percyfal ratatosk issues

percyfal / ratatosk

Apache License 2.0

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issues

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Use new luigi visualizer

#49 percyfal opened 11 years ago
0
Add java job runner

#48 percyfal closed 11 years ago
0
Syntax error in utils

#47 percyfal closed 11 years ago
1
Add support for merging vcf files in HaloPlex using CombineVariants

#46 percyfal closed 11 years ago
0
Merge sam files target list not unique

#45 percyfal closed 11 years ago
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global config not updated correctly

#44 percyfal opened 11 years ago
0
Resolve option update order

#43 percyfal closed 11 years ago
0
opt_to_dict in wrapper script squashes list options

#42 percyfal closed 11 years ago
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Fixed check for 'settings' to be done before it's needed

#41 vals closed 11 years ago
0
Better SLURM/drmaa integration

#40 percyfal opened 11 years ago
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Control number of threads / worker

#39 percyfal opened 11 years ago
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Hadoop integration

#38 percyfal opened 11 years ago
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Implement restarting functions

#37 percyfal opened 11 years ago
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Clean up intermediate output

#36 percyfal opened 11 years ago
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Implement pipes

#35 percyfal closed 11 years ago
0
Task event timing

#34 percyfal opened 11 years ago
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Central planner

#33 percyfal opened 11 years ago
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Class validation of parent task

#32 percyfal opened 11 years ago
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Target grouping in table output

#31 percyfal opened 11 years ago
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Reimplement server.py, importing and subclassing only the necessary

#30 percyfal opened 11 years ago
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Use cloudbiolinux references

#29 percyfal opened 11 years ago
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Configuration improvements

#28 percyfal closed 11 years ago
2
Check for program versions

#27 percyfal opened 11 years ago
0
Dynamic calculation of target names

#26 percyfal opened 11 years ago
0
a.move(b) doesn't seem to work

#25 percyfal opened 11 years ago
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Fix unit tests

#24 percyfal closed 11 years ago
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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 percyfal closed 11 years ago
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Function opts() is inconsistent at present. Best is probably to init empty list and do a join on return.

#22 percyfal closed 11 years ago
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Make exe() use self.executable and remove exe() from all subclasses.

#21 percyfal closed 11 years ago
0
Fix path handling so relative paths can be used (see e.g. run method in fastq)

#20 percyfal closed 11 years ago
0
There is still a dependency on cement that should be removed

#19 percyfal closed 11 years ago
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 percyfal closed 11 years ago
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 percyfal closed 11 years ago
0
Modify graph representation so only task name is shown

#16 percyfal closed 11 years ago
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 percyfal closed 11 years ago
0
Pickling states doesn't currently seem to work?

#14 percyfal closed 11 years ago
0
File suffixes and string substitutions in file names are

#13 percyfal closed 11 years ago
0
Command-line options should override settings in config file - not

#12 percyfal closed 11 years ago
0
Add general task config option `--target` to mimic Make behaviour

#11 percyfal closed 11 years ago
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Implement dry run

#10 percyfal closed 11 years ago
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Implement dry run

#9 percyfal closed 11 years ago
0
Implement dry run

#8 percyfal closed 11 years ago
0
Implement dry run

#7 percyfal closed 11 years ago
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Try: modify repr(Task) for better visualization in graphs via a

#6 percyfal closed 11 years ago
0
Sort out dependencies between IndelRealigner and

#5 percyfal closed 11 years ago
0
Sort out dependencies between IndelRealigner and

#4 percyfal closed 11 years ago
0
Sort out dependencies between IndelRealigner and

#3 percyfal closed 11 years ago
0
Try: modify repr(Task) for better visualization in graphs via a

#2 percyfal closed 11 years ago
0
Make opts() and args() more consistent

#1 percyfal closed 11 years ago
0