Using preprocessing/alignment functions on the server
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).