.09=pl526_0
- perl-xsloader=0.24=pl526_0
- pillow=8.1.2=py38ha0e1e83_0
- pip=21.0.1=pyhd8ed1ab_0
- protobuf=3.15.5=py38h709712a_0
- psutil=5.8.0=py38h497a2fe_1
- pulp=2.4=py38h578d9bd_0
- pyasn1=0.4.8=py_0
- pyasn1-modules=0.2.8=py_0
- pycosat=0.6.3=py38h497a2fe_1006
- pycparser=2.20=pyh9f0ad1d_2
- pyopenssl=20.0.1=pyhd8ed1ab_0
- pyparsing=2.4.7=pyh9f0ad1d_0
- pyrsistent=0.17.3=py38h497a2fe_2
- pysam=0.16.0.1=py38hbdc2ae9_1
- pysocks=1.7.1=py38h578d9bd_3
- python=3.8.0=h357f687_5
- python-dateutil=2.8.1=py_0
- python-slugify=4.0.1=pyh9f0ad1d_0
- python_abi=3.8=1_cp38
- pytimeparse=1.1.8=py_0
- pytz=2021.1=pyhd8ed1ab_0
- pyyaml=5.4.1=py38h497a2fe_0
- ratelimiter=1.2.0=py38h32f6830_1001
- readline=8.0=he28a2e2_2
- reproc=14.2.1=h36c2ea0_0
- reproc-cpp=14.2.1=h58526e2_0
- requests=2.25.1=pyhd3deb0d_0
- rsa=4.7.2=pyh44b312d_0
- ruamel_yaml=0.15.87=py38h7b6447c_1
- s3transfer=0.3.4=pyhd8ed1ab_0
- samtools=1.10=h2e538c0_3
- scikit-learn=0.23.1=py38h3a94b23_0
- scipy=1.6.1=py38hf56f3a7_0
- sdsl-lite=2.1.1=hc9558a2_1001
- setuptools=52.0.0=py38h06a4308_0
- six=1.15.0=pyh9f0ad1d_0
- smart_open=4.2.0=pyhd8ed1ab_0
- smmap=3.0.5=pyh44b312d_0
- snakemake-minimal=6.0.2=py_0
- snp-sites=2.5.1=hed695b0_0
- sqlalchemy=1.4.2=py38h497a2fe_0
- sqlite=3.34.0=h74cdb3f_0
- sra-tools=2.10.9=pl526haddd2b5_0
- sysroot_linux-64=2.12=h77966d4_13
- tabix=0.2.6=ha92aebf_0
- text-unidecode=1.3=py_0
- threadpoolctl=2.1.0=pyh5ca1d4c_0
- tk=8.6.10=h21135ba_1
- toposort=1.6=pyhd8ed1ab_0
- tornado=6.1=py38h497a2fe_1
- tqdm=4.58.0=pyhd8ed1ab_0
- traitlets=5.0.5=py_0
- typing-extensions=3.7.4.3=0
- typing_extensions=3.7.4.3=py_0
- tzdata=2021a=he74cb21_0
- unidecode=1.2.0=pyhd8ed1ab_0
- urllib3=1.26.3=pyhd8ed1ab_0
- wheel=0.36.2=pyhd3deb0d_0
- wrapt=1.12.1=py38h497a2fe_3
- xlrd=2.0.1=pyhd8ed1ab_3
- xz=5.2.5=h516909a_1
- yaml=0.2.5=h516909a_0
- yarl=1.5.1=py38h1e0a361_0
- zipp=3.4.1=pyhd8ed1ab_0
- zlib=1.2.11=h516909a_1010
- zstd=1.4.9=ha95c52a_0
- pip:
- pangolearn==2021-04-01
- pangolin==2.3.8