binder env

binder/postBuild

@@ -8,4 +8,4 @@ resources/demon_model/src/demon.cpp \
 -I/srv/conda/envs/notebook/include/ \
 -lm
 
-bash ../prepare-environments.sh
+bash prepare-environments.sh

binder/prepare-environments.sh

@@ -0,0 +1,39 @@
+###############################################################################
+#
+#   Create internal conda envs with all dependencies
+#
+#   AUTHOR: Maciej_Bak
+#   CONTACT: wsciekly.maciek@gmail.com
+#
+###############################################################################
+
+# exit at a first command that exits with a !=0 status
+set -eo pipefail
+
+$CONDA_PREFIX/bin/snakemake \
+    --snakefile="workflow/Snakefile" \
+    --configfile="tests/localtest/config-template.yml" \
+    --config workflow_repo_path="$PWD" workflow_analysis_outdir="$PWD/tests/localtest/output" \
+    --use-conda \
+    --conda-create-envs-only \
+    --conda-frontend=conda \
+    --cores 1 \
+    --nolock \
+    all
+
+for file in .snakemake/conda/*.yaml; do
+    if [ -f "$file" ]; then
+        if grep -q "name: warlock-r" "$file"; then
+            ENVPATH="${file%.yaml}"
+            break
+        fi
+    fi
+done
+
+eval "$(conda shell.bash hook)"
+conda deactivate
+conda activate $ENVPATH
+
+# strange error often appears, installation needs to be called twice
+Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)" || true
+Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)" || true