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bcgsc / transabyss

de novo assembly of RNA-seq data using ABySS
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Library conflict #13

Closed weedcentipede closed 5 years ago

weedcentipede commented 6 years ago

Hi, Just reporting an issue with Python3,

Traceback (most recent call last):
  File "/home/bio/anaconda3/bin/transabyss", line 4, in <module>
    __import__('pkg_resources').run_script('transabyss==1.54', 'transabyss')
  File "/home/bio/anaconda3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 658, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/bio/anaconda3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1438, in run_script
    exec(code, namespace, namespace)
  File "/home/bio/anaconda3/lib/python3.6/site-packages/transabyss-1.54-py3.6.egg-info/scripts/transabyss", line 19, in <module>
    from transabyss.adj_utils import has_edges
  File "/home/bio/anaconda3/lib/python3.6/site-packages/transabyss/adj_utils.py", line 7, in <module>
    import igraph
  File "/home/bio/anaconda3/lib/python3.6/site-packages/igraph/__init__.py", line 8, in <module>
    raise DeprecationWarning("To avoid name collision with the igraph project, "
DeprecationWarning: To avoid name collision with the igraph project, this visualization library has been renamed to 'jgraph'. Please upgrade when convenient.

Cheers! Luis Alfonso.

kmnip commented 6 years ago

I think I know what happened... FYI: https://stackoverflow.com/questions/36200707/error-with-igraph-library-deprecated-library

It looks like a Python package called igraph was installed instead of python-igraph. So, you need to uninstall igraph and then re-install python-igraph.

weedcentipede commented 5 years ago

Thanks a lot, but it haven't worked. I'm trying to figure it out how to use transabyss inside a virtual enviroment

sjackman commented 5 years ago

One option is to install it using Linuxbrew / Homebrew.

brew install brewsci/bio/transabyss