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Isolate R to look for packages in container only #586

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Mar 16, 2020
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,10 @@

## v1.10dev

### Template

* Isolate R library paths to those in container [#541](https://github.com/nf-core/tools/issues/541)

### Linting

* Refactored PR branch tests to be a little clearer.
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Expand Up @@ -11,3 +11,7 @@ ENV PATH /opt/conda/envs/{{ cookiecutter.name_noslash }}-{{ cookiecutter.version

# Dump the details of the installed packages to a file for posterity
RUN conda env export --name {{ cookiecutter.name_noslash }}-{{ cookiecutter.version }} > {{ cookiecutter.name_noslash }}-{{ cookiecutter.version }}.yml

# Instruct R processes to use these empty files instead of clashing with a local version
RUN touch .Rprofile
RUN touch .Renviron
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Expand Up @@ -78,9 +78,11 @@ if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
}

// Export this variable to prevent local Python libraries from conflicting with those in the container
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}

// Capture exit codes from upstream processes when piping
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