1.3/workflow-examples/analysis/
utterances-bot opened this issue · 5 comments
Complete Example - RAPIDS
When I am running the command "./rapids -j1 --profile example_profile" I'm getting below error
AttributeError in line 1 of /Users/qirtasmalik/rapids/example_profile/Snakefile:
'NoneType' object has no attribute 'get'
File "/Users/qirtasmalik/rapids/example_profile/Snakefile", line 1, in
Moreover, where can I find the code for the whole "Modules of our analysis workflow example" since I want to make few changes as per my use case. Thank you!
Can someone please help me with this?
Hi @Qirtas,
This is likely because your conda environment is not active or is not installed. Can you double check this please? If you run the following command you should see snakemake as the output: conda list | grep "snakemake".
The code for the modeling is here https://github.com/carissalow/rapids/tree/master/src/models/workflow_example. If you want to know what input/output files each script uses you can check the rules https://github.com/carissalow/rapids/blob/master/rules/models.smk
That being said, we just fixed a crash with the example profile so I would recommend switching to the develop branch or waiting until we release 1.4 today or tomorrow.
Hope this helps and let us know if you have any more questions.
Hi, thank you for the reply.
I have just checked by running the command you asked for and I got below output
"snakemake 6.4.1 pypi_0 pypi".
I guess my conda environment is working fine since I'm able to extract behavioral features for some other CSV files but getting issue only when I'm trying to run this example profile and the error is below
AttributeError in line 1 of /Users/qirtasmalik/rapids/example_profile/Snakefile:
'NoneType' object has no attribute 'get'
File "/Users/qirtasmalik/rapids/example_profile/Snakefile", line 1, in
Which means the error is related to a specific attribute which is mentioned here. I'm running this on mac m1.
Oh yes, sorry, I did not notice the edit on your first comment. For future reference for anyone reading this:
"/bin/sh: snakemake: command not found" this error is likely because of the conda environment not being active.
AttributeError in line 1 of /Users/qirtasmalik/rapids/example_profile/Snakefile This error will be fixed in v1.4
If you need to run the example now you can to switch to develop otherwise feel free to wait for the v1.4 release coming in the next few days. Thanks for reaching out!