Editing the import file when relocating files

Import and Export
1

Dear colleagues,

I moved the original mrc micrographs to the other disc.

What is the way to modify/edit the first Import micrographs file in the CS project (specifying the new location of the originals) to avoid rerunning all the further time-consuming steps (patch motion correction + CTF estimation)?

Thank you in advance.

Sincerely,
Dmitry

2

Hi,

Instructions involving icli are available in Migration Guide: Use Case A. Although it’s also straightforward to redirect the symlinks in your shell of choice.

For example, in bash:

$ pwd
/path/to/project/folder/J1/imported/
$ readlink 012345678901234567890_mic1.mrc
/disk1/path/to/raw/micrograph/mic1.mrc
$ for symlink in *.mrc; do
> if [[ -L "$symlink" ]]; then
> target=$(readlink "$symlink")
> new_target="${target/disk1/disk2}"
> ln -sf "$new_target" "$symlink"
> fi
> done
$ readlink 012345678901234567890_mic1.mrc
/disk2/path/to/raw/micrograph/mic1.mrc

EDIT: typo in ln -sf command.

Cheers,
Yang

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