Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unable to laod jbrowse.conf #549

Closed
verne91 opened this issue Dec 17, 2014 · 5 comments

Comments

Projects
None yet
2 participants
@verne91
Copy link

commented Dec 17, 2014

After I modified "[aboutThisBrowser]" and "[trackSelector]" in the file of jbrowse.conf, my jbrowse didn 't change.
Above all, After I changed "dataRoot" in the file of jbrowse.conf, I must type "?data=dataroot" after "http://my.machine.address/jbrowse/" to visit my Jbrowse.

@cmdcolin

This comment has been minimized.

Copy link
Contributor

commented Dec 18, 2014

I'm not sure about your problem with [aboutThisBrowser] and [trackSelector] are but i think the dataRoot could be a bug. I notice that it gives the "Congratulations JBrowse is on the web" / "Could not load reference sequence definitions. RequestError: Unable to load data/seq/refSeqs.json status: 404." even if dataRoot is set to somewhere else.

@cmdcolin

This comment has been minimized.

Copy link
Contributor

commented Dec 18, 2014

That said, if data/seq/refSeqs.json is initialized with some random data, it will then redirect the dataRoot to what was specified after loading JBrowse.

@verne91

This comment has been minimized.

Copy link
Author

commented Dec 19, 2014

Thank you.
After I wipped cache of my browser, the "[aboutThisBrowser]" and "[trackSelector]" became normal.
However, the condition you said still exists.

While I was running bin/prepare-refseqs.pl, I used the "--out" option. And data/seq/refSeqs.json didn't exitst.
So, how to fix this bug?

@cmdcolin

This comment has been minimized.

Copy link
Contributor

commented Dec 19, 2014

If it's possible, you can create a file in data/seq/refSeqs.json and then it will properly use the dataRoot variable afterwards. I think it is a bug that it doesn't instead check for {dataRoot}/seq/refSeqs.json in the first place

@verne91

This comment has been minimized.

Copy link
Author

commented Dec 20, 2014

After I copied from original refSeqs.json to data/seq/, the Jbrowser became normal.
Thank you!

@verne91 verne91 closed this Dec 20, 2014

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.