Feedback on new uploader
The new uploader looks awesome. Works great for me. And I like that it's a command-line application now.
Below are some comments I have:
Could you incorporate the instructions for installing the software into the docs (instead of just in the
README.md)? I found myself going back and forth between the readthedocs page and the README to figure out how to install and run.
Could you rename
upload.shto something like
irida-upload)? Also, allow it to be runnable outside of main directory (that is, don't use
source ./.virtualenv/bin/activate, but instead use
source $ROOT_DIR/.virtualenv/bin/activate, where
ROOT_DIRis set like so https://github.com/phac-nml/snvphyl-galaxy/blob/development/scripts/setup_toolshed.sh#L2).
The reason for this is that if we install the uploader to some system-wide directory (or package up in conda) the name will be a bit more descriptive and it will still work no matter which directory you're currently in.
Could you add a usage statement to
upload.shif this is the main method people will run the software (e.g., just running
upload.shshould print out a description of what the program does and how to run it).
I got an error when I tried to upload a miseq directory structure:
2018-12-12 11:42:03,093 ERROR ERROR! An error occurred with directory '/home/aaron/Downloads/irida-sample-data/miseq-run', with message: The directory /home/aaron/Downloads/irida-sample-data/miseq-run has no sample sheet file with the name SampleList.csv
I was fairly confident that this directory is properly formatted as a miseq directory though I may have been missing
CompletedJobInfo.xml. Is this file necessary? Could you maybe add a message to the logs saying something like directory structure not formatted as a MiSeq structure, defaulting to regular directory structure?
I was testing with the
miseq-rundirectory in the IRIDA sample data download (https://irida.corefacility.ca/documentation/downloads/#sample-data). We may have to re-format some of the files/samplesheets in there to get to work with the new uploader (that's okay).
Could you provide an example set of data that is formatted correctly (and linked to in the docs)? You could maybe link to the sample data from IRIDA (https://irida.corefacility.ca/documentation/downloads/#sample-data).