try catch for uninstalled files

ktmeaton · Jul 25, 2020 · e618979 · e618979
1 parent e2128d5
commit e618979
Showing 1 changed file with 29 additions and 25 deletions.
diff --git a/scripts/uninstall.sh b/scripts/uninstall.sh
@@ -10,37 +10,41 @@ REPO=${1:-"ktmeaton/plague-phylogeography"}
 # Number of uninstall steps
 STEPS="5"
 # Get plague-phylogeography conda name
-PHYLO_CONDA_ENV=`grep "name:" ~/.nextflow/assets/${REPO}/environment.yaml |  \
-                 cut -d " " -f 2`
-# Use default as backup if not found
-PHYLO_CONDA_ENV=${PHYLO_CONDA_ENV:-"plague-phylogeography-0.1.4dev"}
-# Get nf-core/eager conda name
-EAGER_CONDA_ENV=`grep "name:" ~/.nextflow/assets/nf-core/eager/environment.yaml |  \
-                cut -d " " -f 2`
-# Use default as backup if not found
-EAGER_CONDA_ENV=${EAGER_CONDA_ENV:-"nf-core-eager-2.2.0dev"}
-# Get nextstrain conda name
-NEXTSTRAIN_CONDA_ENV=`grep "name:" ~/.nextflow/assets/${REPO}/config/nextstrain.yaml |  \
-                 cut -d " " -f 2`
-# Use default as backup if not found
-NEXTSTRAIN_CONDA_ENV=${NEXTSTRAIN_CONDA_ENV:-"nextstrain-8.0.0"}
+PHYLO_CONDA_ENV="plague-phylogeography-0.1.4dev"
+if [[ `ls ~/.nextflow/assets/${REPO}/environment.yaml` ]]; then
+  PHYLO_CONDA_ENV=`grep "name:" ~/.nextflow/assets/${REPO}/environment.yaml |  \
+                   cut -d " " -f 2`
+fi
 
 
-# Remove the plague-phylogeography pipeline
+# Remove the plague-phylogeography pipeline and conda environment
 echo "[1/${STEPS}] Removing the plague-phylogeography nextflow pipeline."
-nextflow drop ${REPO}
-# Remove the plague-phylogeography conda env
-echo "[2/${STEPS}] Removing the plague-phylogeography conda environment."
-conda remove -n ${PHYLO_CONDA_ENV} --all
+if [[ `ls ~/.nextflow/assets/${REPO}/environment.yaml` ]]; then
+  PHYLO_CONDA_ENV=`grep "name:" ~/.nextflow/assets/${REPO}/environment.yaml |  \
+                   cut -d " " -f 2`
+  nextflow drop ${REPO}
+  echo "[2/${STEPS}] Removing the plague-phylogeography conda environment."
+  conda remove -n ${PHYLO_CONDA_ENV} --all
+else
+  echo "[2/${STEPS}] Removing the plague-phylogeography conda environment...Skip."
+fi
 
 # Remove the nfcore/eager pipeline
 echo "[3/${STEPS}] Removing the nf-core/eager nextflow pipeline."
-nextflow drop nf-core/eager
-# Remove the nfcore/eager conda env
-echo "[4/${STEPS}] Removing the nf-core/eager conda environment."
-conda remove -n ${EAGER_CONDA_ENV} --all
+if [[ `ls ~/.nextflow/assets/nf-core/eager/environment.yaml` ]]; then
+  EAGER_CONDA_ENV=`grep "name:" ~/.nextflow/assets/nf-core/eager/environment.yaml |  \
+                   cut -d " " -f 2`
+  nextflow drop nf-core/eager
+  echo "[4/${STEPS}] Removing the nf-core/eager conda environment."
+  conda remove -n ${EAGER_CONDA_ENV} --all
+else
+  echo "[4/${STEPS}] Removing the nf-core/eager conda environment...Skip."
+fi
 
 # Remove the nextstrain conda env
 echo "[5/${STEPS}] Removing the nextstrain conda environment."
-echo "conda remove -n ${NEXTSTRAIN_CONDA_ENV} --all"
-conda remove -n ${NEXTSTRAIN_CONDA_ENV} --all
+if [[ `ls ~/.nextflow/assets/${REPO}/config/nextstrain.yaml` ]]; then
+  NEXTSTRAIN_CONDA_ENV=`grep "name:" ~/.nextflow/assets/${REPO}/config/nextstrain.yaml |  \
+                   cut -d " " -f 2`
+  conda remove -n ${NEXTSTRAIN_CONDA_ENV} --all
+fi