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PyClone的安装报错及解决

1、 PyClone 安装，报错及解决

1.1、 安装

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conda install PyClone

命令如下：

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PyClone run_analysis_pipeline --in_files SRR385938.tsv SRR385939.tsv SRR385940.tsv SRR385941.tsv --working_dir ./tt

1.2、 报错：

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Traceback (most recent call last):
  File "/home/lixy/miniconda2/envs/ngs2/bin/PyClone", line 11, in <module>
    load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')()
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/pyclone/cli.py", line 78, in main
    args.func(args)
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/pyclone/run.py", line 97, in run_analysis_pipeline
    args.thin
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/pyclone/run.py", line 409, in _cluster_plot
    samples=samples,
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/pyclone/post_process/plot/clusters.py", line 58, in density_plot
    fig = pp.figure(figsize=(width, height))
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 534, in figure
    **kwargs)
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 170, in new_figure_manager
    return cls.new_figure_manager_given_figure(num, fig)
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 176, in new_figure_manager_given_figure
    canvas = cls.FigureCanvas(figure)
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/matplotlib/backends/backend_qt5agg.py", line 35, in __init__
    super(FigureCanvasQTAggBase, self).__init__(figure=figure)
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py", line 235, in __init__
    _create_qApp()
  File "/home/lixy/miniconda2/envs/ngs2/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py", line 122, in _create_qApp
    raise RuntimeError('Invalid DISPLAY variable')
RuntimeError: Invalid DISPLAY variabl

1.3、 解决：

aroth85 ：

Please check user group (https://groups.google.com/forum/#!forum/pyclone-user-group) for threads on this.

There is another bit in the links about changing your "matplotlibrc" file, instead of the code. This will globally set the backend for all Python scripts to Agg which is what you likely want for a remote server. You should not need to edit the code if you set this file up correctly. See the matplotlib help page with search terms matplotlibrc for details.

具体：

  1. 报错的原因是 matplotlib的配置文件没有设置好：
  2. 找到配置文件：

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>>> import matplotlib
>>> matplotlib.matplotlib_fname()
'/home/foo/.config/matplotlib/matplotlibrc'
参考 1. 编辑你的 matplotlibrc (第44行) ：

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vim /home/foo/.config/matplotlib/matplotlibrc :
backend      : Agg

再次执行命令，成功！