I’m new to bioinformatics and Galaxy. I’m trying to map a genome using the Linear Genome Plot Tool but am having some trouble. I looked into the publication but it referred to some other program… or in the very least a program that is being used to run this tool. Does anybody know where I can find a manual or a tutorial for how to use this tool?
I have some sequence data that I already have annotated, I just want a visual graphic to supplement my findings.
You’re supposed to use this tool through a Galaxy instance, specifically through Galaxy | CPT Public
If you really want to use it from the command line, you should be able to run the python code of it (galaxy-tools/tools/genome_viz/linear_genome_plot.py at master · TAMU-CPT/galaxy-tools · GitHub) by first installing the requirements listed in galaxy-tools/tools/genome_viz/macros.xml at c43f5a7706fb64615b7c050a5a9e5fc20ca33873 · TAMU-CPT/galaxy-tools · GitHub into a conda environment, then executing the python code with that environment activated.