Viash 0.2.1

Docker chown by default

New Release
Author

Viash Team

Published

September 11, 2020

Docker chown by default

Running a script using a Docker platform will now chown output files by default, as well as any temporary files. You can turn off this feature by specifying chown: false in the yaml of a Docker platform.

[NXF] Data references

Data references in Map form can now have values being lists. In other words, we can have multiple options which have one or more values.

viash ns build -P docker –parallel –setup

viash ns build has been greatly improved! You can automatically build the docker container by adding --setup to the command, as well as make the whole thing run in parallel using the --parallel or -l flag.

To build a docker container, you can run either of the following:

viash run -f path/to/config.yaml -P docker -- ---setup
viash build -f path/to/functionality.yaml -P docker -o target/docker/path/to --setup

Note that the first will only build the docker container, whereas the second will build the executable and then build the docker container.

To build a lot of them all at once, run:

viash ns build -P docker --parallel --setup

Custom order of platform requirements

You can now choose the order in which platform requirements are installed!

Before:

type: docker
image: rocker/tidyverse
target_image: "viash_test/r"
r:
  cran:
  - optparse
  github:
  - dynverse/dynutils@devel
  bioc:
  - limma
apt:
  packages:
  - libhdf5-serial-dev
docker:
  build_arg:
  - GITHUB_PAT="$GITHUB_PAT"
  run:
  - git clone --depth 1 https://github.com/data-intuitive/viash_docs.git && rm -r viash_docs/.git
↑ in which order will these three components be run? Who knows!

Now:

type: docker
image: rocker/tidyverse
target_image: "viash_test/r"
setup:
- type: docker
  build_arg:
  - GITHUB_PAT="$GITHUB_PAT"
- type: apt
  packages:
  - libhdf5-serial-dev
- type: r
  cran:
  - optparse
  - dynutils
  github:
  - rcannood/princurve@devel
  bioc:
  - limma
- type: docker
  run:
  - git clone --depth 1 https://github.com/data-intuitive/viash_docs.git && rm -r viash_docs/.git

This will ensure that the setup instructions are installed in the given order.

Full changelog:

NEW FEATURES

  • NXF: Data references in Map form can now have values being lists. In other words, we can have multiple options which have one or more values.
  • viash ns build: Added –parallel and –setup flag.
  • viash build`: Added –setup flag.
  • Allow changing the order of setup commands using the setup: variable.
  • Do not escape ${VIASH_...} elements in default values and descriptions!

MINOR CHANGES

  • Remove ---chown flag, move to platform.docker.chown; is set to true by default.
  • Perform chown during both run and test using a Docker platform.

BUG FIXES

  • Issue trying to parse positional arguments even when none is provided.