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claraqin / neonMicrobe

Processing NEON soil microbe marker gene sequence data into ASV tables.
GNU Lesser General Public License v3.0
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can't knit vignette download-neon-data #28

Closed lstanish closed 3 years ago

lstanish commented 3 years ago

The .rmd file will not knit. I added my file directory in the knitr::opts_knit$set function, but I think the params.R file is causing the problem, since the file paths are hard-coded. Is it worth updating so that I can knit the .rmd, or should I instead just send text edits to you?

yyachung commented 3 years ago

I also tried last week and had similar problems knitting, but held off commenting since I hadn't exhausted all options yet. Happy to just send text edits if that would be helpful.

claraqin commented 3 years ago

Hi Lee and Anny,

Sorry for the slow response – I'm just now returning from leave. To clarify, you definitely should update the parameters in the params.R file, as I specified in issue #27.

I realize that the params.R file is somewhat clunky, and if there is a better way for the user to enter parameters that are specific to their computing system, I'm open to suggestions.

Best, Clara

lstanish commented 3 years ago

@claraqin @yyachung Thanks for directing me to those instructions. I was able to get the workaround file to work, but also made a couple tweaks to the main vignette rmd and that knitted for me as well. I found and fixed a couple bugs in the downloadSequenceMetadata() function and the function now splits up 16S and ITS metadata if 'all' is specified. Working through updates to the downloadSequenceData() function, expect those to be ready for review next week.

lstanish commented 3 years ago

issue resolved, closing ticket