installs wrong

[flying-sheep]

here is a tutorial how to do it. the main errors are:

1. you should use relative or absolute imports. import IO_utils should be from .IO_utils import ... or from sircel import IO_utils
2. py_modules isn’t for dependencies, it‘s for listing your own stuff. check the tutorial above for how to specify dependencies.
3. you shouldn’t do what you do here. the final location of the package is in .../site-packages. the directory where you called setup.py from should be deletable immediately after running python3 setup.py install
4. after installing, python -m sircel or just sircel should be enough to run it. for the former, rename Sircel_master.py to __main__.py. for the latter, see the packaging tutorial i linked to at the start (chapter “Command line scripts”)
5. kallisto in params.json should be set to "kallisto" per default. the normal way to call binaries is to put them into some directory in your $PATH, where they can then be found automatically and without configuration.
6. --osx is superfluous. you should detect that automatically.

furthermore: python modules shouldn’t be named with uppercase letters

[flying-sheep]

to sum up:

if which kallisto prints a path on my system, the following should work no matter the OS:

wget https://github.com/pachterlab/sircel/archive/master.zip
unzip master.zip
pip3 install sircel-master
rm -rf master.zip sircel-master
python3 -m sircel --help