I am trying to set up an esATAC pipeline, however I am running into a few issues when I am trying to set the genome for the file.
Code:
library(esATAC)
library(magrittr)
dir.create("./esATAC_pipeline")
dir.create("./esATAC_pipeline/refdir")
dir.create("./esATAC_pipeline/result")
#configure reference path, result path, the max number of threads, genome
setRefDir("esATAC_pipeline/refdir")
setTmpDir("esATAC_pipeline/result")
setThreads(2)
setGenome("mm10")
Error:
Configure fasta ...
Error in .Call2("write_XStringSet_to_fasta", x, filexp_list, width, lkup, :
write error
Error in .Call2("write_XStringSet_to_fasta", x, filexp_list, width, lkup, :
write error
Error in .Call2("write_XStringSet_to_fasta", x, filexp_list, width, lkup, :
write error
Configure fasta finished
Configure bt2Idx ...
--threads 2
Error in system(call, intern = TRUE, show.output.on.console = TRUE) :
'python' not found