Common stuff:


  • Projector: Code 1988
  • Workstations: student hookem

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


  • 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 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 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?


  • 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 - DA to trim, then SPHS ask Vicki/heather to print/laminate
  • SPSH edit flowchart icncluding quafelkfuyt.
  • Refer folks to linux intro tutorials - 
  • 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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