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higlass / higlass-manage

A utility script to manage local docker instances of HiGlass
http://docs.higlass.io
MIT License
23 stars 9 forks source link

Problem in quickly viewing a dataset #82

Open Soh-hyon opened 2 years ago

Soh-hyon commented 2 years ago

Hello,

I got an error when I tried to quickly view a .mcool file using higlass-manage view file_name.mcool OSError: [Errno 18] Invalid cross-device link: '../HiChIP/KCl_H3K27ac/Processed_KCl_0h/KCl_0h_matrix_1kb.mcool' -> '/tmp/higlass-docker/KCl_0h_matrix_1kb.mcool'

What should I do now? Is the location of my .mcool file important? I ran the command inside the folder where .mcool file is located.

Thank you in advance!

pkerpedjiev commented 2 years ago

Hi, sorry for the delayed response. That's usually the error you get when mounting a network drive in Docker. Is your mcool file on a NFS volume? Would it be possible to move the file to a local directory?

luoxun-xl commented 1 year ago

Hello,

I got an error when I tried to quickly view a .mcool file using higlass-manage view file_name.mcool OSError: [Errno 18] Invalid cross-device link: '../HiChIP/KCl_H3K27ac/Processed_KCl_0h/KCl_0h_matrix_1kb.mcool' -> '/tmp/higlass-docker/KCl_0h_matrix_1kb.mcool'

What should I do now? Is the location of my .mcool file important? I ran the command inside the folder where .mcool file is located.

Thank you in advance!

This may be due to the file system inconsistency between the folder where the cool files are located and the /tmp folder. You can use the df-TH command to view the folder system on your system.

To solve this problem, you can move the files to a folder consistent with the /tmp file system, and then use higlass-manage view