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try to fix locale

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This commit is contained in:
Moritz E. Beber 2022-04-02 15:44:39 +02:00
parent 4e22bc9610
commit 41526e8a64
2 changed files with 9 additions and 1 deletions
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8
.github/workflows/ci.yml vendored
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@ -46,6 +46,14 @@ jobs:
wget -qO- get.nextflow.io | bash wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
- name: Show current locale
run: locale
- name: Set UTF-8 enabled locale
run: |
sudo locale-gen en_US.UTF-8
sudo update-locale LANG=en_US.UTF-8
- name: Run pipeline with test data - name: Run pipeline with test data
# TODO nf-core: You can customise CI pipeline run tests as required # TODO nf-core: You can customise CI pipeline run tests as required
# For example: adding multiple test runs with different parameters # For example: adding multiple test runs with different parameters

2
nextflow.config
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@ -159,7 +159,7 @@ if (!params.igenomes_ignore) {
env { env {
PYTHONNOUSERSITE = '1' PYTHONNOUSERSITE = '1'
PYTHONUTF8 = '1' // MetaPhlAn3 may fail with a UnicodeDecodeError if the locale is not set appropriately. // PYTHONUTF8 = '1' // MetaPhlAn3 may fail with a UnicodeDecodeError if the locale is not set appropriately.
R_PROFILE_USER = "/.Rprofile" R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron" R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia" JULIA_DEPOT_PATH = "/usr/local/share/julia"