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backend { | |
# Override the default backend. | |
#default = "LocalWithDocker" | |
# The list of providers. | |
providers { | |
# The local provider is included by default in the reference.conf. This is an example. | |
# Define a new backend provider. | |
LocalWithDocker { | |
# The actor that runs the backend. In this case, it's the Shared File System (SFS) ConfigBackend. | |
actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory" | |
# The backend custom configuration. | |
config { | |
# Optional limits on the number of concurrent jobs | |
#concurrent-job-limit = 5 | |
# The list of possible runtime custom attributes. | |
runtime-attributes = """ | |
String? docker | |
String? docker_user | |
String? cpu | |
String? memory_mb | |
""" | |
# Submit string when there is no "docker" runtime attribute. | |
submit = "/usr/bin/env bash ${script}" | |
# Submit string when there is a "docker" runtime attribute. | |
submit-docker = """ | |
docker run \ | |
--rm -i \ | |
${"--cpus=" + cpu} \ | |
${"--memory=" + memory_mb + "m" } \ | |
${"--user " + docker_user} \ | |
--entrypoint ${job_shell} \ | |
-v ${cwd}:${docker_cwd} \ | |
${docker} ${script} | |
""" | |
# Root directory where Cromwell writes job results. This directory must be | |
# visible and writeable by the Cromwell process as well as the jobs that Cromwell | |
# launches. | |
root = "cromwell-executions" | |
# Root directory where Cromwell writes job results in the container. This value | |
# can be used to specify where the execution folder is mounted in the container. | |
# it is used for the construction of the docker_cwd string in the submit-docker | |
# value above. | |
dockerRoot = "/cromwell-executions" | |
# File system configuration. | |
filesystems { | |
# For SFS backends, the "local" configuration specifies how files are handled. | |
local { | |
# Try to hard link (ln), then soft-link (ln -s), and if both fail, then copy the files. | |
localization: [ | |
"hard-link", "soft-link", "copy" | |
] | |
# Call caching strategies | |
caching { | |
# When copying a cached result, what type of file duplication should occur. Attempted in the order listed below: | |
duplication-strategy: [ | |
"hard-link", "soft-link", "copy" | |
] | |
# Possible values: file, path | |
# "file" will compute an md5 hash of the file content. | |
# "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link", | |
# in order to allow for the original file path to be hashed. | |
hashing-strategy: "file" | |
# When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash. | |
# If false or the md5 does not exist, will proceed with the above-defined hashing strategy. | |
check-sibling-md5: false | |
} | |
} | |
} | |
# The defaults for runtime attributes if not provided. | |
default-runtime-attributes { | |
failOnStderr: false | |
continueOnReturnCode: 0 | |
cpu: 1 | |
memory: "4 MB" | |
} | |
} | |
} | |
} | |
} |
yes! thank you for noticing -- fixed
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Is there supposed to be a
\
at the end of line 37?