fix ci

AngryMaciek · Mar 6, 2024 · 8838077 · 8838077
1 parent 00b0388
commit 8838077
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -56,6 +56,16 @@ jobs:
             -I/usr/share/miniconda3/envs/warlock/include
             -lm
 
+      - name: Prepare internal conda envs (Ubuntu)
+        shell: bash -l {0}
+        run: >
+            snakemake
+            --snakefile="workflow/Snakefile" \
+            --configfile="tests/test1/config-Ubuntu.yml" \
+            --use-conda \
+            --conda-create-envs-only \
+            all
+
       # Run the tests sequentially;
       # This could be parallelized in the CI but setting up conda
       # is expensive; its faster to run the tests one-by-one.

diff --git a/prepare-environments.sh b/prepare-environments.sh
@@ -34,5 +34,5 @@ conda deactivate
 conda activate $ENVPATH
 
 # strange error often appears, installation needs to be called twice
-Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)"
-Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)"
+Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)" || true
+Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)" || true