PyQT4 error when running Moving Pictures tutorial

jorvis · April 25, 2017, 8:14pm

I installed a new instance of Qiime2 (2017.4) within a Docker image with this definition:

###########
## Qiime ##

# Dependency: miniconda
RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda
ENV PATH $PATH:/opt/miniconda/bin
RUN rm Miniconda3-latest-Linux-x86_64.sh

# Attempt to resolve python Click library errors
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8

# Primary: Qiime2-2017.2
RUN conda create -n qiime2-2017.4 --file https://data.qiime2.org/distro/core/qiime2-2017.4-conda-linux-64.txt

This worked without error. But I get a PyQt4 error when I run through the tutorial.

source activate qiime2-2017.4

mkdir qiime2-moving-pictures-tutorial
cd qiime2-moving-pictures-tutorial
wget -O "sample-metadata.tsv" "https://data.qiime2.org/2017.4/tutorials/moving-pictures/sample_metadata.tsv"
mkdir emp-single-end-sequences
wget -O "emp-single-end-sequences/barcodes.fastq.gz" "https://data.qiime2.org/2017.4/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz"
wget -O "emp-single-end-sequences/sequences.fastq.gz" "https://data.qiime2.org/2017.4/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz"

(qiime2-2017.4) root@8ed7c1cdb0b5:/qiime2-moving-pictures-tutorial# qiime tools import --type EMPSingleEndSequences --input-path emp-single-end-sequences --output-path emp-single-end-sequences.qza
Traceback (most recent call last):
  File "/opt/miniconda/envs/qiime2-2017.4/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/q2cli/tools.py", line 62, in import_data
    view_type=source_format)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/result.py", line 155, in import_data
    type_ = qiime2.sdk.parse_type(type_)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
    pm = qiime2.sdk.PluginManager()
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
    self._init()
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 58, in _init
    plugin = entry_point.load()
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2258, in load
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2264, in resolve
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/q2_diversity/__init__.py", line 9, in <module>
    from ._alpha import (alpha, alpha_phylogenetic, alpha_group_significance,
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/q2_diversity/_alpha/__init__.py", line 10, in <module>
    from ._method import (alpha, alpha_phylogenetic, phylogenetic_metrics,
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/q2_diversity/_alpha/_method.py", line 11, in <module>
    import skbio.diversity
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/skbio/__init__.py", line 13, in <module>
    import skbio.io  # noqa
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/skbio/io/__init__.py", line 238, in <module>
    import_module('skbio.io.format.lsmat')
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in <module>
    from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/skbio/stats/distance/__init__.py", line 192, in <module>
    from ._base import (DissimilarityMatrixError, DistanceMatrixError,
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 12, in <module>
    import matplotlib.pyplot as plt
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/matplotlib/pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/matplotlib/backends/__init__.py", line 32, in pylab_setup
    globals(),locals(),[backend_name],0)
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py", line 16, in <module>
    from .backend_qt5 import QtCore
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/matplotlib/backends/backend_qt5.py", line 26, in <module>
    import matplotlib.backends.qt_editor.figureoptions as figureoptions
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
    import matplotlib.backends.qt_editor.formlayout as formlayout
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 56, in <module>
    from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
  File "/opt/miniconda/envs/qiime2-2017.4/lib/python3.5/site-packages/matplotlib/backends/qt_compat.py", line 137, in <module>
    from PyQt4 import QtCore, QtGui
ImportError: No module named 'PyQt4'

thermokarst · April 25, 2017, 8:18pm

Hi @jorvis —

We have an official Docker image, I would suggest starting there! We have done all the necessary configuration to get it up and running in a container format for you!

To comment on your specific error, because Docker is running in a headless environment (e.g. Docker), you have to configure your Matplotlib Backend as such. Moving forward though I would recommend our official QIIME 2 Docker image! Thanks!

thermokarst · April 25, 2017, 9:36pm

@jorvis, I should note, you can still create a custom image based on the official one, since Docker supports inheritance:

FROM qiime2/core:2017.4

RUN some_custom_script.sh

Good luck!

jorvis · April 26, 2017, 12:48pm

I’ll work on the reconfiguration of matplotlib, as you suggested. For technical reasons, I’m not sure the custom qiime2 docker image is an option.

system · May 27, 2017, 6:50pm

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