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madscatt / zazzie

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ds-DNA issues #11

Open madscatt opened 8 years ago

madscatt commented 8 years ago
  1. run_ directories are not following protocol
  2. "hacked in alignment code used in some cases" needs to be reviewed
  3. move test cases from early state debugging to a comprehensive set of tests
  4. $ID flag set on some files in TAMC and not others. Needs to be reviewed and if used, use it everywhere.
StevenCHowell commented 8 years ago
  1. Not sure which directories so cannot comment on why.
  2. The alignment code I use is in the B-DNA gui_mimic files. I put this together to use the existing code in a more intuitive manner. We should discuss adapting this to general use.
  3. no comments
  4. The SVN $ID: $ flags were helpful when using that version control. Git does not use any equivalent. We should remove them.
madscatt commented 8 years ago
  1. Try running a few of the gui_mimic scripts (dna related) and see what folders are created. Maybe I misinterpreted what I saw.
  2. Github can query a similar syntax with the commit hash.
StevenCHowell commented 8 years ago

What folders should be created? The DNA gui mimic scripts create the <run folder> with a monte_carlo subfolder, and all the pertinent files within that subfolder. The names for <run folder> in the DNA gui mimics is typically more descriptive than the other gui mimic files (usually use run_0.

Is this naming difference the issue?