Process for CAVATICA access/analysis

[jharenza]

We should flush out this process - giving people access to CAVATICA to analyze data, ability to use virtual notebooks to do analyses, then submission of their code/figures/notebooks to github.

[cgreene]

Short summary:

• We will create a CAVATICA user that has access to the PBTA data.
• We will generate an API key.
• We will use that API key in our download scripts to obtain the PBTA data files.

[cgreene]

Current instructions from @yuankunzhu

curl -s https://pbta-open-access-data.s3.amazonaws.com/downloader.sh | sh # primary download
curl -s https://pbta-open-access-data.s3.amazonaws.com/downloader-or.sh | sh # overwrite download

About to convert this into a download script.

[jharenza]

Current instructions from @yuankunzhu

curl -s https://pbta-open-access-data.s3.amazonaws.com/downloader.sh | sh # primary download
curl -s https://pbta-open-access-data.s3.amazonaws.com/downloader-or.sh | sh # overwrite download

About to convert this into a download script.

As an FYI for anyone downloading this data, we will be updating the download dataset to include some additional CNV/SV analyses by the end of next week.

[cgreene]

@jharenza - what do you think about closing this issue now that we have determined a process and taking a look at #2 and adding additional requirements (if any) in there? Also, are you and @yuankunzhu going to take a stab at putting the download code together?

[jharenza]

sure - I think @yuankunzhu will work on this during this sprint!