https://github.com/jhmarcus/feems-analysis
Raw File
Tip revision: f2d7330f25f8a11124db09000918ae38ae00d4a7 authored by Joseph Marcus on 16 May 2021, 23:59:23 UTC
made C larger in supp fig 13
Tip revision: f2d7330
environment.yml
name: feems_analysis_e
channels:
  - r
  - defaults
  - conda-forge
  - bioconda
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - _r-mutex=1.0.0=anacondar_1
  - admixture=1.3.0=0
  - alabaster=0.7.12=py_0
  - argon2-cffi=20.1.0=py38h25fe258_2
  - async_generator=1.10=py_0
  - attrs=20.3.0=pyhd3deb0d_0
  - babel=2.9.0=pyhd3deb0d_0
  - backcall=0.2.0=pyh9f0ad1d_0
  - backports=1.0=py_2
  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
  - binutils_impl_linux-64=2.31.1=h6176602_1
  - binutils_linux-64=2.31.1=h6176602_9
  - bleach=3.3.0=pyh44b312d_0
  - brotlipy=0.7.0=py38h8df0ef7_1001
  - bwidget=1.9.11=1
  - bzip2=1.0.8=h7b6447c_0
  - c-ares=1.17.1=h27cfd23_0
  - ca-certificates=2021.4.13=h06a4308_1
  - cairo=1.14.12=h8948797_3
  - cartopy=0.18.0=py38hc1e57b6_5
  - certifi=2020.12.5=py38h06a4308_0
  - cffi=1.14.5=py38h261ae71_0
  - chardet=4.0.0=py38h578d9bd_1
  - cryptography=3.2.1=py38h7699a38_0
  - curl=7.76.1=h979ede3_1
  - dbus=1.13.16=hb2f20db_0
  - decorator=5.0.7=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - docutils=0.17.1=py38h578d9bd_0
  - entrypoints=0.3=pyhd8ed1ab_1003
  - expat=2.2.9=he1b5a44_2
  - fontconfig=2.13.0=h9420a91_0
  - freetype=2.10.4=h7ca028e_0
  - fribidi=1.0.10=h7b6447c_0
  - gcc_impl_linux-64=7.3.0=habb00fd_1
  - gcc_linux-64=7.3.0=h553295d_9
  - geos=3.8.1=he1b5a44_0
  - gfortran_impl_linux-64=7.3.0=hdf63c60_1
  - gfortran_linux-64=7.3.0=h553295d_9
  - glib=2.68.1=h36276a3_0
  - graphite2=1.3.14=h23475e2_0
  - gsl=2.4=h14c3975_4
  - gst-plugins-base=1.14.0=hbbd80ab_1
  - gstreamer=1.14.0=h28cd5cc_2
  - gxx_impl_linux-64=7.3.0=hdf63c60_1
  - gxx_linux-64=7.3.0=h553295d_9
  - harfbuzz=2.8.0=h6f93f22_0
  - icu=58.2=hf484d3e_1000
  - idna=2.10=pyh9f0ad1d_0
  - imagesize=1.2.0=py_0
  - importlib-metadata=3.10.1=py38h578d9bd_0
  - ipykernel=5.5.3=py38hd0cf306_0
  - ipython=7.22.0=py38hd0cf306_0
  - ipython_genutils=0.2.0=py_1
  - ipywidgets=7.6.3=pyhd3deb0d_0
  - jedi=0.18.0=py38h578d9bd_2
  - jinja2=2.11.3=pyh44b312d_0
  - jpeg=9d=h36c2ea0_0
  - json5=0.9.5=pyh9f0ad1d_0
  - jsonschema=3.2.0=pyhd8ed1ab_3
  - jupyter=1.0.0=py38h578d9bd_6
  - jupyter_client=6.1.12=pyhd8ed1ab_0
  - jupyter_console=6.4.0=pyhd8ed1ab_0
  - jupyter_core=4.7.1=py38h578d9bd_0
  - jupyterlab=2.1.5=py_0
  - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
  - jupyterlab_server=1.2.0=py_0
  - jupyterlab_widgets=1.0.0=pyhd8ed1ab_1
  - krb5=1.17.2=h926e7f8_0
  - ld_impl_linux-64=2.33.1=h53a641e_7
  - libblas=3.9.0=8_openblas
  - libcblas=3.9.0=8_openblas
  - libcurl=7.76.1=hc4aaa36_1
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h7b6447c_0
  - libffi=3.3=he6710b0_2
  - libgcc-ng=9.3.0=h2828fa1_19
  - libgfortran-ng=7.5.0=h14aa051_19
  - libgfortran4=7.5.0=h14aa051_19
  - libgomp=9.3.0=h2828fa1_19
  - 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=h21135ba_2
  - libsodium=1.0.18=h36c2ea0_1
  - libssh2=1.9.0=hab1572f_5
  - libstdcxx-ng=9.3.0=h6de172a_19
  - libtiff=4.1.0=hc3755c2_3
  - libuuid=1.0.3=h1bed415_2
  - libxcb=1.13=h14c3975_1002
  - libxml2=2.9.9=h13577e0_2
  - lz4-c=1.9.2=he1b5a44_3
  - make=4.2.1=h1bed415_1
  - markupsafe=1.1.1=py38h8df0ef7_2
  - metis=5.1.0=h58526e2_1006
  - mistune=0.8.4=py38h25fe258_1002
  - nbclient=0.5.3=pyhd8ed1ab_0
  - nbconvert=6.0.7=py38h578d9bd_3
  - nbformat=5.1.3=pyhd8ed1ab_0
  - nbsphinx=0.7.1=pyh9f0ad1d_0
  - ncurses=6.2=he6710b0_1
  - nest-asyncio=1.5.1=pyhd8ed1ab_0
  - notebook=6.3.0=pyha770c72_1
  - openssl=1.1.1k=h27cfd23_0
  - packaging=20.9=pyh44b312d_0
  - pandoc=2.12=h7f98852_0
  - pandocfilters=1.4.2=py_1
  - pango=1.45.3=hd140c19_0
  - parso=0.8.2=pyhd8ed1ab_0
  - pcre=8.44=he1b5a44_0
  - pexpect=4.8.0=pyh9f0ad1d_2
  - pickleshare=0.7.5=py_1003
  - pip=21.0.1=py38h06a4308_0
  - pixman=0.40.0=h7b6447c_0
  - plink=1.90b6.21=h516909a_0
  - proj=7.1.1=h966b41f_3
  - prometheus_client=0.10.1=pyhd8ed1ab_0
  - prompt-toolkit=3.0.18=pyha770c72_0
  - prompt_toolkit=3.0.18=hd8ed1ab_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - ptyprocess=0.7.0=pyhd3deb0d_0
  - pycparser=2.20=pyh9f0ad1d_2
  - pygments=2.8.1=pyhd8ed1ab_0
  - pyopenssl=20.0.1=pyhd8ed1ab_0
  - pyparsing=2.4.7=pyh9f0ad1d_0
  - pyqt=5.9.2=py38h05f1152_4
  - pyrsistent=0.17.3=py38h25fe258_1
  - pyshp=2.1.3=pyh44b312d_0
  - pysocks=1.7.1=py38h578d9bd_3
  - python=3.8.3=hcff3b4d_2
  - python-dateutil=2.8.1=py_0
  - python_abi=3.8=1_cp38
  - pytz=2021.1=pyhd8ed1ab_0
  - pyzmq=20.0.0=py38h1d1b12f_1
  - qt=5.9.7=h5867ecd_1
  - qtconsole=5.0.3=pyhd8ed1ab_0
  - qtpy=1.9.0=py_0
  - r-askpass=1.0=r36h14c3975_0
  - r-assertthat=0.2.1=r36h6115d3f_0
  - r-backports=1.1.4=r36h96ca727_0
  - r-base=3.6.1=haffb61f_2
  - r-base64enc=0.1_3=r36h96ca727_4
  - r-bh=1.69.0_1=r36h6115d3f_0
  - r-broom=0.5.2=r36h6115d3f_0
  - r-callr=3.2.0=r36h6115d3f_0
  - r-cellranger=1.1.0=r36h6115d3f_0
  - r-cli=1.1.0=r36h6115d3f_0
  - r-clipr=0.6.0=r36h6115d3f_0
  - r-clisymbols=1.2.0=r36h6115d3f_0
  - r-colorspace=1.4_1=r36h96ca727_0
  - r-crayon=1.3.4=r36h6115d3f_0
  - r-curl=3.3=r36h96ca727_0
  - r-dbi=1.0.0=r36h6115d3f_0
  - r-dbplyr=1.4.0=r36h6115d3f_0
  - r-desc=1.2.0=r36h6115d3f_0
  - r-devtools=2.0.2=r36h6115d3f_0
  - r-dichromat=2.0_0=r36h6115d3f_4
  - r-digest=0.6.18=r36h96ca727_0
  - r-dplyr=0.8.0.1=r36h29659fb_0
  - r-ellipsis=0.1.0=r36h96ca727_0
  - r-evaluate=0.13=r36h6115d3f_0
  - r-fansi=0.4.0=r36h96ca727_0
  - r-forcats=0.4.0=r36h6115d3f_0
  - r-foreign=0.8_71=r36h96ca727_0
  - r-fs=1.2.7=r36h29659fb_0
  - r-generics=0.0.2=r36h6115d3f_0
  - r-ggplot2=3.1.1=r36h6115d3f_0
  - r-gh=1.0.1=r36h6115d3f_0
  - r-git2r=0.25.2=r36h96ca727_0
  - r-glue=1.3.1=r36h96ca727_0
  - r-gtable=0.3.0=r36h6115d3f_0
  - r-haven=2.1.0=r36h29659fb_0
  - r-highr=0.8=r36h6115d3f_0
  - r-hms=0.4.2=r36h6115d3f_0
  - r-htmltools=0.3.6=r36h29659fb_0
  - r-httr=1.4.0=r36h6115d3f_0
  - r-ini=0.3.1=r36h6115d3f_0
  - r-jsonlite=1.6=r36h96ca727_0
  - r-knitr=1.22=r36h6115d3f_0
  - r-labeling=0.3=r36h6115d3f_4
  - r-lattice=0.20_38=r36h96ca727_0
  - r-lazyeval=0.2.2=r36h96ca727_0
  - r-lubridate=1.7.4=r36h29659fb_0
  - r-magrittr=1.5=r36h6115d3f_4
  - r-maps=3.3.0=r36h96ca727_0
  - r-maptools=0.9_5=r36h96ca727_0
  - r-markdown=0.9=r36h96ca727_0
  - r-mass=7.3_51.3=r36h96ca727_0
  - r-matrix=1.2_17=r36h96ca727_0
  - r-memoise=1.1.0=r36h6115d3f_0
  - r-mgcv=1.8_28=r36h96ca727_0
  - r-mime=0.6=r36h96ca727_0
  - r-modelr=0.1.4=r36h6115d3f_0
  - r-munsell=0.5.0=r36h6115d3f_0
  - r-nlme=3.1_139=r36ha65eedd_0
  - r-openssl=1.3=r36h96ca727_0
  - r-pillar=1.3.1=r36h6115d3f_0
  - r-pkgbuild=1.0.3=r36h6115d3f_0
  - r-pkgconfig=2.0.2=r36h6115d3f_0
  - r-pkgload=1.0.2=r36h29659fb_0
  - r-plogr=0.2.0=r36h6115d3f_0
  - r-plyr=1.8.4=r36h29659fb_0
  - r-prettyunits=1.0.2=r36h6115d3f_0
  - r-processx=3.3.0=r36h96ca727_0
  - r-progress=1.2.0=r36h6115d3f_0
  - r-ps=1.3.0=r36h96ca727_0
  - r-purrr=0.3.2=r36h96ca727_0
  - r-r6=2.4.0=r36h6115d3f_0
  - r-raster=2.8_19=r36h29659fb_0
  - r-rcmdcheck=1.3.2=r36h6115d3f_0
  - r-rcolorbrewer=1.1_2=r36h6115d3f_0
  - r-rcpp=1.0.1=r36h29659fb_0
  - r-rcppeigen=0.3.3.5.0=r36h29659fb_0
  - r-readr=1.3.1=r36h29659fb_0
  - r-readxl=1.3.1=r36h29659fb_0
  - r-rematch=1.0.1=r36h6115d3f_0
  - r-remotes=2.0.4=r36h6115d3f_0
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  - r-reshape2=1.4.3=r36h29659fb_0
  - r-rgeos=0.5_5=r36hb2de1b9_0
  - r-rlang=0.3.4=r36h96ca727_0
  - r-rmarkdown=1.12=r36h6115d3f_0
  - r-rprojroot=1.3_2=r36h6115d3f_0
  - r-rstudioapi=0.10=r36h6115d3f_0
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  - r-scales=1.0.0=r36h29659fb_0
  - r-selectr=0.4_1=r36h6115d3f_0
  - r-sessioninfo=1.1.1=r36h6115d3f_0
  - r-sp=1.3_1=r36h96ca727_0
  - r-stringi=1.4.3=r36h29659fb_0
  - r-stringr=1.4.0=r36h6115d3f_0
  - r-sys=3.2=r36h96ca727_0
  - r-tibble=2.1.1=r36h96ca727_0
  - r-tidyr=0.8.3=r36h29659fb_0
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  - r-tidyverse=1.2.1=r36h6115d3f_0
  - r-tinytex=0.12=r36h6115d3f_0
  - r-usethis=1.5.0=r36h6115d3f_0
  - r-utf8=1.1.4=r36h96ca727_0
  - r-viridislite=0.3.0=r36h6115d3f_0
  - r-whisker=0.3_2=r36h6115d3f_4
  - r-withr=2.1.2=r36h6115d3f_0
  - r-xfun=0.6=r36h6115d3f_0
  - r-xml2=1.2.0=r36h29659fb_0
  - r-xopen=1.0.0=r36h6115d3f_0
  - r-yaml=2.2.0=r36h96ca727_0
  - readline=8.1=h27cfd23_0
  - requests=2.25.1=pyhd3deb0d_0
  - rpy2=3.4.3=py38r36hb5d20a5_0
  - scikit-sparse=0.4.4=py38h956cf04_1004
  - send2trash=1.5.0=py_0
  - shapely=1.7.1=py38h2765ab7_1
  - simplegeneric=0.8.1=py38_2
  - sip=4.19.13=py38he6710b0_0
  - six=1.15.0=pyh9f0ad1d_0
  - snowballstemmer=2.1.0=pyhd8ed1ab_0
  - sphinx=3.1.2=py_0
  - sphinx-autodoc-typehints=1.12.0=pyhd8ed1ab_0
  - sphinx_rtd_theme=0.5.0=pyh9f0ad1d_0
  - sphinxcontrib-applehelp=1.0.2=py_0
  - sphinxcontrib-devhelp=1.0.2=py_0
  - sphinxcontrib-htmlhelp=1.0.3=py_0
  - sphinxcontrib-jsmath=1.0.1=py_0
  - sphinxcontrib-qthelp=1.0.3=py_0
  - sphinxcontrib-serializinghtml=1.1.4=py_0
  - sqlite=3.35.4=hdfb4753_0
  - suitesparse=5.7.2=h717dc36_0
  - tbb=2020.2=hc9558a2_0
  - terminado=0.9.4=py38h578d9bd_0
  - testpath=0.4.4=py_0
  - tk=8.6.10=hbc83047_0
  - tktable=2.10=h14c3975_0
  - tornado=6.1=py38h25fe258_0
  - traitlets=5.0.5=py_0
  - tzlocal=2.1=py38_0
  - urllib3=1.26.4=pyhd8ed1ab_0
  - wcwidth=0.2.5=pyh9f0ad1d_2
  - webencodings=0.5.1=py_1
  - wheel=0.36.2=pyhd3eb1b0_0
  - widgetsnbextension=3.5.1=py38h578d9bd_4
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xz=5.2.5=h7b6447c_0
  - zeromq=4.3.3=h58526e2_3
  - zipp=3.4.1=pyhd8ed1ab_0
  - zlib=1.2.11=h7b6447c_3
  - zstd=1.4.5=h6597ccf_2
  - pip:
    - amply==0.1.4
    - appdirs==1.4.4
    - click==7.1.2
    - click-plugins==1.1.1
    - cligj==0.7.1
    - cloudpickle==1.6.0
    - configargparse==1.4
    - cycler==0.10.0
    - dask==2021.4.0
    - datrie==0.8.2
    - deprecated==1.2.12
    - feems==1.0.0
    - filelock==3.0.12
    - fiona==1.8.13.post1
    - flake8==3.8.3
    - fsspec==2021.4.0
    - gitdb==4.0.7
    - gitpython==3.1.14
    - joblib==1.0.1
    - kiwisolver==1.3.1
    - locket==0.2.1
    - matplotlib==3.2.2
    - mccabe==0.6.1
    - more-itertools==8.7.0
    - msprime==1.0.0
    - munch==2.5.0
    - networkx==2.4
    - newick==1.1.0
    - numpy==1.18.5
    - pandas==1.2.4
    - pandas-plink==2.0.4
    - partd==1.2.0
    - pep8==1.7.1
    - pluggy==0.13.1
    - psutil==5.8.0
    - pulp==2.4
    - py==1.10.0
    - pyaml==20.4.0
    - pycodestyle==2.6.0
    - pyflakes==2.2.0
    - pyproj==2.6.1.post1
    - pytest==5.4.3
    - pyyaml==5.4.1
    - ratelimiter==1.2.0.post0
    - scikit-learn==0.23.1
    - scipy==1.5.0
    - setuptools==49.1.0
    - smart-open==5.0.0
    - smmap==4.0.0
    - snakemake==6.1.1
    - svgwrite==1.4.1
    - threadpoolctl==2.1.0
    - toolz==0.11.1
    - toposort==1.6
    - tqdm==4.60.0
    - tskit==0.3.5
    - wrapt==1.12.1
    - xarray==0.17.0
    - xlrd==2.0.1
    - zstandard==0.15.2
prefix: /project2/jnovembre/jhmarcus/src/miniconda3/envs/feems_analysis_e
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