Merge pull request #3159 from mahesh-panchal/patch_conda_gitpod

Add --update-all flag to conda in Gitpod
nf-core · Sep 5, 2024 · d6bd738 · d6bd738
2 parents 308baef + 1c6b577
commit d6bd738
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -83,6 +83,7 @@
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
 - Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
 - fix syncing a pipeline from current directory ([#3143](https://github.com/nf-core/tools/pull/3143))
+- Patch gitpod conda setup to not use defaults channel ([#3159](https://github.com/nf-core/tools/pull/3159))
 
 ## Version updates
 

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
@@ -45,7 +45,7 @@ USER gitpod
 RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
-    conda install --quiet --yes --name base \
+    conda install --quiet --yes --update-all --name base \
     nextflow \
     nf-test \
     prettier \