desc.conf is not used ?

maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

https://github.com/ucscGenomeBrowser/cellBrowser/

GNU General Public License v3.0

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desc.conf is not used ? #161

Closed drbecavin closed 2 years ago

drbecavin commented 4 years ago

Hello, To create my cellbrowser I was trying to use desc.conf as mentionned in the readthedoc Is it still a thing ? Does not seem to be taken into consideration. Thanks

matthewspeir commented 4 years ago

Hello @drbecavin !

Yes, the desc.conf is still used to control the abstract, methods, etc. for your dataset.

Can you provide more details about the issue you're running into?

A few things it might be:

The desc.conf should be in the same directory where you are running cbBuild.
It's also possible that you're running into some browser caching issues. Have you tried doing a hard refresh of the web page? I think on Mac it's cmd+shift+R, I'm not sure about Linux or Windows. Or try it in a web browser you don't use.

drbecavin commented 4 years ago

First of all when running the cbBuild,n I got this:

cbBuild -i cellbrowser.conf -o /ipmc/......../HCA
INFO:root:Loading settings from cellbrowser.conf
INFO:root:/home/becavin/hca/summary.html does not exist
INFO:root:/home/becavin/hca/methods.html does not exist
INFO:root:/home/becavin/hca/downloads.html does not exist
INFO:root:Getting md5 of /home/becavin/hca/metadata_FINAL_corrected.tsv

Should I get something like INFO:root:Loading settings from desc.conf ?

matthewspeir commented 4 years ago

Those three files (summary/methods/downloads.html) were the previous way of describing a dataset and its download files. However, those were replaced with desc.conf quite a few versions ago. The latest pip version (0.7.7, I think) should be looking for the desc.conf file.

What version of the "cellbrowser" package do you have installed?

matthewspeir commented 3 years ago

Hi, @drbecavin!

Is this still a problem? If not, maybe we can close this issue.

Thanks!

matthewspeir commented 2 years ago

I'm going to close this issue, but please feel free to re-open if you feel something is still unaddressed here.