linnarsson-lab / loom-viewer

Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format
BSD 2-Clause "Simplified" License
35 stars 6 forks source link

Question regarding Loom CLI #129

Closed JobLeonard closed 6 years ago

JobLeonard commented 6 years ago

Am I correct in understanding that the loom CLI tool is officially deprecated, not maintained, and not used anywhere in the pipeline other than serving the viewer? Does that mean I can safely strip anything non-viewer related, so stuff like creating Loom files from other files, uploading to a server, using BackSPIN, and so on?

I'd like to do some code clean-up on the Python side of the loom-viewer code, and there's a lot of old stuff I haven't looked at in over a year and I don't know what is and isn't relevant at this stage.

slinnarsson commented 6 years ago

Yes, correct. The only use for it now is to extract loom files for the server.

/Sten

-- Sten Linnarsson, PhD Professor of Molecular Systems Biology Karolinska Institutet Unit of Molecular Neurobiology Department of Medical Biochemistry and Biophysics Scheeles väg 1, 171 77 Stockholm, Sweden +46 8 52 48 75 77 (office) +46 70 399 32 06 (mobile)

On 22 Oct 2017, at 17:49, Job van der Zwan notifications@github.com wrote:

Am I correct in understanding that the loom CLI tool is officially deprecated, not maintained, and not used anywhere in the pipeline other than serving the viewer? Does that mean I can safely strip anything non-viewer related, so stuff like creating Loom files from other files, uploading to a server, using BackSPIN, and so on?

I'd like to do some code clean-up on the Python side of the loom-viewer code, and there's a lot of old stuff I haven't looked at in over a year and I don't know what is and isn't relevant at this stage.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.

JobLeonard commented 6 years ago

Time to do some spring autumn cleaning!

JobLeonard commented 6 years ago

I assume loom_pipeline.py can be deleted as a whole?

slinnarsson commented 6 years ago

Yes!

-- Sten Linnarsson, PhD Professor of Molecular Systems Biology Karolinska Institutet Unit of Molecular Neurobiology Department of Medical Biochemistry and Biophysics Scheeles väg 1, 171 77 Stockholm, Sweden<x-apple-data-detectors://1/0> +46 8 52 48 75 77<tel:+46%208%2052%2048%2075%2077> (office) +46 70 399 32 06<tel:+46%2070%20399%2032%2006> (mobile)

25 okt. 2017 kl. 15:49 skrev Job van der Zwan notifications@github.com<mailto:notifications@github.com>:

I assume loom_pipeline.py can be deleted as a whole?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHubhttps://github.com/linnarsson-lab/loom-viewer/issues/129#issuecomment-339335734, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKKag9Y9bxx4zCTYsZmOq6JhC3KkmX3_ks5svzxDgaJpZM4QB_zi.