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Roth-Lab / pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.
https://bitbucket.org/aroth85/pyclone/wiki/Home
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is tcltk necessary? can I run in non-interactive mode? #23

Closed xmzhuo closed 3 years ago

xmzhuo commented 3 years ago

Traceback (most recent call last): File "/opt/conda/bin/PyClone", line 10, in sys.exit(main()) File "/opt/conda/lib/python2.7/site-packages/pyclone/cli.py", line 78, in main args.func(args) File "/opt/conda/lib/python2.7/site-packages/pyclone/run.py", line 97, in run_analysis_pipeline args.thin File "/opt/conda/lib/python2.7/site-packages/pyclone/run.py", line 409, in _cluster_plot samples=samples, File "/opt/conda/lib/python2.7/site-packages/pyclone/post_process/plot/clusters.py", line 58, in density_plot fig = pp.figure(figsize=(width, height)) File "/opt/conda/lib/python2.7/site-packages/matplotlib/pyplot.py", line 533, in figure **kwargs) File "/opt/conda/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 161, in new_figure_manager return cls.new_figure_manager_given_figure(num, fig) File "/opt/conda/lib/python2.7/site-packages/matplotlib/backends/_backend_tk.py", line 1046, in new_figure_manager_given_figure window = Tk.Tk(className="matplotlib") File "/opt/conda/lib/python2.7/lib-tk/Tkinter.py", line 1825, in init self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable

environment:

packages in environment at /opt/conda:

#

Name Version Build Channel

_libgcc_mutex 0.1 main
asn1crypto 1.0.1 py27_0
backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge backports_abc 0.5 py_1 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge cffi 1.12.3 py27h2e261b9_0
chardet 3.0.4 py27_1003
conda 4.8.3 py27h8c360ce_1 conda-forge conda-package-handling 1.6.0 py27h7b6447c_0
cryptography 2.7 py27h1ba5d50_0
cycler 0.10.0 py_2 conda-forge enum34 1.1.6 py27_1
freetype 2.10.4 h7ca028e_0 conda-forge funcsigs 1.0.2 py_3 conda-forge functools32 3.2.3.2 py_3 conda-forge futures 3.3.0 py27_0
icu 64.2 he1b5a44_1 conda-forge idna 2.8 py27_0
ipaddress 1.0.22 py27_0
kiwisolver 1.1.0 py27h9e3301b_1 conda-forge libblas 3.9.0 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.5.0 h14aa051_18 conda-forge libgfortran4 7.5.0 h14aa051_18 conda-forge liblapack 3.9.0 8_openblas conda-forge libllvm8 8.0.1 hc9558a2_0 conda-forge libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0
llvmlite 0.31.0 py27h5ee40b5_1 conda-forge matplotlib-base 2.2.5 py27h250f245_1 conda-forge ncurses 6.1 he6710b0_1
numba 0.47.0 py27hb3f55d8_0 conda-forge numpy 1.16.5 py27h95a1406_0 conda-forge openssl 1.1.1h h516909a_0 conda-forge pandas 0.24.2 py27hb3f55d8_0 conda-forge patsy 0.5.1 py_0 conda-forge pip 19.2.3 py27_0
pyclone 0.13.1 py_0 bioconda pycosat 0.6.3 py27h14c3975_0
pycparser 2.19 py27_0
pydp 0.2.4 py_0 bioconda pyopenssl 19.0.0 py27_0
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pysocks 1.7.1 py27_0
python 2.7.16 h9bab390_7
python-dateutil 2.8.1 py_0 conda-forge python_abi 2.7 1_cp27mu conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge pyyaml 5.1.2 py27h516909a_0 conda-forge readline 7.0 h7b6447c_5
requests 2.22.0 py27_0
ruamel_yaml 0.15.46 py27h14c3975_0
scipy 1.2.1 py27h921218d_2 conda-forge seaborn 0.9.0 py_2 conda-forge setuptools 41.4.0 py27_0
singledispatch 3.6.1 pyh44b312d_0 conda-forge six 1.12.0 py27_0
sqlite 3.30.0 h7b6447c_0
statsmodels 0.10.2 py27hc1659b7_0 conda-forge subprocess32 3.5.4 py27h516909a_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge tornado 5.1.1 py27h14c3975_1000 conda-forge tqdm 4.36.1 py_0
urllib3 1.24.2 py27_0
wheel 0.33.6 py27_0
yaml 0.1.7 had09818_2
zlib 1.2.11 h7b6447c_3

xmzhuo commented 3 years ago

update:

work after set matplotlib in agg mode sed -i 's/(backend : ).$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )

aroth85 commented 3 years ago

Sorry I missed this. This and several other issues have been answered on the user group for future reference https://groups.google.com/g/pyclone-user-group. Really need an FAQ page at some point.