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dnanexus / dxda

CLI tool to manage the download of large quantities of files from DNAnexus
Apache License 2.0
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Issue downloading data from DNAnexus to external HPC cluster #87

Closed prasundutta87 closed 3 months ago

prasundutta87 commented 3 months ago

Hi,

I wish to download some shared datasets in DNAnexus to my own university cluster. I am using this software to do the same. I have been trying to download this client on my cluster, but I am caught up with some errors and I would be grateful if I could be helped with this and also let me know if this method is the correct way to download data to an external HPC environment.

` pip3 install git+git://github.com/dnanexus/dxda.git Collecting git+git://github.com/dnanexus/dxda.git Cloning git://github.com/dnanexus/dxda.git to /tmp/pip-req-build-m_xipr3h Running command git clone --quiet git://github.com/dnanexus/dxda.git /tmp/pip-req-build-m_xipr3h fatal: unable to connect to github.com: github.com[0: 20.26.156.215]: errno=Connection timed out

error: subprocess-exited-with-error

× git clone --quiet git://github.com/dnanexus/dxda.git /tmp/pip-req-build-m_xipr3h did not run successfully. │ exit code: 128 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× git clone --quiet git://github.com/dnanexus/dxda.git /tmp/pip-req-build-m_xipr3h did not run successfully. │ exit code: 128 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. `

Regards, Prasun

prasundutta87 commented 3 months ago

This issue can be closed--I followed this method- https://documentation.dnanexus.com/user/login-and-logout#generating-an-authentication-token and this- https://hemtools.readthedocs.io/en/latest/content/Bioinformatics_tools/dnanexus.html