bulker problem with bedToBigBed

[jpsmith5]

bedToBigBed is called by R script. So it can't call the bedToBigBed container...Not sure how to go about resolving this one, short of adding bedToBigBed to the rpipe container?

> `Rscript tools/PEPATAC.R bigbed -i /mnt/storage/processed/tutorial/results_pipeline/tutorial/peak_calling_hg38/tutorial_peaks.narrowPeak -c /mnt/storage/genomes/hg38/fasta/default/hg38.chrom.sizes -t bedToBigBed` (2175)
<pre>
Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
sh: 1: bedToBigBed: not found
Warning message:
In system2(paste(ucsc_tool), args = c(paste("-as=", as_file, sep = ""),  :
  error in running command
[1] TRUE
</pre>

[nsheff]

yep that's what we'd have to do. Or, make the call outside of R from within the pipeline instead.

[nsheff]

did this get solved?

[jpsmith5]

Converted this approach to python instead of R.