I would highly recommend using nextflow or some other workflow manager as they are designed precisely for the task you are describing.
You can write a simple script to read in the bam files, and execute the cufflinks command. Using the -with-docker flag will tell it to run it inside the container where your tools are.
Something like:
#!/usr/bin nextflow
params.bams = "/path/to/bams/*.bam"
Channel
.frompath( params.bams )
.set{ bams }
params.genome = "/path/to/hg19.fa"
genome_file = file(params.genome)
params.gtf = "path/to/hg19.gtf"
gtf_file = file(params.gtf)
process cufflinks{
publishDir "Results", mode:'copy'
input:
file bam from bams
file genome from genome_file
file gtf from gtf_file
output:
file "*.gtf" into outputs
script:
"""
cufflinks -b $genome -g $gtf -u $bam
"""
}
Should be more than enough to get you up and running there. Nextflow is easy to install and you will not run into sudo problems (assuming you are on a HPC with 700+ bams).