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Zymo-Research / figaro

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
GNU General Public License v3.0
80 stars 25 forks source link

Installed successfully but command line doesn't work #58

Closed WJH58 closed 1 year ago

WJH58 commented 1 year ago

Hi thank you for developing this tool. I have installed it following your documentation. Below is the installation info:

$python setup.py bdist_wheel

running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/figaro
copying figaro/figaro.py -> build/lib/figaro
copying figaro/defaultParser.py -> build/lib/figaro
copying figaro/fastqAnalysis.py -> build/lib/figaro
copying figaro/__init__.py -> build/lib/figaro
copying figaro/expectedErrorCurve.py -> build/lib/figaro
copying figaro/qualityScoreHandler.py -> build/lib/figaro
copying figaro/gzipIdentifier.py -> build/lib/figaro
copying figaro/trimParameterPrediction.py -> build/lib/figaro
copying figaro/easyMultiprocessing.py -> build/lib/figaro
copying figaro/fastqHandler.py -> build/lib/figaro
copying figaro/environmentParameterParser.py -> build/lib/figaro
copying figaro/fileNamingStandards.py -> build/lib/figaro
creating build/lib/figaro/defaults
copying figaro/defaults/standard.py -> build/lib/figaro/defaults
copying figaro/defaults/__init__.py -> build/lib/figaro/defaults
copying figaro/defaults/environment.py -> build/lib/figaro/defaults
running egg_info
creating figaro.egg-info
writing figaro.egg-info/PKG-INFO
writing dependency_links to figaro.egg-info/dependency_links.txt
writing entry points to figaro.egg-info/entry_points.txt
writing requirements to figaro.egg-info/requires.txt
writing top-level names to figaro.egg-info/top_level.txt
writing manifest file 'figaro.egg-info/SOURCES.txt'
reading manifest file 'figaro.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'figaro.egg-info/SOURCES.txt'
/Users/flora/miniconda3/envs/figaro/lib/python3.7/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  setuptools.SetuptoolsDeprecationWarning,
installing to build/bdist.macosx-10.9-x86_64/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-x86_64
creating build/bdist.macosx-10.9-x86_64/wheel
creating build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/figaro.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/defaultParser.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/fastqAnalysis.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/expectedErrorCurve.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/qualityScoreHandler.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
creating build/bdist.macosx-10.9-x86_64/wheel/figaro/defaults
copying build/lib/figaro/defaults/standard.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro/defaults
copying build/lib/figaro/defaults/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro/defaults
copying build/lib/figaro/defaults/environment.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro/defaults
copying build/lib/figaro/gzipIdentifier.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/trimParameterPrediction.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/easyMultiprocessing.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/fastqHandler.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/environmentParameterParser.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
copying build/lib/figaro/fileNamingStandards.py -> build/bdist.macosx-10.9-x86_64/wheel/figaro
running install_egg_info
Copying figaro.egg-info to build/bdist.macosx-10.9-x86_64/wheel/figaro-0.1-py3.7.egg-info
running install_scripts
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
creating build/bdist.macosx-10.9-x86_64/wheel/figaro-0.1.dist-info/WHEEL
creating 'dist/figaro-0.1-py3-none-any.whl' and adding 'build/bdist.macosx-10.9-x86_64/wheel' to it
adding 'figaro/__init__.py'
adding 'figaro/defaultParser.py'
adding 'figaro/easyMultiprocessing.py'
adding 'figaro/environmentParameterParser.py'
adding 'figaro/expectedErrorCurve.py'
adding 'figaro/fastqAnalysis.py'
adding 'figaro/fastqHandler.py'
adding 'figaro/figaro.py'
adding 'figaro/fileNamingStandards.py'
adding 'figaro/gzipIdentifier.py'
adding 'figaro/qualityScoreHandler.py'
adding 'figaro/trimParameterPrediction.py'
adding 'figaro/defaults/__init__.py'
adding 'figaro/defaults/environment.py'
adding 'figaro/defaults/standard.py'
adding 'figaro-0.1.dist-info/LICENSE'
adding 'figaro-0.1.dist-info/METADATA'
adding 'figaro-0.1.dist-info/WHEEL'
adding 'figaro-0.1.dist-info/entry_points.txt'
adding 'figaro-0.1.dist-info/top_level.txt'
adding 'figaro-0.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-x86_64/wheel
$pip install --force-reinstall dist/*.whl

Processing ./dist/figaro-0.1-py3-none-any.whl
Collecting scipy>=1.2.1
  Using cached scipy-1.7.3-cp37-cp37m-macosx_10_9_x86_64.whl (33.0 MB)
Collecting matplotlib>=3.0.2
  Using cached matplotlib-3.5.3-cp37-cp37m-macosx_10_9_x86_64.whl (7.3 MB)
Collecting numpy>=1.13.1
  Using cached numpy-1.21.6-cp37-cp37m-macosx_10_9_x86_64.whl (16.9 MB)
Collecting pyparsing>=2.2.1
  Using cached pyparsing-3.1.1-py3-none-any.whl (103 kB)
Collecting python-dateutil>=2.7
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.4.5-cp37-cp37m-macosx_10_9_x86_64.whl (67 kB)
Collecting cycler>=0.10
  Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0
  Using cached fonttools-4.38.0-py3-none-any.whl (965 kB)
Collecting packaging>=20.0
  Using cached packaging-23.1-py3-none-any.whl (48 kB)
Collecting pillow>=6.2.0
  Using cached Pillow-9.5.0-cp37-cp37m-macosx_10_10_x86_64.whl (3.4 MB)
Collecting six>=1.5
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting typing-extensions; python_version < "3.8"
  Using cached typing_extensions-4.7.1-py3-none-any.whl (33 kB)
Installing collected packages: numpy, scipy, pyparsing, six, python-dateutil, typing-extensions, kiwisolver, cycler, fonttools, packaging, pillow, matplotlib, figaro
Successfully installed cycler-0.11.0 figaro-0.1 fonttools-4.38.0 kiwisolver-1.4.5 matplotlib-3.5.3 numpy-1.21.6 packaging-23.1 pillow-9.5.0 pyparsing-3.1.1 python-dateutil-2.8.2 scipy-1.7.3 six-1.16.0 typing-extensions-4.7.1

At this step, installation has been finished and no error was reported yet. However, when I run figaro, I got this error:

Traceback (most recent call last):
  File "/Users/flora/miniconda3/envs/figaro/bin/figaro", line 8, in <module>
    sys.exit(main())
  File "/Users/flora/miniconda3/envs/figaro/lib/python3.7/site-packages/figaro/figaro.py", line 207, in main
    setLogging()
  File "/Users/flora/miniconda3/envs/figaro/lib/python3.7/site-packages/figaro/figaro.py", line 142, in setLogging
    loggingParameters = getLoggingParameters()
  File "/Users/flora/miniconda3/envs/figaro/lib/python3.7/site-packages/figaro/figaro.py", line 132, in getLoggingParameters
    os.makedirs(logFilePath)
  File "/Users/flora/miniconda3/envs/figaro/lib/python3.7/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/Users/flora/miniconda3/envs/figaro/lib/python3.7/os.py", line 223, in makedirs
    mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/data'

Could you please indicate what's wrong with my installation? Thank you!