New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Nextflow launch script: improving search for JAVA_CMD #4830
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…n installation Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
✅ Deploy Preview for nextflow-docs-staging canceled.
|
I would not bind so strictly to SDKman. It would be preferable just report that |
… detailed Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Have a look at this iteration:
|
pditommaso
reviewed
Mar 20, 2024
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
pditommaso
reviewed
Mar 20, 2024
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
pditommaso
approved these changes
Mar 20, 2024
@marcodelapierre thanks! |
nschan
pushed a commit
to nschan/nextflow
that referenced
this pull request
Apr 3, 2024
Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Signed-off-by: Niklas Schandry <niklas@bio.lmu.de>
nschan
pushed a commit
to nschan/nextflow
that referenced
this pull request
Apr 3, 2024
Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Signed-off-by: Niklas Schandry <niklas@bio.lmu.de>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR aims to address #4653, and as such applies a few small edits to the main
nextflow
script:JAVA_CMD=java
/usr/libexec/java_home
is found but not working, silently fallback toJAVA_CMD=java
, for a less confusing error (I think that path search only works on a Mac and if a system Java has been installed)