percyfal/ratatosk

Issues

• Use new luigi visualizer

  #49 opened 11 years ago by percyfal
  0

• Add java job runner

  #48 opened 11 years ago by percyfal
  0

• Syntax error in utils

  #47 opened 11 years ago by percyfal
  1

• Add support for merging vcf files in HaloPlex using CombineVariants

  #46 opened 12 years ago by percyfal
  0

• Merge sam files target list not unique

  #45 opened 12 years ago by percyfal
  0

• opt_to_dict in wrapper script squashes list options

  #42 opened 12 years ago by percyfal
  0

• Resolve option update order

  #43 opened 12 years ago by percyfal
  0

• global config not updated correctly

  #44 opened 12 years ago by percyfal
  0

• Configuration improvements

  #28 opened 12 years ago by percyfal
  2

• Implement pipes

  #35 opened 12 years ago by percyfal
  0

• Fix unit tests

  #24 opened 12 years ago by percyfal
  0

• Better SLURM/drmaa integration

  #40 opened 12 years ago by percyfal
  0

• Control number of threads / worker

  #39 opened 12 years ago by percyfal
  0

• Hadoop integration

  #38 opened 12 years ago by percyfal
  0

• Implement restarting functions

  #37 opened 12 years ago by percyfal
  0

• Clean up intermediate output

  #36 opened 12 years ago by percyfal
  0

• Task event timing

  #34 opened 12 years ago by percyfal
  0

• Central planner

  #33 opened 12 years ago by percyfal
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• Class validation of parent task

  #32 opened 12 years ago by percyfal
  0

• Target grouping in table output

  #31 opened 12 years ago by percyfal
  0

• Reimplement server.py, importing and subclassing only the necessary

  #30 opened 12 years ago by percyfal
  0

• Use cloudbiolinux references

  #29 opened 12 years ago by percyfal
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• Check for program versions

  #27 opened 12 years ago by percyfal
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• Dynamic calculation of target names

  #26 opened 12 years ago by percyfal
  0

• a.move(b) doesn't seem to work

  #25 opened 12 years ago by percyfal
  0

• Modify graph representation so only task name is shown

  #16 opened 12 years ago by percyfal
  0

• Have had weird problems with cutadapt. Using the '-o' flag should generate gzipped output. However, the job runner uses tmp files, which by default don't use 'gz'-suffix. A workaround for now is to add the suffix in CutadaptJobRunner. This works on Linux,

  #17 opened 12 years ago by percyfal
  0

• Currently they live in ratatosk.scilife, but the principle is clear. Add ratatosk.pipeline in which pipeline wrappers are put. In the main script then import different pre-defined pipelines so one could change them via the command line following luigi rul

  #18 opened 12 years ago by percyfal
  0

• Function opts() is inconsistent at present. Best is probably to init empty list and do a join on return.

  #22 opened 12 years ago by percyfal
  0

• Speaking of file suffixes, currently assume all fastq files are gzipped. EDIT: actually, this is a good thing. If a program can't take gzipped input, use pipes.

  #23 opened 12 years ago by percyfal
  0

• There is still a dependency on cement that should be removed

  #19 opened 12 years ago by percyfal
  0

• Fix path handling so relative paths can be used (see e.g. run method in fastq)

  #20 opened 12 years ago by percyfal
  0

• Make exe() use self.executable and remove exe() from all subclasses.

  #21 opened 12 years ago by percyfal
  0

• File suffixes and string substitutions in file names are hard-coded. Turning substitutions into options would maybe solve the issue of input parameter generation for tasks that are run s

  #15 opened 12 years ago by percyfal
  0

• File suffixes and string substitutions in file names are

  #13 opened 12 years ago by percyfal
  0

• Pickling states doesn't currently seem to work?

  #14 opened 12 years ago by percyfal
  0

• Command-line options should override settings in config file - not

  #12 opened 12 years ago by percyfal
  0

• Add general task config option `--target` to mimic Make behaviour

  #11 opened 12 years ago by percyfal
  0

• Implement dry run

  #10 opened 12 years ago by percyfal
  0

• Implement dry run

  #7 opened 12 years ago by percyfal
  0

• Implement dry run

  #8 opened 12 years ago by percyfal
  0

• Implement dry run

  #9 opened 12 years ago by percyfal
  0

• Try: modify repr(Task) for better visualization in graphs via a

  #2 opened 12 years ago by percyfal
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• Sort out dependencies between IndelRealigner and

  #3 opened 12 years ago by percyfal
  0

• Sort out dependencies between IndelRealigner and

  #4 opened 12 years ago by percyfal
  0

• Sort out dependencies between IndelRealigner and

  #5 opened 12 years ago by percyfal
  0

• Try: modify repr(Task) for better visualization in graphs via a

  #6 opened 12 years ago by percyfal
  0

• Make opts() and args() more consistent

  #1 opened 12 years ago by percyfal
  0