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stephenslab / dsc-log-fold-change

dsc to compare approaches to estimating/testing log-fold-change from counts
https://stephenslab.github.io/dsc-log-fold-change/
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Declare module specific R libraries #2

Closed gaow closed 6 years ago

gaow commented 6 years ago

@jhsiao999 I've got 2 comments for DESeq2 module:

  1. You might want to add a @CONF: R_libs=DESeq2 or @CONF: R_libs = DESeq2, voom, ... if there are more libraries used. That way the library not only gets automatically installed when others run it, but also gets loaded. Otherwise even your code as is would not work due to missing load lib statements.

  2. Maybe consider putting the code under code folder instead? See my get_data.R example

Now you can make the changes and add your module to benchmark.dsc and give it a go using --target get_data * run_DESeq2 :)

jhsiao999 commented 6 years ago

Great. Thanks. I've made changes accordingly. Will push the changes now.

gaow commented 6 years ago

Looking good! except here (and the line under it) will have to be conventional R variable, so remove $(). After that it should run?

jhsiao999 commented 6 years ago

I got this error message:

ERROR: sequence item 0: expected str instance, NoneType found
jhsiao999 commented 6 years ago

this the line I ran to test my code

dsc benchmark.dsc --target "get_data*DESeq2" --truncate -o testDESeq2
gaow commented 6 years ago

@jhsiao999 oops sorry, fixed in master. Please update. But there is still issue with your data column names ... you can run to find out.