Today I had attempts to write code for automation my pipeline. I tried make It in Jupyter but some packages, for example os.startfile (path[, operation]), not intended for Unix sistem. Now I attempt make it in R-studio and I have some questions:
1) How I should run program? For example, I had attempts run bwa mem and I have problem. I wrote in terminal:
bwa.path <- "/home/valera/Utilits/bwa-0.7.16a/bwakit/" system(paste(bwa.path, "run-bwamem -M /home/valera/bam/GRCh38_latest_genomic.fna /home/valera/bam/Rep2.fastq.gz>/home/valera/bam/Prob_obr.sam","index", sep=""))
and the program makes output
ERROR: failed to locate the BWA index.
2) Second question from first, what I should indicate in "index"?
3) Is It good idea write automatically pipeline on R-language?