Cell Browser data flow and architecture: Difference between revisions

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How does data flow between different machines


Data flow from test->beta->RR
== '''How does data flow between the different machines?''' ==


Diagram here?
[[File:cb-data-flow.png|650]]


How does building a cell browser work?
 
== '''How does building a cell browser work?''' ==
     What files are copied over?
     What files are copied over?
     Which ones are transformed into another format?
     Which ones are transformed into another format?


[[File:cb_sysarchmap.png|1050px]]
1. Data is first deposited in a dataset directory inside <code>/hive/data/inside/cells</code> on <code>hgwdev</code> and then gets built onto [https://cells-test.gi.ucsc.edu/ cells-test] using the command:
<pre>
cbBuild -o alpha
# For datasets with no additional subsets
 
cbBuild -r -o alpha
# For dataset collections you will use the recursive option "-r"
</pre>
 
2. The output files from <code>cbBuild</code> are placed inside <code>/usr/local/apache/htdocs-cells</code>. Note that the original configuration files and expression matrices inside the dataset directory are converted into either JSON or binary files (BIN). These files are used by the Cell Browser to ....... (help) build a cell browser.


System architecture map or something like that
[[File:cb_sysarchmap.png|1045px]]
Where do we we keep input files for cbBuild
Where do we build out to
What are the files in the output directory




[[Category:Cell Browser]]
[[Category:Cell Browser]]

Revision as of 23:07, 25 August 2022

How does data flow between the different machines?

650


How does building a cell browser work?

   What files are copied over?
   Which ones are transformed into another format?

1. Data is first deposited in a dataset directory inside /hive/data/inside/cells on hgwdev and then gets built onto cells-test using the command: 

cbBuild -o alpha
# For datasets with no additional subsets

cbBuild -r -o alpha
# For dataset collections you will use the recursive option "-r"

2. The output files from cbBuild are placed inside /usr/local/apache/htdocs-cells. Note that the original configuration files and expression matrices inside the dataset directory are converted into either JSON or binary files (BIN). These files are used by the Cell Browser to ....... (help) build a cell browser.

Cb sysarchmap.png

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