I am trying to run an alignment using Bowtie2 from Rstudio and following the systemPipeR workflow. Though, after installing Bowtie2 and hisat2 I am unable to run the tools and I get the following error message in Rstudio
sh: 1: bowtie2-build: not found Warning message: In system("bowtie2-build ./data/tair10.fasta ./data/tair10.fasta") : error in running command
`* Is there any way by which I could be able to run it from Rstudio ?? I have added the tools to my PATH variables also. Is there any specific way to add the PATH variable to environment as I have tried in various ways?? Any answers will be very helpful!