installation in isolated (shared) directory
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Wolfgang Resch
Jun 28, 2016, 4:31:55 PM6/28/16
to Nextflow
Hi,
i have a question about installing nextflow into an isolated directory for multiple users. The applications on our cluster all reside in isolated, versioned directories like
/usr/local/apps/<app>/<version>
I can move the nextflow home dir from ~/.nextflow to shared space with NXF_HOME. However, it seems that nextflow modifies that directory at runtime so i'm not sure that's safe.
What is the preferred way of installing nextflow for multiple users? Or should users just install into their space (i.e. ~/.nextflow)?
Thanks,
Wolfgang
i have a question about installing nextflow into an isolated directory for multiple users. The applications on our cluster all reside in isolated, versioned directories like
/usr/local/apps/<app>/<version>
I can move the nextflow home dir from ~/.nextflow to shared space with NXF_HOME. However, it seems that nextflow modifies that directory at runtime so i'm not sure that's safe.
What is the preferred way of installing nextflow for multiple users? Or should users just install into their space (i.e. ~/.nextflow)?
Thanks,
Wolfgang
Wolfgang Resch
Jun 28, 2016, 4:35:23 PM6/28/16
to Nextflow
To answer my own question:
https://github.com/nextflow-io/nextflow/issues/186
should have searched issues/pull requests first i guess
https://github.com/nextflow-io/nextflow/issues/186
should have searched issues/pull requests first i guess
Paolo Di Tommaso
Jun 29, 2016, 1:59:11 PM6/29/16
to nextflow
Sorry for the late reply.
Using a shared path as NXF_HOME is fine (there's a file lock mechanism that prevent race conditions).
Cheers,
Paolo
Wolfgang Resch
Jun 29, 2016, 3:24:55 PM6/29/16
to Nextflow
Paolo,
one more question for clarification - our NFX_HOME is not writable by users. I've patched the wrapper to locate the cached classpath in the user's home. Are there any other situations where NFX_HOME needs to be writable? According to issue #186 this should be fine and my tests have been running without problems but i wanted to make sure that there aren't any conditions that my simple tests missed.
Best,
Wolfgang
one more question for clarification - our NFX_HOME is not writable by users. I've patched the wrapper to locate the cached classpath in the user's home. Are there any other situations where NFX_HOME needs to be writable? According to issue #186 this should be fine and my tests have been running without problems but i wanted to make sure that there aren't any conditions that my simple tests missed.
Best,
Wolfgang
Paolo Di Tommaso
Jun 29, 2016, 5:18:33 PM6/29/16
to nextflow
Well, nextflow stores in the NXF_HOME folder its own dependencies (jar files), the classpath cache files, and eventually pipeline projects downloaded from GitHub.
You may relocate these folder providing some environment variables but at that point would not make much sense to have the NXF_HOME in a not writable folder.
Cheers,
Paolo
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