Rstudio server in Snakemake
Hello, I am new to using Snakemake and I am running a test script calling an R script. I work on a restricted server and I have access to a docker R studio server to run everything. However, it seems I am not able to connect the Snakemake to the Rstudio docker. Is that possible? Or do I need to install R?
This is my R script:
args = commandArgs(trailingOnly = TRUE)
num_cells = args[[1]]
write.table("Cells: 1000", num_cells)
This is the Snakemake script (Snakemake_Test1_PS.txt):
rule test_file:
output:
num_cells="all_cells.txt"
shell:
"Rstudio --no_environ Scripts/testing_snakemake.R {output.num_cells}"
Output:
$ snakemake -s Snakemake_Test1_PS.txt
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 88
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 read_file
1
[Tue Jul 18 12:38:20 2023]
rule read_file:
output: all_cells.txt
jobid: 0
/usr/bin/bash: Rstudio: command not found
[Tue Jul 18 12:38:20 2023]
Error in rule read_file:
jobid: 0
output: all_cells.txt
shell:
Rstudio --no_environ Scripts/testing_snakemake.R all_cells.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Thank you!!
1 answer
There are several ways you could do, I would suggest you make use of the container keyword in the test_file rule (see here Snakemake container). Generally it's also a good idea to use script instead of shell if you call R scripts (see here R script).
Log in to answer this question.
More posts like this
-
Snakemake error AttributeError: 'Resources' object has no attribute 'tmpdir'
written by Begonia_pavonina •
-
Snakemake issue with wrappers
written by Begonia_pavonina •
-
Snakemake: Missing output files:
written by Joshua •
-
Snakemake + singularity fails to locate bwa index files.
written by jkim •
-
r script is not working in snakemake
written by firstorthopedicdoctor •
-
Snakemake bwa mem
written by priya.bmg •
-
Snakemake error with blast
written by kamanovae •
-
Error to run snakemake using conda environment to create a docker image
written by gkaradk •
-
Problem with Snakemake
written by viv3kanand •
-
Error with snakemake
written by Biologist
Why do you run
Rstudioand not simplyR?I would like to run it in the R studio server environment I have. But either way just R doesn't work either. I get the exact same error
So do you run the script inside the docker? Do you run this specific part in the docker?
No, it doesn't work inside the docker because Snakemake isnt recognized. I run the docker using:
but mostly I use the Rstudio webpage interface linked to the docker
sudo, there is a way to run docker without asudo, see here.snakemakein which environment it should run the rule. See here , you should add adocker:label to your rule.Unfortunately I cannot do that. Although I have sudo access I wasn't given the docker account password. I understand that doesn't really make sense.
Running this:
Gives me this error
What version of snakemake are you using?
It is version 5.9.1
container support was introduced in 4.8.0 so it should work, but your version is quite old. I recommend updating to the latest version and giving it another try.
How do you normally use R/Rsudio on the server? It would appear that it is not installed / available. On our server, R is not available by default and requires running
module load Rto make it available. If it is not available at all you will need to install R and Rstudio for these commands to run.I think thats my issue. I don't know how to have the console access the docker while still using the usual bash interface where Snakemake is. Or if that is even possible