Proposal on how to organize this folder
How to connect to the flux, useful unix commands, hints/notes on configurating & running jobs, how to run interactive jobs, maybe miscelleous scripts that aren't clearly placed in other folders. For example, place the blast_quick_guide here
Possibly move SRA_data into it as subfolder
Possibly place the some_useful_scripts in this folder
Possibly place the fantastic script list in this folder
Basic pipeline for quality control, assembly, gene/protein prediction, and gene/protein annotation. For DNA and RNA. The Maker_pipline in here. Possibly place pacbio and hybrid analysis in here. Move the MiSeq_Analysis here.
Possibly place processing_messy_genomic_data in here as a subfolder. Running_ESOM definetly becomes a subfolder of the processing_messy_genomic_data
Everything related to R scripts. Place Will's community analysis stuff here. Subfolders that will be moved here: Creating_NMDS_Plots, MHC-Haplotype_Analyses
As is? Maybe move the whole Spatafora et al. pipeline into a new subdirectory & have other subdirectories for other methods, such as phyluce.
Two subfolders: QUIIME 1 and QIIME 2 with appropriate stuff in both.