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ReproNim / containers

Containers "distribution" for reproducible neuroimaging
Apache License 2.0
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bids/hcppipelines does not expose entrypoint, when original docker container does #35

Open yarikoptic opened 4 years ago

yarikoptic commented 4 years ago 
(dev3) @beast:~/containers$ docker run -it --rm bids/hcppipelines --version
HCP Pielines BIDS App version v3.17.0-18

(dev3) @beast:~/containers$ singularity run images/bids/bids-hcppipelines--3.17.0-18.sing --version
GNU bash, version 4.3.30(1)-release (x86_64-pc-linux-gnu)
...

as you can see -- entry point is "bash" not the "app"... something is not right... probably because of the "custom" Singularity file -- we are not just pulling from docker into an image, we are creating a singularity image based on docker image and do not provide entry point whatsoever! but it is not clear then how it works for others, e.g.:

(dev3) amanelis@beast:~/containers$ singularity run images/bids/bids-mriqc--0.15.1.sing --help | head
usage: mriqc [-h] [--version]
             [--participant_label [PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]]
             [--session-id [SESSION_ID [SESSION_ID ...]]]
             [--run-id [RUN_ID [RUN_ID ...]]]
             [--task-id [TASK_ID [TASK_ID ...]]]
             [-m [MODALITIES [MODALITIES ...]]] [--dsname DSNAME]
             [-w WORK_DIR] [--verbose-reports] [--write-graph] [--dry-run]
             [--profile] [--use-plugin USE_PLUGIN] [--no-sub] [--email EMAIL]
             [-v] [--webapi-url WEBAPI_URL] [--webapi-port WEBAPI_PORT]
...

so the issue might be that container specific. Would be nice to automate tests for all bids apps to provide proper interface

yarikoptic commented 4 years ago

I believe it was due to singularity 2.6 used to build those images... I replicated locally on the bids example one and building with recent singularity "solved" the issue. So we would just need to rebuild them all I guess.