Using cdqr in latest skadi OVA system can't see zip file about skadi

[orlikoski]

Hi @slacker-kb and thank you for asking.

Starting in Skadi 2019.3 the CDQR functions are accomplished using the aorlikoski/CDQR docker. In order to facilitate this transition a CDQR Docker Helper script was created and stored in /usr/local/bin/cdqr. So that script is what you're calling when cdqr is typed at the terminal and then it does some translations and then creates the correct docker run command required to process the data.

There is a slight difference in the command line arguments between cdqr.py and the cdqr helper script. I believe this is what is causing the issue you're having.

I've added links in this response to facilitate research on the script. Here is the modified command, based on your example. That should work

cdqr -p lin --max_cpu in:beast5.zip out:Results --es_kb beast5_sample

[slacker-kb]

Thanks so much! Worked like a charm.