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papaemmelab / toil_container

:whale: Toil + Docker and Singularity.
MIT License
9 stars 6 forks source link

Use --containall and user specific tmp directory for singularity call #15

Closed jsmedmar closed 6 years ago

jsmedmar commented 6 years ago

We need to do something like this, so that every container call uses a new tmp directory:

--workdir $TMP_DIR/${USER}_toi_container_openssl rand -hex 12\

Perhaps cleaning tmp afterwards?

We also need to use --containall so that $HOME is not mapped inside the container

juanesarango commented 6 years ago

Is this issue related with #16?

jsmedmar commented 6 years ago

yep, it seems you can resolve issues if you write resolves #id in the commit