Question: reading a RDS file in galaxy using a R tool
1
gravatar for Nicolas
2.4 years ago by
Nicolas10
Burunid/Bujumbura
Nicolas10 wrote:

Dear Comunity

I am a bit new in galaxy and I am currently trying to adapt a stand alone program (written in R) into galaxy tools.

To communicate beatween the tools, I am using RDS files but I struggle a bit to read them once they are loaded in galaxy.

following this post using R data structure files (rds) as input/output in galaxy tools and some github code from Stef van Lieshout, I was able to create a rds type that is correctly uploaded in galaxy but when I try a readRDS() in R script, it fails to load them into the script.

I tried to read the data file as galaxy display it (in galaxy/database/files/000/dataset_anID.dat) and it is obviously something R won't read with readRDS (it is not a binary)

so I am a little bit lost on how I should handle this. Is the following pipeline correct or did I miss something ?

  1. declaring a new datatype as explained in the link above
  2. uploading a rds file in galaxy
  3. using this data as input of my R-based tool
  4. using readRDS() in the R code to load the file

Thanks

Nicolas

galaxy R • 588 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Nicolas10
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