Common stuff:

Credentials

Projector: Code 1988
Workstations: student hookem

Project allocation for the class, e.g. : 20130520NGS-FAC

Instructors:

Make sure you source the common profile, or if not, be sure to execute umask 002 to make all files you create group writable.
If your primary group is not the NGSC group, do this right after logging so that all files you create will be the NGSC group (G-803889)
```
newgrp - G-803889
umask 002
```

Instructors de-briefing 5/23/13:

Most common confusion in tutorials:
- local computer vs TACC vs idev
- where example commands are being executed (current directory)
1st day overwhelming for non-Unix folks (as usual). Maybe find a way to introduce commands as part of guided lecture?
Three kinds of sections from us: 1) lecture 2) guided lecture (they exec some cmds) 3) tutorial
- Have more 1 & 2 early on, moving to more 2 & 3 as they get more comfortable
- Definitely go through mapping tutorial one step at a time from the front of the class - this should be REALLY clear
Should explore full day for TopHat - maybe yeast in TopHat? More interactive demos on graphing, etc. Theoretically (in Anna's mind) this is already done!
Maintain encouragement to the linux-challenged
Maybe an assembly evaluation tool?
Maybe switch from a genome assembly to a transcriptome assembly (i.e. the yeast subset from the TopHat)
Should move to bowtie2
Need to clarify language: reference, reference genome, indexes (references, bam files)
Need to clarify "commands" file (for launcher_creator.py) vs a bash script
Fix wrap-around with "nowrap" macro instead of "code" macro
Maybe some "speciality" or niche application exposure - metagenomics, IMGT, ddRAD analysis, etc.
Should we describe library prep more? Or things like enrichment?
It was good to have expanded QC discussion.
Maybe manipulatives.
End-of-day review/test - with rewards the next day if they get it right - to build confidence.

Instructors de-briefing 8/23/12:

Need to add a TACC 1-day Linux workshop the week before the class - students must have some linux exp. before class or they fall behind
Limit class size to 30 with two instructors and four volunteers so there is ample personal instruction
Use the large-monitor TACC machines, not personal PC's, for instruction, but offer to help people setup their own laptops in an enrichment section or two
John F. will figure out how to test whether corral is running before sourcing the ngs_user_profile script (in case corral is down)
Need to have back-up of data on SCRATCH - best idea is the following:
- Have students copy the entire tree of data/examples/etc on day 1
- Have a "fix my data" rsync script that corrects it on subsequent days, in case they accidentally corrupt their local copy
Re-structure so that each major section has:
- Clearly stated learning objectives
- A theoretical overview
- An overview of the exact workflow steps the students will do and finally
  - Recommended sections for a tutorial: Data (where to get it, description of what it is), Toolbox/Recipe (introduce new commands/programs/basic workflow), Exercises (questions about the data analysis or what options in the program are doing).
- Time - for the students to work through the exact commands themselves; instructors & volunteers going around to help one-on-one instead of watching the instructor type commands and students trying to follow along.
  - As we see what many people struggle with, we can pull everyone's attention up to the screen occasionally to go over a specific command.
  - Since this will take longer, we might want to co-opt the later "enrichment section" time for one of the self-paced lessons each day (i.e, have an introduction to a topic that ends at 4:30), and only use time before class for real enrichment sessions on other topics.
  - This will also encourage people to try things on their own data?
- Re-cap learning objectives
- Test whether students have met the learning objectives (homework, scavenger hunts, etc.)
We can reserve nodes for iDev in the future - we need to ask for Tommy's help about a week to 10 days in advance
Prune content - fewer commands, focus on what they're doing
Maybe use ssh -Y which John F. believes will forward not only from a login node but also from an idev node

Older to-dos

Our project is: 20120820NGS

Use this when list a command to submit to the queue, not run interactively

Submit via qsub

Use launcher_creator.py followed by qsub to submit this command.

Launcher creator - update - with usage(), output what it's doing - Aaron
Explain SAM format when we look at data in IGV
Create more intro materials - SPHS/JB
Any other visualization tools?

Done:

Obtain allocation for Aug course - SPHS
Ask Chris Jordan for NGCS web allocation - SPHS/AB
AB: Add new dir or re-use on /corral-repl/utexas; make new global linking to it.
AB: will email group RE global .profile_user we should use with the right umask.
Hardcopies of http://www.tjhsst.edu/~dhyatt/superap/unixcmd.html - DA to trim, then SPHS ask Vicki/heather to print/laminate
SPSH edit flowchart icncluding quafelkfuyt.
Refer folks to linux intro tutorials -
http://loving.corral.tacc.utexas.edu/bioiteam/ which links to $BI/web

Guidelines on scripting vs. individual commands:

1. On early-on basics (e.g. day 1), try to lead students to do it themselves; copy and paste hidden is OK.

We're going to run R interactively on HN, idev -m <bunch> is backup, local machines is next. John F. looking at other options.

SPHS to move $BI/subdirs into ngs_course and update links

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