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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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define dataRoot via command-line argument or environmental variable? #185

Closed kriemo closed 4 years ago

kriemo commented 4 years ago

Hi, Thanks for developing such a useful tool. I routinely generate cellbrowsers for multiple unrelated projects and have been testing out using dataset hierarchies to organize each independent project. I can make this work currently by changing the global dataRoot in ~/.cellbrowser.conf as needed to point to the project-specific collection of cellbrowsers before running cbBuild. However, I'm wondering if there could be a feature to define the global dataRoot as an environmental variable, a command line option to cbBuild, or as a config parameter set in the top-level directory for each dataset hierarchy.

e.g. as environmental variable

CBDATAROOT="/project1/celldata/"

Thanks!

maximilianh commented 4 years ago

This is a great idea! Do you want to try to add it yourself (there is a function findDataRoot) or shall I?

On Wed 5 Aug 2020 at 16:19, Kent Riemondy notifications@github.com wrote:

Hi, Thanks for developing such a useful tool. I routinely generate cellbrowsers for multiple unrelated projects and have been testing out using dataset hierarchies to organize each independent project. I can make this work currently by changing the global dataRoot in ~/.cellbrowser.conf as needed to point to the project-specific collection of cellbrowsers before running cbBuild. However, I'm wondering if there could be a feature to define the global dataRoot as an environmental variable, a command line option to cbBuild, or as a config parameter set in the top-level directory for each dataset hierarchy.

e.g. as environmental variable

CBDATAROOT="/project1/celldata/"

Thanks!

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kriemo commented 4 years ago

Sure, I can try to add this feature myself. Is there a testing workflow that you typically use after making code changes?

maximilianh commented 4 years ago

Not yet, we’re just making one. But this particular feature wouldn’t affect it anyways. It should be a two-line change... I hope...

On Wed 5 Aug 2020 at 18:41, Kent Riemondy notifications@github.com wrote:

Sure, I can try to add this feature myself. Is there a testing workflow that you typically use after making code changes?

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