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CompEpigen / figeno

Tool for plotting sequencing data along genomic coordinates.
GNU General Public License v3.0
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whether does figeno support URL #13

Closed BenxiaHu closed 2 months ago

BenxiaHu commented 2 months ago

whether does figeno support URL?

e-sollier commented 2 months ago

What do you mean? Figeno only works locally and is not available as a web service, if that's what you want to know.

BenxiaHu commented 2 months ago

no. for example, you depoisted your bigwig files on amazon or google driver. does Figeno can support the URL which links to these bigwig files? IGV does support URLs.

e-sollier commented 2 months ago

Ah, I see. No, figeno currently does not support URLs. I can investigate how feasible this would be to implement, but I expect this might be too much work. However, you can mount a remote filesystem (e.g. with sshfs), and use files from the mounted filesystem.

e-sollier commented 2 months ago

I've added experimental support for remote bigwig files in version v1.3.1 (that can be installed with pip install figeno==1.3.1). If you paste an http url in the "file" field of a bigwig track, figeno should be able to display it, although it will be slower than for a local file. However, this will only work if you have curl installed and if you reinstall pybigwig using pip install --upgrade --force pybigwig --no-binary pybigwig because for some reason the wheels provided for pybigwig do not seem to support remote files. I don't plan to add support for remote files for other file types, as it would take too much time.

As mentioned above, if you want to use remote files, I would suggest mounting a remote filesystem, which allows you to access those files as if they were stored on your computer. You can use sshfs if the files are on an ssh server, or https://github.com/s3fs-fuse/s3fs-fuse for amazon S3, or https://github.com/astrada/google-drive-ocamlfuse for google drive.