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mcmero / SVclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
BSD 3-Clause "New" or "Revised" License
40 stars 10 forks source link

installation//import problem #4

Closed EricDeveaud closed 4 years ago

EricDeveaud commented 4 years ago

Hello

trying to install SVclone. what I did

/local/gensoft2/adm/Python/2.7/bin/python2.7 -m virtualenv /local/gensoft2/exe/SVclone/0.4.0/venv
git clone https://github.com/mcmero/SVclone.git
cd SVclone 
.  /local/gensoft2/exe/SVclone/0.4.0/venv/bin/activate
pip install -r requirements.txt
python setup.py install 
Rscript install_R_requirements.R

and then tried to run SVclone.py. but:

(venv) [gensoft@e211aa82115c SVclone-0.4.0]$ SVclone.py -h 
Traceback (most recent call last):
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/bin/SVclone.py", line 4, in <module>
    __import__('pkg_resources').run_script('SVclone==0.2.1', 'SVclone.py')
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1462, in run_script
    exec(code, namespace, namespace)
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/lib/python2.7/site-packages/SVclone-0.2.1-py2.7.egg/EGG-INFO/scripts/SVclone.py", line 7, in <module>
    from SVclone import run_filter
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/bin/SVclone.py", line 4, in <module>
    __import__('pkg_resources').run_script('SVclone==0.2.1', 'SVclone.py')
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1462, in run_script
    exec(code, namespace, namespace)
  File "/local/gensoft2/exe/SVclone/0.4.0/venv/lib/python2.7/site-packages/SVclone-0.2.1-py2.7.egg/EGG-INFO/scripts/SVclone.py", line 7, in <module>
    from SVclone import run_filter
ImportError: cannot import name run_filter

same problem with the 0.4.0 archive (https://github.com/mcmero/SVclone/archive/v0.4.0.tar.gz)

best regards

Eric

mcmero commented 4 years ago

Hi Eric,

Did you receive any error messages when running python setup.py install? Also try running python SVclone.py -h. Are you able to run the ./run_example.sh script without the error?

If these suggestions don't work, I would also try installing with Python 3 using the latest code in the master branch, or the v1.0.0 release. The Python 2 version will be deprecated in future releases.

Cheers, Marek