hackseq_plan

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#HACKSEQ 2019 PLAN

Day 1: 

   i. MORNING  MEETING: 

       A. Team formation, introductions, overview of Hackathon workflow and Lesson Plan/Analysis Pipeline, Adding everyone to Github, Git overview and push/pull protocols 

       B. Assignment of individuals to either Docs or Interface, Git issue Overview
	***Kate: CRAN documentation and usethis() for R package building
	***Paaksum: YAML file template and course material writing (starting with file types and low level analyses), based on swirlify() YAML file structure
	***Lisa: Interface, working on Radian + Biosyntax convergence 
	***Jackie: '' 
	***Jeremy: ''
			    


       C. Installation of:

	    [ SEE devenv_install ]

            i. Devtools, usethis, knitr, roxygen2, git, vim (Nvim-R)

            ii. Radian, BioSyntax, beRi, Bioconductor 

            iii. scRNA datasets, workflow guides 

            iv. R packages: scRNAseq, Rsamtools, fastqc, rsubread, scater, scran, scpipe, Seurat, heatmapr

            v. IF NEEDED: Rpytools, htmltools, 

        D. Specific Task Assignment 

  ii. DAILY| WORK: 

        A. Docs Team: 

            i. assign lesson plan documentation to individuals based on expertise (Basic Concepts, workflow, low level, high level, or coding practices) 

            ii. encode the YAML files

            iii. gaining a general idea of good hands on lessons, desired input/outputs in terminal  

        B. Interface Team: 

            i. MAIN GOAL: Integration of all resources and file structure aka “Harmony”, interactivity component

            ii. Building the file structure needed and create necessary pointer variables in R, writing install files (including install options), initialization of R package (+ licensing), based on swirlstats structure 

                    c. Building the skeleton lesson plan, prepping gene files for testing and ensuring annotation displays correctly, making sure correct lessons launch with user input  



Day 2: 

   i. MORNING MEETING: 

        A. Team get together, overview of where everyone’s at, carry over tasks left over from day before, and assign new tasks

        B. Documentation refinement, moving from background and theory to hand on coding sections

   ii. DAILY WORK:

        A. Docs Team: working on lesson plans from day before, or moving onto next 

        B. Interface Team: 

             i. Development of Lesson plan structure, importing in YAML files from docs team and organizing structure of lesson plan. Importing of dummy and test gene files to test for annotation and compatibility, 

             ii. “Failteacher” - > git diffs (or equiv) data outputs and gives feedback based on differences (unlikely!!) 

             iii. Begin CRAN documentation 

             iv. Creating launch icon, user settings, allow of radian/terminal option OR Rstudio option, Progress tracking, save/load metadata files for quickstart

             v. [IF THERES TIME] Lesson tester to overview input functionality, purposeful breaking  


Day 3:

   i. MORNING MEETING: 

         A. PRIORITIZATION OF ISSUES

         B. Reassignment to critical areas

         C. Team vote on what to abandon/Keep 

   ii. DAILY WORK: 

         A. Proofreading 

         B. Debug/Finishing touches 

         C. Present work