Update/nextflow container

.travis.yml

@@ -27,9 +27,15 @@ before_deploy:
   - bash _scripts/configure-deploy.sh
 
 deploy:
-  provider: script
-  script: bash _scripts/deploy.sh
-  skip_cleanup: true
-  on:
-    repo: aws-samples/aws-genomics-workflows
-    branch: master
+  - provider: script
+    script: bash _scripts/deploy.sh production
+    skip_cleanup: true
+    on:
+      repo: aws-samples/aws-genomics-workflows
+      branch: release
+  - provider: script
+    script: bash _scripts/deploy.sh test
+    skip_cleanup: true
+    on:
+      repo: aws-samples/aws-genomics-workflows
+      branch: master

README.md

@@ -11,7 +11,7 @@ The documentation is built using mkdocs.
 Install dependencies:
 
 ```bash
-$ conda env create --file enviroment.yaml
+$ conda env create --file environment.yaml
 ```
 
 This will create a `conda` environment called `mkdocs`

_scripts/deploy.sh

@@ -5,30 +5,74 @@ set -e
 bash _scripts/make-artifacts.sh
 mkdocs build
 
+ASSET_BUCKET=s3://aws-genomics-workflows
+ASSET_STAGE=${1:-production}
 
-echo "publishing artifacts:"
-aws s3 sync \
-    --profile asset-publisher \
-    --acl public-read \
-    --delete \
-    ./artifacts \
-    s3://aws-genomics-workflows/artifacts
 
+function s3_uri() {
+    BUCKET=$1
+    shift
 
-echo "publishing templates:"
-aws s3 sync \
-    --profile asset-publisher \
-    --acl public-read \
-    --delete \
-    --metadata commit=$(git rev-parse HEAD) \
-    ./src/templates \
-    s3://aws-genomics-workflows/templates
+    IFS=""
+    PREFIX_PARTS=("$@")
+    PREFIX_PARTS=(${PREFIX_PARTS[@]})
+    PREFIX=$(printf '/%s' "${PREFIX_PARTS[@]%/}")
+
+    echo "${BUCKET%/}/${PREFIX:1}"
+}
 
 
-echo "publishing site"
-aws s3 sync \
-    --acl public-read \
-    --delete \
-    ./site \
-    s3://docs.opendata.aws/genomics-workflows
+function artifacts() {
+    S3_URI=$(s3_uri $ASSET_BUCKET $ASSET_STAGE_PATH "artifacts")
 
+    echo "publishing artifacts: $S3_URI"
+    aws s3 sync \
+        --profile asset-publisher \
+        --acl public-read \
+        --delete \
+        ./artifacts \
+        $S3_URI
+}
+
+function templates() {
+    S3_URI=$(s3_uri $ASSET_BUCKET $ASSET_STAGE_PATH "templates")
+
+    echo "publishing templates: $S3_URI"
+    aws s3 sync \
+        --profile asset-publisher \
+        --acl public-read \
+        --delete \
+        --metadata commit=$(git rev-parse HEAD) \
+        ./src/templates \
+        $S3_URI
+}
+
+function site() {
+    echo "publishing site"
+    aws s3 sync \
+        --acl public-read \
+        --delete \
+        ./site \
+        s3://docs.opendata.aws/genomics-workflows
+}
+
+function all() {
+    artifacts
+    templates
+    site
+}
+
+case $STAGE in
+    production)
+        ASSET_STAGE_PATH=""
+        all
+        ;;
+    test)
+        ASSET_STAGE_PATH="test"
+        artifacts
+        templates
+        ;;
+    *)
+        echo "unsupported staging level"
+        exit 1
+esac