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Use specific 2019-03 nixpkgs#3

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cgevans wants to merge 67 commits intoDNA-and-Natural-Algorithms-Group:masterDNA-and-Natural-Algorithms-Group/SST-sequence-designer:masterfrom cgevans:masterCopy head branch name to clipboard

+3-1

Commits

Commits on Oct 25, 2018

• adding files

  damienwoods

  committed
  695ee2d

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• add random file, rename 6-bit IBC input tileset file

  damienwoods

  committed
  2619445

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• rename 6-bit IBC input tileset file for designing random seqs

  damienwoods

  committed
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• prep of input files, generated random seqs

  damienwoods

  committed
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• added a few more files

  damienwoods

  committed
  22af7d7

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• claned up some input tileset files

  damienwoods

  committed
  a977f1b

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• added TODO.txt

  damienwoods

  committed
  e6eb160

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• todo

  damienwoods

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• adding seq set used for paper

  damienwoods

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Commits on Nov 3, 2018

• adds comments and print commands to atam2ssts.py

  damienwoods

  committed
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• code comments

  damienwoods

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• adding demo.py input file

  damienwoods

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• comments

  damienwoods

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• more comments

  damienwoods

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• nupack license

  damienwoods

  committed
  3877831

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• rm nupack license

  damienwoods

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• LICENSE viennaRNA

  damienwoods

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Commits on Nov 4, 2018

• updated install instructions

  damienwoods

  committed
  ecfffa6

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• moving viennaRNA param files

  damienwoods

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• stuff

  damienwoods

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• loos params file

  damienwoods

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• update TODO.txt

  damienwoods

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• comments

  damienwoods

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• comments

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• comments

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• comments

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• comments

  damienwoods

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• LICENSE changed to MIT

  erikwinfree

  committed
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• typos in example files

  erikwinfree

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  c9b6ab6

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• minor typo

  damienwoods

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Commits on Nov 5, 2018

• unique tile set and comments in atam2ssts

  erikwinfree

  committed
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• Merge branch 'master' of to.dna.caltech.edu:/research/git/sst_seq_design

  erikwinfree

  committed
  13b4f9d

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• fixing stupid typos and errors in comments

  damienwoods

  committed
  7f1ae77

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• small tilesets v num_processors bug

  damienwoods

  committed
  f4e8a43

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• rename variable

  damienwoods

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• pr block test only when tile names have ;s

  damienwoods

  committed
  e6e0f30

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• pr block test only when tile names have ;s

  damienwoods

  committed
  0ba9794

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• edited uniqueNxN demonstration files

  erikwinfree

  committed
  13885d8

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• Fixed issue where glues were only checked on N/W for existence, now also checked on S/E.

  pexatus

  committed
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Commits on Nov 6, 2018

• unique NxN comments updated

  erikwinfree

  committed
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Commits on Nov 7, 2018

• comments

  damienwoods

  committed
  4c13e32

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• Constantines patch to allow running from an arbitrary directory

  damienwoods

  committed
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• NUPACKHOME bug

  damienwoods

  committed
  68983e3

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• comments etc

  damienwoods

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Commits on Nov 8, 2018

• yeah

  damienwoods

  committed
  f3cb9bd

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• pfunc caching turned back ON

  damienwoods

  committed
  587d83b

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• deleted unused function tile_tile_heuristic_interaction(seq1, seq2, temperature)

  damienwoods

  committed
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• Added check for NUPACK and Vienna RNA so that user sees a helpful error message if either is not present.

  pexatus

  committed
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• Turned threading back on.

  pexatus

  committed
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• minor

  damienwoods

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• minor

  damienwoods

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Commits on Nov 9, 2018

• adding python3 nix shell

  damienwoods

  committed
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• Updated to work with python3 and moved python2 version into its own folder.

  dave-doty

  committed
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• Added new atam2ssts.py and moved lru_cache.py to python2 subdirectory.

  dave-doty

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Commits on Nov 10, 2018

• del comment

  damienwoods

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• I hate git?

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  damienwoods

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• nix shell for python3

  damienwoods

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• del script

  damienwoods

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• rm 37

  damienwoods

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• sequence analysis tool

  damienwoods

  committed
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• work towards getting analysis code to work for non-algrithmic tile sets

  damienwoods

  committed
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Commits on Nov 12, 2018

• Changed python3 version so it runs under python2 as well and deleted subfolder with python2-only version.

  dave-doty

  committed
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• analysis code

  damienwoods

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Commits on Nov 13, 2018

• improving plots

  damienwoods

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• improving plots

  damienwoods

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Commits on Jun 30, 2023

• Split on *at least* two spaces; fix nix and pin to 2019

  cgevans

  committed
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Commits on Oct 19, 2023

• disable viennarna unused packages, add gitignore

  cgevans

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