Script 'scripts/collapse_isoforms_by_sam.py' not found in metadata

Hi, I am trying to install cupcake from the git repo and I am doing it in the following way:

conda create --name cupcake python=3.7 anaconda
conda activate cupcake
pip install bcbio-gff pysam sklearn biopython bx-python
git clone https://github.com/Magdoll/cDNA_Cupcake.git
cd cDNA_Cupcake.git
python setup.py build
python setup.py install
> which collapse_isoforms_by_sam.py
~/.conda/envs/cupcake/bin/collapse_isoforms_by_sam.py
> collapse_isoforms_by_sam.py --help
Traceback (most recent call last):
  File "/home/user/jmontenegro/.conda/envs/cupcake/bin/collapse_isoforms_by_sam.py", line 4, in <module>
    __import__('pkg_resources').run_script('cupcake==15.1.0', 'collapse_isoforms_by_sam.py')
  File "/home/user/jmontenegro/.conda/envs/cupcake/lib/python3.7/site-packages/pkg_resources/__init__.py", line 665, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/user/jmontenegro/.conda/envs/cupcake/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    .format(**locals()),
pkg_resources.ResolutionError: Script 'scripts/collapse_isoforms_by_sam.py' not found in metadata at '/proj/jmontenegro/software/cDNA_Cupcake/cupcake.egg-info'

I found that installation formula after playing with several different combinations of installation commands. This formula is the only one that does not produce any errors and yet I get this error after installing the cupcake git repo.

Any suggestions how to get around this issue would be more than welcome.

Regards,

Juan D. Montenegro

[moschmi]

It seems to work if I omit PYTHONPATH below export PYTHONPATH=~/cDNA_Cupcake/sequence/:$PYTHONPATH export PYTHONPATH=~/cDNA_Cupcake/:$PYTHONPATH

[Magdoll]

Hi @moschmi , Oh yeeah that is the reason why. You probably should be doing this instead:

export PATH=$PATH:<path_to_cDNA_Cupcake>/sequence

You want to make sure $PATH comes first. Also, it is <path_to_cDNA_Cupcake>/sequence that contains the scripts you may want to call directly.