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R2915/UniBe/singularity_pipeline/sample_pipeline.yaml
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sample_pipeline.yaml
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## Those will be used in default image name
name: CowSay
version: 1
## Those are purely informative at the moment
author: Alexander Kashev
author_org: UniBe
source:
## Extra substitutions for commands
## {image} is always available; in some contexts,
## To use literal {foo} in commands, double the braces: {{foo}}
substitutions:
text: "Moo"
## Bind specifications (souce:destination) to be passed to Singularity
binds:
- "/var/tmp:/var/tmp"
## Build instructions
build:
## Currently supported: bootstrap (will run sudo), pull, docker2singularity, custom
type: pull
## Size in MB; optional for pull
size: 512
## Extra options to pass to corresponding singularity build command; string
# options: "--some-option"
## For bootstrap, should be a local Singularity file
## For pull, shub / docker URL
## For docker2singularity, should be a local Dockerfile file
source: docker://chuanwen/cowsay
## Only for build type "custom".
## Additional substitutions: {source}, {size} (as "--size XXX") and {options}
# commands:
# - "singularity ..."
## Credentials for docker regsiteries
## Passed to singularity as environment variables
# credentials:
# username: foo
# password: bar
## Run instructions
run:
## An array of scripts to be executed in shell
## Preset substitutions:
## * {exec} for "singularity exec [-B <bind specification>] <image name>"
## * {run} for "singularity run [-B <bind specification>] <image name>"
## * {binds} for "[-B <bind specification>]"
## * {image} for container file name
## will be substituted; for literal {} (e.g. shell) use {{}}
commands:
- "{exec} /usr/games/cowsay {text} > cowsay.txt 2> /dev/null"
## Test instructions
test:
## Files required for testing; will run prepare_commands if any doesn't exist or --force specified
test_files:
- cowsay.md5
## An array of scripts to be executed in shell to prepare test_files
prepare_commands:
- "echo '548c5e52a6c1abc728a6b8e27f5abdd4 cowsay.txt' > cowsay.md5"
## An array of scripts to be executed in shell after running
validate_commands:
- "md5sum -c cowsay.md5"
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