tetedange13
commented
3 years ago Hi @TheMuffinMan563,
Not an author of CNVkit, but I think this error means attempt to run 1st CNVkit command for testing failed
=>More precisely, looks like the term "python" (called by make comand) is not recognized as a valid command
Being inside your container, simply type "python" and if I am correct you should get the same "python: Command not found" error
=> Sometimes to call "Python3", one needs to explicitely type "python3" instead of just "python" (which often refers to "Python2" version of this language)
=> So could you please type "python3" inside your container and see if this "Command not found" error is gone (if so you should enter "Python interpreter" starting with >>> sign, that can be exited typing "CTRL+D" on you keyboard)
Still if this was root cause of your issue, you will have to correct the Makefile within your "test/" directory too
=> At line 6 of your Makefile, replace "python" by "python3" and re-run your make command again
=> You may also need to replace "python" term at this line by full absolute path leading to your Python executable
Hope this helps. Have a nice day. Felix.
TheMuffinMan563
Hello, i am trying to run cnvkit test using Docker (tried both with your image and a github repo one), i am in the container but when i run the make test as per instructions "You can test your installation by running the CNVkit pipeline on the example files in the test/ directory. The pipeline is implemented as a Makefile and can be run with the make command (standard on Unix/Linux/Mac OS X systems):" , i get the following error :
make: python: Command not found make: *** [Makefile:50: build/reference-picard.cnn] Error 127
I tried googling the error but i am unable to find a solution at the moment. What am i doing wrong?
Thank you