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YangLab / CIRCexplorer

A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)
http://yanglab.github.io/CIRCexplorer
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unsuccessful installation #17

Closed timedreamer closed 6 years ago

timedreamer commented 6 years ago

Hi there,

When I use pip install CIRCexplorer, I can install sucessfully. But when I call CIRCexplorer.py, i got the following message:

Traceback (most recent call last):
  File "/home5/jhuang/software/anaconda3/bin/CIRCexplorer.py", line 7, in <module>
    from circ.CIRCexplorer import main
  File "/home5/jhuang/software/anaconda3/lib/python3.6/site-packages/circ/CIRCexplorer.py", line 31, in <module>
    from genomic_interval import Interval
ModuleNotFoundError: No module named 'genomic_interval'
jhuang@pauper:~/projects/Misc/drought-stress/CIRCexplorer$ CIRCexplorer.py
Traceback (most recent call last):
  File "/home5/jhuang/software/anaconda3/bin/CIRCexplorer.py", line 7, in <module>
    from circ.CIRCexplorer import main
  File "/home5/jhuang/software/anaconda3/lib/python3.6/site-packages/circ/CIRCexplorer.py", line 31, in <module>
    from genomic_interval import Interval
ModuleNotFoundError: No module named 'genomic_interval'

When I try to install through conda, I got the following warning that did not success:

Fetching package metadata .............
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - circexplorer -> python 3.4* -> xz 5.0.5
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.

I also tried install from source, but no luck.

Any idea how I can fix?

Thanks in advance!

timedreamer commented 6 years ago

I just tried to install in Python 3.4 environment using conda install circexplorer --channel bioconda. The installation went well. But still got warnings when I call CIRCexplorer.py.

Traceback (most recent call last):
  File "/home5/jhuang/software/anaconda3/envs/py34/bin/CIRCexplorer.py", line 9, in <module>
    load_entry_point('CIRCexplorer==1.1.8', 'console_scripts', 'CIRCexplorer.py')()
  File "/home5/jhuang/software/anaconda3/envs/py34/lib/python3.4/site-packages/setuptools-27.2.0-py3.4.egg/pkg_resources/__init__.py", line 565, in load_entry_point
  File "/home5/jhuang/software/anaconda3/envs/py34/lib/python3.4/site-packages/setuptools-27.2.0-py3.4.egg/pkg_resources/__init__.py", line 2598, in load_entry_point
  File "/home5/jhuang/software/anaconda3/envs/py34/lib/python3.4/site-packages/setuptools-27.2.0-py3.4.egg/pkg_resources/__init__.py", line 2258, in load
  File "/home5/jhuang/software/anaconda3/envs/py34/lib/python3.4/site-packages/setuptools-27.2.0-py3.4.egg/pkg_resources/__init__.py", line 2264, in resolve
  File "/home5/jhuang/software/anaconda3/envs/py34/lib/python3.4/site-packages/CIRCexplorer-1.1.8-py3.4.egg/circ/CIRCexplorer.py", line 29, in <module>
  File "/home5/jhuang/software/anaconda3/envs/py34/lib/python3.4/site-packages/pysam/__init__.py", line 5, in <module>
    from pysam.libchtslib import *
ImportError: libhts.so.1: cannot open shared object file: No such file or directory
xingma commented 6 years ago

It's caused by that CIRCexplorer isn't compatible with python3 and we won't add python3 support to CIRCexplorer. In addition, CIRCexplorer2 has supported python3.

timedreamer commented 6 years ago

Thank you. That works. May be add this in the CIRCexplorer documentation?