PMC

(http://github.com/galaxyproject/training-material). The material is organized in different topics, each topic in a dedicated directory. Inside each topic’s directory, the structure is the same: a metadata file, a directory with the topic introduction slide decks, a directory with the tutorials and a directory with the Dockerfile describing the details to build a container for the topic that would contain a dedicated Galaxy instance with all tools relevant for the tutorials. Inside the topic directory, each tutorial related to the topic has its own subdirectory with several files: a tutorial file written in Markdown with hands-on, an optional slides file to support the tutorial, a directory with Galaxy Interactive Tours to reproduce the tutorial, a directory with workflows extracted from the tutorial, a file with the links to the input data needed for the tutorial and a file with the description of needed tools to run the tutorial. The process of development of new content is shown at the bottom of the figure.

DiCoExpress workspace. A visual representation of the DiCoExpress Workspace. a Sources directory contains all R functions implemented in DiCoExpress. b Template_scripts directory is the directory where an analysis script for each project analyzed must be saved. c Data directory is the directory where for each project, the input files (target and count tables) must be saved. If an annotation file used to describe biologically the different result tables as well as an reference file for the enrichment analysis are available, they must be also be saved in this directory. d Results directory contains all results obtained for each project

EpiDiverse EWAS pipeline output directory structure. EpiDiverse EWAS pipeline generates input directory as default and positions directory with methylation calls, DMPs, and regions directory DMRs. Input directory covers gxe.txt, snps.txt, cov.txt, and env.txt files and bed directory with merged bedGraph files as unfiltered and filtered and missing data estimated. Both positions and regions directories have three subdirectories for outputs and graphs with Emodel, Gmodel, and GxE names. Q–Q plots and histograms are produced with all models.

Directory structure for RELION data processing. Directories made by the user are named in black, directories created by the RELION GUI are shown in gray, symbolic links are shown in blue, and micrograph files are shown in green. This directory structure permits multiple RELION analysis directories to sit within a project folder, while keeping the raw data outside of the “relion” processing folder. Critically important is that the path from the RELION processing directory to the micrograph's directory avoids a parent directory reference (“..”), which would otherwise cause havoc for RELION's auto‐generated directory structures.