Issue while installing TF-comb

[VenkateshLab]

Im trying to install TF-comb using mamba i'm facing an error saying Could not solve for environment specs

mamba create -n tfcomb_env --file required_packages.txt
The following packages are incompatible
├─ pybigwig   does not exist (perhaps a typo or a missing channel);
├─ pysam   does not exist (perhaps a typo or a missing channel);
├─ tobias   does not exist (perhaps a typo or a missing channel);
└─ uropa   does not exist (perhaps a typo or a missing channel).

while trying to installing using pip pip install TF-COMB

im facing an error with matlab

can you help to fix this issue.

[vheger]

Hi @VenkateshLab,

thank you for your interest in TF-COMB.

Regarding the mamba issue: it seems like you missing the bioconda channel on your mamba installation, can you please try mamba create -n tfcomb_env --file required_packages.txt --channel bioconda and see if it works for you?

Regarding the matplotlib Issue: can you please check you matplotlib version, e.g. with pip show matplotlib ? If it's below 3.6.0 you will encounter this deprecation warning. Updating matplotlib to a version above 3.6.0 should make the warning disappear. However you should be able to use tfcomb besides the warning. Can you please try tfcomb.__version__ after the warning? like

>>> import tfcomb
/python3.9/site-packages/tfcomb/network.py:16: MatplotlibDeprecationWarning:
The mpl_toolkits.axes_grid module was deprecated in Matplotlib 2.1 and will be removed two minor releases later. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist, which provide the same functionality instead.
  from mpl_toolkits.axes_grid.inset_locator import inset_axes
>>> tfcomb.__version__
'1.0.3'

If you see a version like 1.0.3 you could proceed with the usage of tfcomb. Please note we highly recommend to use the newest version, if you see a version below 1.0.3 please consider updating tfcomb as well.

I hope this solves your problem, if not please let me know and I'm happy to assist you further.

[VenkateshLab]

I have installed the TF-comb using mamba. and now i have an error called no modlule named 'tfcomb.counting'

Now the Pip installtion is also saying the same error

[vheger]

Hi !

I can not see the folder you are executing python from. Are you executing python from within the TF-COMB folder ? For the mamba installation: After pip install . can you try moving to another folder (e.g. one folder up)?
The reason for this is: the python interpreter tries to import the local module from the folder you are in instead of the installed module (see my attached screenshot).

The same problem exists when installed via pip but python is executed from within the TF-COMB folder.

I see this is a caveat we should mention in the installation section, I will update our Readme accordingly, thank you.

If this does not solve the problem in your case, please let me know.

[VenkateshLab]

Thanks @vheger, i just went to a different location. it started working.