looper

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sample_modifiers and project_modifiers in looper config file

14

I just got a bit tripped up with the command extra stuff, and realized: in `looper.cli` you have to use `command-extra`, but in `sample_modifiers.append` you use `command_extra`. This all makes...

nsheff

add support for bulker

1

adding support for bulker would be sweet. here's what we'd need to do: - [x] pipeline interface adds `bulker_crate` attribute - [ ] on `--bulker` flag, looper first runs a...

nsheff

when proceeding under local compute mode, looper should more gracefully handle keyboard interrupts, passing them on the to command it was running and allowing that command a few seconds to...

nsheff

Feature request: Skip pipeline location check

2

For running a pipeline within a container there is a need to skip the check for pipeline location verification as the pipeline of interest in hidden from looper's view within...

jpsmith5

Make suggested changes to `looper init`

4

- [x] remove pause. - [x] it currently erroneously complains if you give it a registry path. - [x] remove asking if the user would wish to follow tutorial (assume...

donaldcampbelljr

- [ ] Ensure docs are updated: https://github.com/pepkit/pepspec/pull/34

donaldcampbelljr

Remove printed dict at looper finish

1

Currently looper prints a statement in dict format for the commands/jobs submitted: ``` Looper finished Samples valid for job generation: 2 of 2 {'Pipestat compatible': False, 'Commands submitted': '2 of...

donaldcampbelljr

divvy list error

1

I can't seem to `divvy list` on a fresh install of looper 2.0.0a1: ``` divvy list Using divvy config: /home/nsheff/Dropbox/env/divvy_config/vole.yaml Traceback (most recent call last): File "/home/nsheff/.local/bin/divvy", line 8, in...

nsheff

Just keeping for myself a list of TODO things for looper docs update: - [ ] Howto: Run looper from PEPhub (this shows up in the hello world docs, but...

nsheff

how do to parallel-process files with looper locally -- lump them together, this will group several commands in one like:

1

> how do to parallel-process files with looper locally -> originally a divvy idea. > issue: 100 files -> divvy submits to cluster no problem, if local they will run...

donaldcampbelljr