Code

Parallel blast#280

Code

Open

necrolyte2 wants to merge 18 commits intodevVDBWRAIR/pathdiscov:devfrom parallel_blastVDBWRAIR/pathdiscov:parallel_blastCopy head branch name to clipboard

+169-51

Commits

Commits on Aug 14, 2015

• parallel blast beginnings. Will be a drop in replacment for par_block_blast.pl

  necrolyte2

  committed
  7e9cae0

• merging test_built.py

  necrolyte2

  committed
  94ccd51

Commits on Aug 17, 2015

• Added GNU Parallel install to pavement

  necrolyte2

  committed
  1341483

• ready to test blasting in parallel. Still need to figure out how to handle diamond

  necrolyte2

  committed
  66bcbf8

• Hopefully fixed implementation of parallel_blast. Will run tomorrow to verify it runs functionally

  necrolyte2

  committed
  2490afa

Commits on Aug 18, 2015

• distinquishes between single node and multi node jobs via PE_HOSTFILE or PBS_NODEFILE entries

  necrolyte2

  committed
  b19d34c

Commits on Aug 19, 2015

• This seems to be the correct variation of options and arguments. Took way too much time debugging shell things

  necrolyte2

  committed
  815fc66

• Blast is working. Now to parallelize diamond

  necrolyte2

  committed
  61aa85a

• Diamond seems to be implemented now although it keeps gobbling up all my ram and being killed so will need to test some other way

  necrolyte2

  committed
  f5cfc1f

Commits on Aug 20, 2015

• Now detects if blastn or blastp/blastx are being run and excludes the -task option

  necrolyte2

  committed
  c0bb5dd

Commits on Aug 21, 2015

• Addressing #281. Pipeline now downloads diamond from github. Shows what version of diamond is used

  necrolyte2

  committed
  22cef86

• Preparing for bio_pieces parallel_blast

  necrolyte2

  committed
  3487ea8

Commits on Aug 24, 2015

• iterative blast tests now run step1 if needed. Fixed bug with iter blast phylo where orf_filter was being incorrectly called for contig

  necrolyte2

  committed
  c510483

• Touched up diamond db buliding docs. Closes #281

  necrolyte2

  committed
  8baab70

Commits on Sep 2, 2015

• Fixes a bug where orf_filter output fasta file was not being used to extract reads from

  necrolyte2

  committed
  205b9a4

• parallel_blast injection for pipeline instead of par_block_blast

  necrolyte2

  committed
  5ef8d78

Commits on Sep 3, 2015

• deltat now will print command that it is for

  necrolyte2

  committed
  8a971a2

• Fixes a bug where blastx was ignored. Fixes #283

  necrolyte2

  committed
  fb28016