Closed heavywatal closed 3 months ago
thanks for alerting me to this. I actually didn't realize it was working in any state. we can try to restore it back to where it was at least
Thank you. But I understand that you don't want to revert and keep incomplete functionalities. So I would suggest not to revert the code, but just to amend the help doc and error messages to guide users properly.
For example, the error message "Error: Please either provide a default session file" was not clear:
[-s <value>]
now mandatory? If so, it should not be an optional argument, but should be a required argument (but making it a positional argument breaks compatibility). The leading title of the help "Set a default session with views and tracks" may be also misleading. Maybe "Set a default session from an existing session file"?If I understand it correctly, I think I can handle it by creating a session.json
from scratch and reading it with -s
.
These two lines in EXAMPLES
section do not work, I guess:
jbrowse set-default-session --target /path/to/jb2/installation/config.json
jbrowse set-default-session --view LinearGenomeView, --name newName
@heavywatal I went ahead and made your suggested documentation fixes!
I think a longer term effort will be to make it so that "defaultSession" format is easier to use, so that it can be hand edited or programmatically generated without as much effort.
There are a couple PR that are open for this but it is a tricky one, so will take some time. Thanks for reporting this though
The related PRs...
https://github.com/GMOD/jbrowse-components/pull/4444 https://github.com/GMOD/jbrowse-components/pull/4148
Confirmed 2.12.0 works as expected. I am using hand-made session.json
s to feed set-default-session -s
. Thank you for the quick action.
Describe the bug
I have been using
jbrowse set-default-session
with--view
and--tracks
options. Unfortunately they were removed in 2.10.2. The removal was announced as a bug fix, but actually that was a breaking change in the existing API, which I think deserves at least a minor version bump. Anyway, now I am struggling to build a new pipeline to setup a new session via CLI in newer versions. The first attempt was to simply remove--view
and--tracks
options from the command, but the command resulted in an error "Error: Please either provide a default session file". It does not make sense.To Reproduce
jbrowse create ...
jbrowse add-assembly ...
;jbrowse add-track ...
jbrowse set-default-session ...
Expected behavior
A default session can be created with a view and tracks. Even though the previous behavior of
set-default-session
was not perfect as stated in #2708 and #4146, it was much better than "not provided at all".Screenshots
Version:
Additional context