problem running executable "charger" file

[nitinroper]

After installing the program, I type charger as suggested to view executable options and I receive the following error:

File "/home/[username]/mycharger/bin/charger", line 256 print "CharGer ERROR: Command not recognized" ^ SyntaxError: Missing parentheses in call to 'print

Any advice on how to fix this? Thank you

[amilacsw]

Thanks @nitinroper for reaching to us. This error should be coming from syntax difference between Python 2 and 3. Charger is built for Python 2. It seems like you are using Python 3. Please follow the installation steps given in the README to install Charger in a Python 2 environment.

[nitinroper]

I followed the installation steps exactly as listed in README. Any other potential reason for this issue?

[amilacsw]

Could you check your python version (enter python -V in terminal) and let us know what you see? Thanks!

[nitinroper]

python -V

Python 3.4.5 :: Continuum Analytics, Inc.

However, I also have python 2 installed and I uninstalled python3.4.5 but have the same issue

[fernanda-rodrigues]

@nitinroper Sorry for the delay in addressing your issue. I have updated the README file, including instructions on how to install CharGer within a conda environment. That might solve your issue. Please try it and let me know if you're still having problems.

Thanks!

[ghost]

I am currently in /home//anaconda2/CharGer directory (base) $conda activate CharGer (CharGer) $python -V Python 2.7.18 :: Anaconda, Inc.

now I want to test the vcf file

(CharGer) $ charger -f tests/examples/grch38_brca2_ashkenazi_jewish_founder.vcf -o testfile.vcf command 'charger' not found, did you mean blabla

I did follow each of the steps in README.md. Please enlighten me.