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jvivian / gene-outlier-detection

A Bayesian model for identifying gene expression outliers for individual single samples (N-of-1) when compared to a cohort of background datasets.
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installation error #79

Open bschilder opened 3 years ago

bschilder commented 3 years ago

Hi there, i really like this concept, was just looking for a tool that does exactly this.

Been running into some install issues within my conda env though.

Conda env

conda list

# packages in environment at /opt/anaconda3/envs/ukb: # # Name Version Build Channel appnope 0.1.2 py38h50d1736_1 conda-forge argon2-cffi 20.1.0 py38h5406a74_2 conda-forge async_generator 1.10 py_0 conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.3 pyhd8ed1ab_0 conda-forge biothings_client 0.2.5 pyh3252c3a_0 bioconda bleach 3.3.0 pyh44b312d_0 conda-forge bokeh 2.3.0 pypi_0 pypi bokehheat 0.0.4 pypi_0 pypi brotlipy 0.7.0 py38h5406a74_1001 conda-forge ca-certificates 2020.12.5 h033912b_0 conda-forge certifi 2020.12.5 py38h50d1736_1 conda-forge cffi 1.14.5 py38ha97d567_0 conda-forge chardet 4.0.0 py38h50d1736_1 conda-forge chart-studio 1.1.0 pyh9f0ad1d_0 conda-forge cryptography 3.4.7 py38h1fa4640_0 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 ha13b53f_2 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge entrypoints 0.3 pyhd8ed1ab_1003 conda-forge et_xmlfile 1.0.1 py_1001 conda-forge expat 2.3.0 he49afe7_0 conda-forge fastcluster 1.1.26 py38h6be0db6_2 conda-forge freetype 2.10.4 h4cff582_1 conda-forge gettext 0.19.8.1 h7937167_1005 conda-forge glib 2.68.0 he49afe7_2 conda-forge glib-tools 2.68.0 he49afe7_2 conda-forge icu 68.1 h74dc148_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge importlib-metadata 3.8.0 py38h50d1736_0 conda-forge ipykernel 5.5.0 py38h9bb44b7_1 conda-forge ipython 7.22.0 py38h6c79ece_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge jdcal 1.4.1 py_0 conda-forge jedi 0.18.0 py38h50d1736_2 conda-forge jinja2 2.11.3 pyh44b312d_0 conda-forge joblib 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9d hbcb3906_0 conda-forge jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge jupyter 1.0.0 py38h50d1736_6 conda-forge jupyter_client 6.1.12 pyhd8ed1ab_0 conda-forge jupyter_console 6.4.0 pyhd8ed1ab_0 conda-forge jupyter_contrib_core 0.3.3 py_2 conda-forge jupyter_contrib_nbextensions 0.5.1 pyhd8ed1ab_2 conda-forge jupyter_core 4.7.1 py38h50d1736_0 conda-forge jupyter_highlight_selected_word 0.2.0 py38h50d1736_1002 conda-forge jupyter_latex_envs 1.4.6 pyhd8ed1ab_1002 conda-forge jupyter_nbextensions_configurator 0.4.1 py38h50d1736_2 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge kiwisolver 1.3.1 py38hd9c93a9_1 conda-forge krb5 1.17.2 h60d9502_0 conda-forge lcms2 2.12 h577c468_0 conda-forge libblas 3.9.0 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libclang 11.1.0 default_he082bbe_0 conda-forge libcxx 11.1.0 habf9029_0 conda-forge libedit 3.1.20191231 h0678c8f_2 conda-forge libffi 3.3 h046ec9c_2 conda-forge libgfortran 5.0.0 9_3_0_h6c81a4c_20 conda-forge libgfortran5 9.3.0 h6c81a4c_20 conda-forge libglib 2.68.0 hd556434_2 conda-forge libiconv 1.16 haf1e3a3_0 conda-forge liblapack 3.9.0 8_openblas conda-forge libllvm10 10.0.1 h009f743_3 conda-forge libllvm11 11.1.0 hd011deb_0 conda-forge libopenblas 0.3.12 openmp_h54245bb_1 conda-forge libpng 1.6.37 h7cec526_2 conda-forge libpq 13.1 h052a64a_2 conda-forge libsodium 1.0.18 hbcb3906_1 conda-forge libtiff 4.2.0 h355d032_0 conda-forge libuv 1.41.0 hbcf498f_0 conda-forge libwebp-base 1.2.0 h0d85af4_2 conda-forge libxml2 2.9.10 h802ca4f_3 conda-forge libxslt 1.1.33 h5739fc3_2 conda-forge llvm-openmp 11.1.0 hda6cdc1_0 conda-forge llvmlite 0.36.0 py38h872f124_0 conda-forge lxml 4.6.3 py38h6ea4786_0 conda-forge lz4-c 1.9.3 h046ec9c_0 conda-forge markupsafe 1.1.1 py38h5406a74_3 conda-forge matplotlib 3.3.4 py38h50d1736_0 conda-forge matplotlib-base 3.3.4 py38hb24f337_0 conda-forge mistune 0.8.4 py38h5406a74_1003 conda-forge mygene 3.2.1 pyh3252c3a_0 bioconda mysql-common 8.0.23 h694c41f_1 conda-forge mysql-libs 8.0.23 hbeb7981_1 conda-forge nb_conda_kernels 2.3.1 py38h50d1736_0 conda-forge nbclient 0.5.3 pyhd8ed1ab_0 conda-forge nbconvert 5.6.1 py38h32f6830_1 conda-forge nbformat 5.1.2 pyhd8ed1ab_1 conda-forge ncurses 6.2 h2e338ed_4 conda-forge nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge nodejs 15.12.0 hb529b34_0 conda-forge notebook 6.3.0 py38h50d1736_0 conda-forge nspr 4.30 hcd9eead_0 conda-forge nss 3.47 hc0980d9_0 conda-forge numba 0.53.1 py38h8fd2267_0 conda-forge numpy 1.20.1 py38h64deac9_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openpyxl 3.0.7 pyhd8ed1ab_0 conda-forge openssl 1.1.1k h0d85af4_0 conda-forge packaging 20.9 pyh44b312d_0 conda-forge pandas 1.2.3 py38h1588c1c_0 conda-forge pandoc 2.13 h0d85af4_0 conda-forge pandocfilters 1.4.2 py_1 conda-forge parso 0.8.1 pyhd8ed1ab_0 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.44 hb1e8313_0 conda-forge pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.1.2 py38h83525de_0 conda-forge pip 21.0.1 pyhd8ed1ab_0 conda-forge plotly 4.14.3 pyh44b312d_0 conda-forge prometheus_client 0.9.0 pyhd3deb0d_0 conda-forge prompt-toolkit 3.0.18 pyha770c72_0 conda-forge prompt_toolkit 3.0.18 hd8ed1ab_0 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.8.1 pyhd8ed1ab_0 conda-forge pynndescent 0.5.2 pyh44b312d_0 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py38h50d1736_7 conda-forge pyqt-impl 5.12.3 py38h721a93c_7 conda-forge pyqt5-sip 4.19.18 py38h5745d40_7 conda-forge pyqtchart 5.12 py38h721a93c_7 conda-forge pyqtwebengine 5.12.1 py38h721a93c_7 conda-forge pyrsistent 0.17.3 py38h5406a74_2 conda-forge pysocks 1.7.1 py38h50d1736_3 conda-forge python 3.8.8 h4e93d89_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.8 1_cp38 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 pypi_0 pypi pyzmq 22.0.3 py38hd3b92b6_1 conda-forge qt 5.12.9 h126340a_4 conda-forge qtconsole 5.0.3 pyhd8ed1ab_0 conda-forge qtpy 1.9.0 py_0 conda-forge readline 8.1 h05e3726_0 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge retrying 1.3.3 py_2 conda-forge scikit-learn 0.24.1 py38hfd19401_0 conda-forge scipy 1.6.1 py38h41e0fa8_0 conda-forge seaborn 0.11.1 hd8ed1ab_1 conda-forge seaborn-base 0.11.1 pyhd8ed1ab_1 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py38h50d1736_3 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.35.3 h44b9ce1_0 conda-forge statsmodels 0.12.2 py38ha1b04c9_0 conda-forge tbb 2020.2 h940c156_4 conda-forge terminado 0.9.3 py38h50d1736_0 conda-forge testpath 0.4.4 py_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 h0419947_1 conda-forge tornado 6.1 py38h5406a74_1 conda-forge traitlets 5.0.5 py_0 conda-forge typing-extensions 3.7.4.3 pypi_0 pypi umap-learn 0.5.1 py38h50d1736_0 conda-forge urllib3 1.26.4 pyhd8ed1ab_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge widgetsnbextension 3.5.1 py38h50d1736_4 conda-forge xlrd 2.0.1 pyhd8ed1ab_3 conda-forge xz 5.2.5 haf1e3a3_1 conda-forge yaml 0.2.5 haf1e3a3_0 conda-forge zeromq 4.3.4 h1c7c35f_0 conda-forge zipp 3.4.1 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h7795811_1010 conda-forge zstd 1.4.9 h582d3a0_0 conda-forge

Error log

I had to take out the middle of this because it was way over GitHub's character limit, but here's the crux of it.

pip install gene-outlier-detection

Collecting gene-outlier-detection Downloading gene_outlier_detection-1.0-py3-none-any.whl (15 kB) Collecting pymc3<4.0,>=3.8 Downloading pymc3-3.11.2-py3-none-any.whl (869 kB) |████████████████████████████████| 869 kB 3.0 MB/s Requirement already satisfied: scipy<2.0,>=1.2 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from gene-outlier-detection) (1.6.1) Collecting sklearn<0.0.1,>=0.0.0 Downloading sklearn-0.0.tar.gz (1.1 kB) Requirement already satisfied: numpy<2.0,>=1.16 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from gene-outlier-detection) (1.20.1) Collecting seaborn<0.10.0,>=0.9.0 Downloading seaborn-0.9.1-py2.py3-none-any.whl (216 kB) |████████████████████████████████| 216 kB 12.3 MB/s Collecting tables<4.0,>=3.5 Using cached tables-3.6.1-cp38-cp38-macosx_10_9_x86_64.whl (4.3 MB) Collecting pandas<0.25.0,>=0.24.1 Downloading pandas-0.24.2.tar.gz (11.8 MB) |████████████████████████████████| 11.8 MB 12.0 MB/s Collecting tqdm<5.0,>=4.31 Downloading tqdm-4.59.0-py2.py3-none-any.whl (74 kB) |████████████████████████████████| 74 kB 2.8 MB/s Collecting theano<2.0.0,>=1.0.4 Downloading Theano-1.0.5.tar.gz (2.8 MB) |████████████████████████████████| 2.8 MB 64.8 MB/s Collecting arviz<0.5.0,>=0.4.0 Downloading arviz-0.4.1-py3-none-any.whl (1.3 MB) |████████████████████████████████| 1.3 MB 18.8 MB/s Requirement already satisfied: matplotlib<4.0,>=3.0 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from gene-outlier-detection) (3.3.4) Collecting black<20.0,>=19.10b0 Downloading black-19.10b0-py36-none-any.whl (97 kB) |████████████████████████████████| 97 kB 17.4 MB/s Collecting click<8.0,>=7.0 Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting netcdf4 Downloading netCDF4-1.5.6-cp38-cp38-macosx_10_9_x86_64.whl (4.0 MB) |████████████████████████████████| 4.0 MB 19.9 MB/s Collecting xarray Downloading xarray-0.17.0-py3-none-any.whl (759 kB) |████████████████████████████████| 759 kB 37.4 MB/s Collecting toml>=0.9.4 Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB) Requirement already satisfied: attrs>=18.1.0 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from black<20.0,>=19.10b0->gene-outlier-detection) (20.3.0) Collecting appdirs Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) Collecting regex Downloading regex-2021.3.17-cp38-cp38-macosx_10_9_x86_64.whl (284 kB) |████████████████████████████████| 284 kB 26.1 MB/s Collecting typed-ast>=1.4.0 Downloading typed_ast-1.4.2-cp38-cp38-macosx_10_9_x86_64.whl (225 kB) |████████████████████████████████| 225 kB 36.0 MB/s Collecting pathspec<1,>=0.6 Using cached pathspec-0.8.1-py2.py3-none-any.whl (28 kB) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from matplotlib<4.0,>=3.0->gene-outlier-detection) (2.4.7) Requirement already satisfied: pillow>=6.2.0 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from matplotlib<4.0,>=3.0->gene-outlier-detection) (8.1.2) Requirement already satisfied: python-dateutil>=2.1 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from matplotlib<4.0,>=3.0->gene-outlier-detection) (2.8.1) Requirement already satisfied: cycler>=0.10 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from matplotlib<4.0,>=3.0->gene-outlier-detection) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from matplotlib<4.0,>=3.0->gene-outlier-detection) (1.3.1) Requirement already satisfied: six in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from cycler>=0.10->matplotlib<4.0,>=3.0->gene-outlier-detection) (1.15.0) Requirement already satisfied: pytz>=2011k in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from pandas<0.25.0,>=0.24.1->gene-outlier-detection) (2021.1) Requirement already satisfied: patsy>=0.5.1 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from pymc3<4.0,>=3.8->gene-outlier-detection) (0.5.1) Collecting dill Downloading dill-0.3.3-py2.py3-none-any.whl (81 kB) |████████████████████████████████| 81 kB 27.5 MB/s Collecting fastprogress>=0.2.0 Downloading fastprogress-1.0.0-py3-none-any.whl (12 kB) Collecting semver Downloading semver-2.13.0-py2.py3-none-any.whl (12 kB) Collecting pymc3<4.0,>=3.8 Downloading pymc3-3.11.1-py3-none-any.whl (868 kB) |████████████████████████████████| 868 kB 88.5 MB/s Downloading pymc3-3.11.0-py3-none-any.whl (866 kB) |████████████████████████████████| 866 kB 28.4 MB/s Collecting theano-pymc==1.1.0 Downloading Theano-PyMC-1.1.0.tar.gz (1.8 MB) |████████████████████████████████| 1.8 MB 44.5 MB/s Collecting pymc3<4.0,>=3.8 Downloading pymc3-3.10.0-py3-none-any.whl (1.9 MB) |████████████████████████████████| 1.9 MB 54.4 MB/s Downloading pymc3-3.9.3-py3-none-any.whl (1.9 MB) |████████████████████████████████| 1.9 MB 50.4 MB/s Downloading pymc3-3.9.2-py3-none-any.whl (1.9 MB) |████████████████████████████████| 1.9 MB 30.2 MB/s Downloading pymc3-3.9.1-py3-none-any.whl (1.9 MB) |████████████████████████████████| 1.9 MB 43.7 MB/s Collecting h5py>=2.7.0 Downloading h5py-3.2.1-cp38-cp38-macosx_10_9_x86_64.whl (2.9 MB) |████████████████████████████████| 2.9 MB 32.3 MB/s Collecting pymc3<4.0,>=3.8 Downloading pymc3-3.9.0-py3-none-any.whl (1.9 MB) |████████████████████████████████| 1.9 MB 16.0 MB/s Downloading pymc3-3.8-py3-none-any.whl (908 kB) |████████████████████████████████| 908 kB 24.8 MB/s Requirement already satisfied: scikit-learn in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from sklearn<0.0.1,>=0.0.0->gene-outlier-detection) (0.24.1) Collecting numexpr>=2.6.2 Downloading numexpr-2.7.3-cp38-cp38-macosx_10_9_x86_64.whl (99 kB) |████████████████████████████████| 99 kB 11.5 MB/s Collecting cftime Downloading cftime-1.4.1-cp38-cp38-macosx_10_9_x86_64.whl (287 kB) |████████████████████████████████| 287 kB 31.5 MB/s Requirement already satisfied: threadpoolctl>=2.0.0 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from scikit-learn->sklearn<0.0.1,>=0.0.0->gene-outlier-detection) (2.1.0) Requirement already satisfied: joblib>=0.11 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from scikit-learn->sklearn<0.0.1,>=0.0.0->gene-outlier-detection) (1.0.1) Requirement already satisfied: setuptools>=40.4 in /opt/anaconda3/envs/ukb/lib/python3.8/site-packages (from xarray->arviz<0.5.0,>=0.4.0->gene-outlier-detection) (49.6.0.post20210108) Collecting xarray Using cached xarray-0.16.2-py3-none-any.whl (736 kB) Downloading xarray-0.16.1-py3-none-any.whl (720 kB) |████████████████████████████████| 720 kB 15.2 MB/s Downloading xarray-0.16.0-py3-none-any.whl (704 kB) |████████████████████████████████| 704 kB 20.8 MB/s Downloading xarray-0.15.1-py3-none-any.whl (668 kB) |████████████████████████████████| 668 kB 22.1 MB/s Downloading xarray-0.15.0-py3-none-any.whl (650 kB) |████████████████████████████████| 650 kB 27.2 MB/s Downloading xarray-0.14.1-py3-none-any.whl (634 kB) |████████████████████████████████| 634 kB 28.1 MB/s Building wheels for collected packages: pandas, sklearn, theano Building wheel for pandas (setup.py) ... error ERROR: Command errored out with exit status 1: command: /opt/anaconda3/envs/ukb/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/pip-install-2whgw2ts/pandas_c7e99d6a5b6b41b18d2bfe77e803509d/setup.py'"'"'; __file__='"'"'/private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/pip-install-2whgw2ts/pandas_c7e99d6a5b6b41b18d2bfe77e803509d/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/pip-wheel-wvm9s1ju cwd: /private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/pip-install-2whgw2ts/pandas_c7e99d6a5b6b41b18d2bfe77e803509d/ ... ... ... ... Moving to /opt/anaconda3/envs/ukb/lib/python3.8/site-packages/pandas/util/ from /opt/anaconda3/envs/ukb/lib/python3.8/site-packages/pandas/~til ERROR: Command errored out with exit status 1: /opt/anaconda3/envs/ukb/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/pip-install-2whgw2ts/pandas_c7e99d6a5b6b41b18d2bfe77e803509d/setup.py'"'"'; __file__='"'"'/private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/pip-install-2whgw2ts/pandas_c7e99d6a5b6b41b18d2bfe77e803509d/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T/pip-record-x_gqql8i/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/ukb/include/python3.8/pandas Check the logs for full command output. Thanks! Looking forward to using this. Best, Brian