ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview: pip install --upgrade --force-reinstall genomeview

[moldach]

This is a follow up to #62 (which was on a shared academic HPC).

I've now tried to download/run svviz2 from Linux machine where I have root privileges.

sudo apt install python3-pip
sudo -H pip3 install rpy2==2.9.3
sudo snap install inkscape
mkdir svviz2; cd svviz2
wget http://tandem.bu.edu/trf/downloads/trf409.linux64
chmod +x trf409.linux64
echo "alias trf="/snap/trf409.linux64" >> ~/.bash_aliases
sudo apt-get install python3-venv
sudo python3 -m venv .venv
source .venv/bin/activate
sudo pip3 install cython
sudo pip3 install genomeview
sudo pip3 install -U git+git://github.com/nspies/svviz2.git

Then calling svviz2 I see the error:

(svviz2) mtg@pop-os:/snap$ svviz2
ssw library not found
ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview: 
  pip install --upgrade --force-reinstall genomeview
Traceback (most recent call last):
  File "/usr/local/bin/svviz2", line 6, in <module>
    from svviz2.app.main import main
  File "/home/mtg/.local/lib/python3.7/site-packages/svviz2/app/main.py", line 7, in <module>
    from svviz2.visualize import visualize
  File "/home/mtg/.local/lib/python3.7/site-packages/svviz2/visualize/visualize.py", line 8, in <module>
    from genomeview import Document, ViewRow, GenomeView
  File "/home/mtg/.local/lib/python3.7/site-packages/genomeview/__init__.py", line 24, in <module>
    from genomeview.bamtrack import *
  File "/home/mtg/.local/lib/python3.7/site-packages/genomeview/bamtrack.py", line 6, in <module>
    from genomeview import MismatchCounts
ImportError: cannot import name 'MismatchCounts' from 'genomeview' (/home/mtg/.local/lib/python3.7/site-packages/genomeview/__init__.py)

running sudo pip3 install --upgrade --force-reinstall genomeview followed by svviz2

(svviz2) mtg@pop-os:/snap$ sudo pip3 install --upgrade --force-reinstall genomeview
Collecting genomeview
Collecting pysam (from genomeview)
Collecting numpy (from genomeview)
  Using cached https://files.pythonhosted.org/packages/b7/ce/d0b92f0283faa4da76ea82587ff9da70104e81f59ba14f76c87e4196254e/numpy-1.18.2-cp37-cp37m-manylinux1_x86_64.whl
Installing collected packages: pysam, numpy, genomeview
  Found existing installation: pysam 0.15.4
    Uninstalling pysam-0.15.4:
      Successfully uninstalled pysam-0.15.4
  Found existing installation: numpy 1.18.2
    Uninstalling numpy-1.18.2:
      Successfully uninstalled numpy-1.18.2
  Found existing installation: genomeview 1.0.1
    Uninstalling genomeview-1.0.1:
      Successfully uninstalled genomeview-1.0.1
Successfully installed genomeview-1.0.1 numpy-1.18.2 pysam-0.15.4
(svviz2) mtg@pop-os:/snap$ svviz2
ssw library not found
ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview: 
  pip install --upgrade --force-reinstall genomeview
Traceback (most recent call last):
  File "/usr/local/bin/svviz2", line 6, in <module>
    from svviz2.app.main import main
  File "/home/mtg/.local/lib/python3.7/site-packages/svviz2/app/main.py", line 7, in <module>
    from svviz2.visualize import visualize
  File "/home/mtg/.local/lib/python3.7/site-packages/svviz2/visualize/visualize.py", line 8, in <module>
    from genomeview import Document, ViewRow, GenomeView
  File "/home/mtg/.local/lib/python3.7/site-packages/genomeview/__init__.py", line 24, in <module>
    from genomeview.bamtrack import *
  File "/home/mtg/.local/lib/python3.7/site-packages/genomeview/bamtrack.py", line 6, in <module>
    from genomeview import MismatchCounts
ImportError: cannot import name 'MismatchCounts' from 'genomeview' (/home/mtg/.local/lib/python3.7/site-packages/genomeview/__init__.py)

Here is my system information:

(svviz2) mtg@pop-os:/snap$ uname -a
Linux pop-os 5.3.0-7625-generic #27~1576774560~19.10~f432cd8-Ubuntu SMP Thu Dec 19 20:35:37 UTC  x86_64 x86_64 x86_64 GNU/Linux