Code

Accessory binary tree#155

Code

Merged

andrewjpage merged 46 commits intosanger-pathogens:mastersanger-pathogens/Roary:masterfrom andrewjpage:accessory_binary_treeandrewjpage/Roary:accessory_binary_treeCopy head branch name to clipboardJun 22, 2015

+1,699-653

Commits

Commits on Jun 15, 2015

• add sudo to the install

  andrewjpage

  committed
  3fc550e

• initial binary tree

  andrewjpage

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  1ee132f

• remove dumper statement

  andrewjpage

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  2f6be5d

• Merge branch 'accessory_tree' into core_gene_lookup

  Show description for 070ee34
  andrewjpage

  committed
  070ee34

• move exec checker to role

  andrewjpage

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  8fbc747

• create binary fasta file

  andrewjpage

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  c496b28

Commits on Jun 16, 2015

• kraken preload

  andrewjpage

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  f27990f

• readme versions tested against

  andrewjpage

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  6334215

• fasttree binaries

  andrewjpage

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  436485e

• run fasttree in post analysis

  andrewjpage

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  414fa6f

• test against more versions of perl

  andrewjpage

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  3acbe37

• strict upper limit on number of genes to look at in accessory genome

  andrewjpage

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  9b1fa7c

• allow for using multicpus to do cd-hit in post analysis

  andrewjpage

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  f4d0f0f

• large gene accessory test

  andrewjpage

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  60cde19

• create sample weights

  andrewjpage

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  11d50cc

Commits on Jun 17, 2015

• try to do travis builds on containers

  andrewjpage

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  6898229

• dont run perl dependancy tests

  andrewjpage

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  e757ec0

• dont use sudo for travis

  andrewjpage

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  85067d6

• cpanm notest

  andrewjpage

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  0b3abae

• fix blast download directory and mcl path

  andrewjpage

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  9769f84

• remove unneeded test plot files

  andrewjpage

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  0e9315e

• mcxdeblast run by perl exec directly since shbang assumes perl in particular location

  andrewjpage

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  a932491

• rename sample weights variable

  andrewjpage

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  df989bc

• tidy

  andrewjpage

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  25d21c0

• weight graph by clusters

  andrewjpage

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  0811c46

• fix test with looser clustering

  andrewjpage

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  5ac0417

• instructions for centos

  andrewjpage

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• more centos instructions

  andrewjpage

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  f8cb68a

• graph nodes are undirected so mask out

  andrewjpage

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  2fc9afa

• sort core genes by file name so tests pass consistently

  andrewjpage

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  5dbdc59

Commits on Jun 18, 2015

• cache dependancy build directories

  andrewjpage

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  8e7b840

• check if build directories exist for travis

  andrewjpage

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  b8101d4

• check for binaries before rebuilding

  andrewjpage

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  b87583b

• order genes by clusters

  andrewjpage

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  4e8f740

• allow for more logging

  andrewjpage

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  08362d4

• more logging

  andrewjpage

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  899128f

• print out contents of bedtools dir

  andrewjpage

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  196a256

Commits on Jun 19, 2015

• take largest cluster then sort predictably by name

  andrewjpage

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  ef21be6

• heatmap of colours

  andrewjpage

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  22d81df

• array ref

  andrewjpage

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  66d948c

• reuntar

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  9b3283c

• colour blocks as heatmap

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  921949b

• travis debug

  andrewjpage

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  e8a1a5a

• change back to build directory

  andrewjpage

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  3f66d55

• check if blast directory avaialble

  andrewjpage

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  aa5dcbb

• tidy

  andrewjpage

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  08b3945