Using preprocessing/alignment functions on the server I am new to bash and the processes behind cluster computing in general and need some help with understanding some basics.

After looking all over the internet and this forum (+ askUbuntu) I found nothing that addresses this issue.

I have a series of raw RNA sequencing files: .bam and wish to utilize samtools (or others) to begin the data preprocessing steps defined in many workflows.

I have installed samtools and many other programs necessary for the workflow, however, once I am on the remote server in bash, and try and run a function over the files of interest, it gives me the error: -bash-samtools: command not found

When I try to install the package, say samtools, by running sudo apt install samtools, I get an error stating I do not have permission to do such.

What do I do? Must I bring up this issue to the server provider or is there a way around it?

Thank you for your time,
The short answer is to use conda. In the bioconda channel we have most of the tools used in bioinformatics, such as samtools. You do not need administrator permissions to install conda or packages with it, so your lack of sudo ability is not an issue.


  I have installed samtools and many other programs necessary for the workflow, however, once I am on the remote server in bash, and try and run a function over the files of interest, it gives me the error


Installing packages on your local machine won't affect the remote server unless they share a file system, so this is expected.

As an aside, BAM files aren't really "raw", they're considered processed data (fastq/fast5 files are considered truly "raw" data in the sequencing world).