We are trying to unzip the MRI task and rest data using jupyterLab. The project directory is read only. home/dnanexus/<my_project>; Is there a way for us to have read write access to a permanent directory. We have a student account.
I believe that "("cannot download data, can only access data via the RAP)" means you cannot download data outside of RAP, but using "dx download", i.e. to transfer data from your project to the execution env, should be possible.
So to your "Can I still use dx download ? (download the file rom the DNAnexus project to the execution enviroment)",
YES, it should be possible. I would do some testing, e.g. by accessing Terminal from JupyterLab. In the terminal, you can try "dx ls" command, which should list the files in your project. Each dnanexus file has its own unique id, it might worth to try first "dx download file-XYZXYZ".
Via GUI, I can get information about the project path and file ID:
Feel free to share a screenshot of what you are trying to do. You may want to also troubleshoot it with ukbiobank-support@dnanexus.com.
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In JupyterLab, there are basically two approaches of Accessing data:
https://documentation.dnanexus.com/user/jupyter-notebooks#accessing-data
I would also recommend reading this whole page: https://documentation.dnanexus.com/user/jupyter-notebooks
As for more example on reading/download MRI zipped data, this thread could also help: https://community.dnanexus.com/s/question/0D5t000004EtXLYCA3/is-there-a-way-to-extract-the-bulk-imaging-data-using-the-spark-jupyter-notebook
Thank you, I read the documentations.
If I have student application ("cannot download data, can only access data via the RAP)
Can I still use dx download ? (download the file rom the DNAnexus project to the execution enviroment)
Could not find a project named "project-<My ID application>"
I understand correctly home/dnanexus/<my_project> have only "read" access.
I really don't now what to do :(
Hi {@005t000000BBxUMAA1}?,
I believe that "("cannot download data, can only access data via the RAP)" means you cannot download data outside of RAP, but using "dx download", i.e. to transfer data from your project to the execution env, should be possible.
So to your "Can I still use dx download ? (download the file rom the DNAnexus project to the execution enviroment)",
YES, it should be possible. I would do some testing, e.g. by accessing Terminal from JupyterLab. In the terminal, you can try "dx ls" command, which should list the files in your project. Each dnanexus file has its own unique id, it might worth to try first "dx download file-XYZXYZ".
Via GUI, I can get information about the project path and file ID:
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