From d4658db6562002c28a8073c4aa0262efb3e44833 Mon Sep 17 00:00:00 2001
From: Andrew Crabb <crabba@amazon.com>
Date: Fri, 19 Mar 2021 19:49:38 -0400
Subject: [PATCH 1/5] Use absolute paths, add verbose flag

---
 _scripts/deploy.sh    |   6 +--
 _scripts/make-dist.sh | 115 ++++++++++++++++++++++++++++--------------
 2 files changed, 81 insertions(+), 40 deletions(-)
 mode change 100644 => 100755 _scripts/deploy.sh

diff --git a/_scripts/deploy.sh b/_scripts/deploy.sh
old mode 100644
new mode 100755
index 199455dd4..a0644e662
--- a/_scripts/deploy.sh
+++ b/_scripts/deploy.sh
@@ -2,9 +2,10 @@
 
 set -e
 
-bash _scripts/make-dist.sh
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+bash ${DIR}/make-dist.sh
 mkdocs build
-
+exit
 SITE_BUCKET=s3://docs.opendata.aws/genomics-workflows
 ASSET_BUCKET=s3://aws-genomics-workflows
 ASSET_STAGE=test
@@ -44,7 +45,6 @@ while (( "$#" )); do
             ;;
     esac
 done
-
 eval set -- "$PARAMS"
 
 ASSET_STAGE=${1:-$ASSET_STAGE}
diff --git a/_scripts/make-dist.sh b/_scripts/make-dist.sh
index d32539adb..015fc9f81 100755
--- a/_scripts/make-dist.sh
+++ b/_scripts/make-dist.sh
@@ -1,5 +1,39 @@
 #!/bin/bash
 
+# make-dist.sh: Create distribution artifacts
+# This script is expected to be in a subdirectory of the top-level directory
+# It accesses the subdirectory 'src', and creates a subdirectory 'dist', in the top-level directory:
+#    .
+#    |-_scripts
+#    |---make-dist.sh
+#    |-dist
+#    |-src
+
+
+VERBOSE=""
+PARAMS=""
+while (( "$#" )); do
+    case "$1" in
+        --verbose)
+            VERBOSE='-v'
+            shift
+            ;;
+        --) # end optional argument parsing
+            shift
+            break
+            ;;
+        -*|--*=)
+            echo "Error: unsupported argument $1" >&2
+            exit 1
+            ;;
+        *) # positional agruments
+            PARAMS="$PARAMS $1"
+            shift
+            ;;
+    esac
+done
+eval set -- "$PARAMS"
+
 echo "checking for dependencies"
 
 DEPENDENCIES=$(cat <<EOF
@@ -25,12 +59,14 @@ done
 set -e
 
 CWD=`pwd`
-SOURCE_PATH=${CWD}/src
-DIST_PATH=${CWD}/dist
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+INSTALL_DIR=`dirname $DIR`
+SOURCE_PATH=$INSTALL_DIR/src
+DIST_PATH=$INSTALL_DIR/dist
 
-TEMP_PATH=${DIST_PATH}/tmp
-ARTIFACT_PATH=${DIST_PATH}/artifacts
-TEMPLATES_PATH=${DIST_PATH}/templates
+TEMP_PATH=$DIST_PATH/tmp
+ARTIFACT_PATH=$DIST_PATH/artifacts
+TEMPLATES_PATH=$DIST_PATH/templates
 
 if [ ! -d $DIST_PATH ]; then
     mkdir -p $DIST_PATH
@@ -39,11 +75,10 @@ fi
 cd $DIST_PATH
 
 # clean up previous dist build
-echo "removing previous dist"
-rm -rf ./*
+echo "removing previous dist in $DIST_PATH"
+[ ! -z $DIR ] && rm -rf $DIST_PATH/*
 
-for d in $TEMP_PATH $ARTIFACT_PATH $TEMPLATES_PATH;
-do
+for d in $TEMP_PATH $ARTIFACT_PATH $TEMPLATES_PATH; do
     if [ ! -d $d ];
     then
         echo "creating $d"
@@ -55,69 +90,75 @@ done
 # combines the latest release of amazon-ebs-autoscale with compatibility shim
 # scripts in ./ebs-autoscale/
 echo "packaging amazon-ebs-autoscale"
-cd ${TEMP_PATH}
+cd $TEMP_PATH
 
 EBS_AUTOSCALE_VERSION=$(curl --silent "https://api.github.com/repos/awslabs/amazon-ebs-autoscale/releases/latest" | jq -r .tag_name)
 curl --silent -L \
     "https://github.com/awslabs/amazon-ebs-autoscale/archive/${EBS_AUTOSCALE_VERSION}.tar.gz" \
     -o ./amazon-ebs-autoscale.tar.gz 
 
-tar -xzvf ./amazon-ebs-autoscale.tar.gz
+echo "copying `tar -tzf ./amazon-ebs-autoscale.tar.gz | wc -l` files from ebs-autoscale $EBS_AUTOSCALE_VERSION into tmp/amazon-ebs-autoscale/"
+tar $VERBOSE -xzf ./amazon-ebs-autoscale.tar.gz
 mv ./amazon-ebs-autoscale*/ ./amazon-ebs-autoscale
 echo $EBS_AUTOSCALE_VERSION > ./amazon-ebs-autoscale/VERSION
 
-cp -Rfv $SOURCE_PATH/ebs-autoscale .
-cp -Rfv ./amazon-ebs-autoscale/* ./ebs-autoscale/
-
-tar -czvf ${ARTIFACT_PATH}/aws-ebs-autoscale.tgz ./ebs-autoscale/
+echo "copying src/ebs-autoscale with `find $SOURCE_PATH/ebs-autoscale/ -type f | wc -l` files to tmp/"
+cp $VERBOSE -Rf $SOURCE_PATH/ebs-autoscale .
+echo "copying `find amazon-ebs-autoscale -type f | wc -l` files from tmp/amazon-ebs-autoscale/ to tmp/ebs-autoscale/"
+cp $VERBOSE -Rf ./amazon-ebs-autoscale/* ./ebs-autoscale/
+echo "creating artifacts/aws-ebs-autoscale.tgz with `find ./ebs-autoscale/ -type f | wc -l` files from tmp/ebs-autoscale/"
+tar $VERBOSE -czf $ARTIFACT_PATH/aws-ebs-autoscale.tgz ./ebs-autoscale/
 
 # add a copy of the release tarball for naming consistency
-tar -czvf ${ARTIFACT_PATH}/amazon-ebs-autoscale.tgz ./amazon-ebs-autoscale
+echo "creating artifacts/amazon-ebs-autoscale.tgz with `find ./amazon-ebs-autoscale/ -type f | wc -l` files from tmp/amazon-ebs-autoscale/"
+tar $VERBOSE -czf $ARTIFACT_PATH/amazon-ebs-autoscale.tgz ./amazon-ebs-autoscale
 
 # add a retrieval script
-cp -vf ${SOURCE_PATH}/ebs-autoscale/get-amazon-ebs-autoscale.sh ${ARTIFACT_PATH}
+cp $VERBOSE -f $SOURCE_PATH/ebs-autoscale/get-amazon-ebs-autoscale.sh $ARTIFACT_PATH
 
 # package crhelper lambda(s)
-cd ${SOURCE_PATH}/lambda
+cd $SOURCE_PATH/lambda
 for fn in `ls .`; do
     echo "packaging crhelper lambda $fn"
-    mkdir -p ${TEMP_PATH}/lambda/$fn
-    cp -Rv ${SOURCE_PATH}/lambda/$fn/. ${TEMP_PATH}/lambda/$fn
-
-    cd ${TEMP_PATH}/lambda/$fn
-    pip install -t . -r requirements.txt
-    zip -r -v $ARTIFACT_PATH/lambda-$fn.zip .
+    mkdir -p $TEMP_PATH/lambda/$fn
+    cp $VERBOSE -R $SOURCE_PATH/lambda/$fn/. $TEMP_PATH/lambda/$fn
+
+    cd $TEMP_PATH/lambda/$fn
+    [ -z $VERBOSE ] && P_QUIET='--quiet' || P_QUIET=''
+    pip $P_QUIET install -t . -r requirements.txt
+    echo "creating artifacts/lambda-${fn}.zip with `find . -type f | wc -l` files"
+    [ -z $VERBOSE ] && Z_QUIET='-q' || Z_QUIET=''
+    zip $Z_QUIET -r $ARTIFACT_PATH/lambda-$fn.zip .
 done
 
-
 # package ecs-additions
 echo "packaging ecs-additions"
 
-cd ${TEMP_PATH}
-mkdir -p ${TEMP_PATH}/ecs-additions
-cp -Rv ${SOURCE_PATH}/ecs-additions/. ${TEMP_PATH}/ecs-additions
+cd $TEMP_PATH
+mkdir -p $TEMP_PATH/ecs-additions
+cp $VERBOSE -R $SOURCE_PATH/ecs-additions/. $TEMP_PATH/ecs-additions
 
 # add the amazon-ebs-autoscale retrieval script to additions
-cp -v ${SOURCE_PATH}/ebs-autoscale/get-amazon-ebs-autoscale.sh ${TEMP_PATH}/ecs-additions
+cp $VERBOSE $SOURCE_PATH/ebs-autoscale/get-amazon-ebs-autoscale.sh $TEMP_PATH/ecs-additions
 
 # keep tarball for backwards compatibilty
-cd ${TEMP_PATH}
-tar -czvf ${ARTIFACT_PATH}/aws-ecs-additions.tgz ./ecs-additions/
+cd $TEMP_PATH
+tar $VERBOSE -czf $ARTIFACT_PATH/aws-ecs-additions.tgz ./ecs-additions/
 
 # zip file for codecommit repo
-cd ${TEMP_PATH}/ecs-additions/
-zip -r -v ${ARTIFACT_PATH}/aws-ecs-additions.zip ./*
+cd $TEMP_PATH/ecs-additions/
+zip $Z_QUIET -r $ARTIFACT_PATH/aws-ecs-additions.zip ./*
 
 
 # package container code
-echo "packaging container definitions"
+echo "packaging container definitions with `find $SOURCE_PATH/containers -type f | wc -l` files"
 cd $SOURCE_PATH/containers
-zip -r -v $ARTIFACT_PATH/containers.zip ./*
+zip $Z_QUIET -r $ARTIFACT_PATH/containers.zip ./*
 
 
 # add templates to dist
-echo "copying cloudformation templates"
-cp -Rv $SOURCE_PATH/templates/. $TEMPLATES_PATH
+echo "copying `find $SOURCE_PATH/templates/ -type f | wc -l` cloudformation templates"
+cp $VERBOSE -R $SOURCE_PATH/templates/. $TEMPLATES_PATH
 
 
 # cleanup

From 984b311256803fb839137f0951b92a603948ad84 Mon Sep 17 00:00:00 2001
From: Andrew Crabb <crabba@amazon.com>
Date: Sun, 21 Mar 2021 19:32:38 -0400
Subject: [PATCH 2/5] Add verbose flag, use absolute paths

---
 _scripts/deploy.sh    | 37 ++++++++++++++++++++++++++++++-------
 _scripts/make-dist.sh | 18 +++++++++---------
 2 files changed, 39 insertions(+), 16 deletions(-)

diff --git a/_scripts/deploy.sh b/_scripts/deploy.sh
index a0644e662..e03003e45 100755
--- a/_scripts/deploy.sh
+++ b/_scripts/deploy.sh
@@ -1,17 +1,16 @@
 #!/bin/bash
 
+# deploy.sh: Create and deploy distribution artifacts
+
 set -e
 
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
-bash ${DIR}/make-dist.sh
-mkdocs build
-exit
 SITE_BUCKET=s3://docs.opendata.aws/genomics-workflows
 ASSET_BUCKET=s3://aws-genomics-workflows
 ASSET_STAGE=test
 ASSET_PROFILE=asset-publisher
 DEPLOY_REGION=us-east-1
 
+VERBOSE=''
 PARAMS=""
 while (( "$#" )); do
     case "$1" in
@@ -31,6 +30,10 @@ while (( "$#" )); do
             DEPLOY_REGION=$2
             shift 2
             ;;
+        --verbose)
+            VERBOSE='--verbose'
+            shift
+            ;;
         --) # end optional argument parsing
             shift
             break
@@ -49,6 +52,9 @@ eval set -- "$PARAMS"
 
 ASSET_STAGE=${1:-$ASSET_STAGE}
 
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+bash ${DIR}/make-dist.sh $VERBOSE
+
 function s3_uri() {
     BUCKET=$1
     shift
@@ -68,20 +74,23 @@ function s3_sync() {
     echo "syncing ..."
     echo "   from: $source"
     echo "     to: $destination"
-    aws s3 sync \
+    cmd="aws s3 sync \
         --profile $ASSET_PROFILE \
         --region $DEPLOY_REGION \
-        --acl public-read \
         --delete \
         --metadata commit=$(git rev-parse HEAD) \
         $source \
-        $destination
+        $destination"
+    echo $cmd
+    eval $cmd
+    exit
 }
 
 function publish() {
     local source=$1
     local destination=$2
 
+    echo "publish(source: $source, destintation: $destination)"
     if [[ $USE_RELEASE_TAG && ! -z "$TRAVIS_TAG" ]]; then
         # create explicit pinned versions "latest" and TRAVIS_TAG
         # pin the TRAVIS_TAG first, since the files are modified inplace
@@ -149,6 +158,13 @@ function templates() {
 
 
 function site() {
+    echo "building site"
+    if [[ ! `command -v mkdocs` ]]; then
+        echo "requirement mkdocs not found. aborting"
+        exit 1
+    fi
+    mkdocs build
+
     echo "publishing site"
     aws s3 sync \
         --region $DEPLOY_REGION \
@@ -166,6 +182,13 @@ function all() {
     site
 }
 
+# Add 's3://' when missing from bucket names
+for bucketname in ASSET_BUCKET SITE_BUCKET; do
+    if [[ ! $(echo ${!bucketname} | grep 's3://') ]]; then
+        newname="s3://${!bucketname}";
+        eval $bucketname=\$newname;
+    fi
+done
 
 echo "DEPLOYMENT STAGE: $ASSET_STAGE"
 case $ASSET_STAGE in
diff --git a/_scripts/make-dist.sh b/_scripts/make-dist.sh
index 015fc9f81..d871adb82 100755
--- a/_scripts/make-dist.sh
+++ b/_scripts/make-dist.sh
@@ -60,7 +60,7 @@ set -e
 
 CWD=`pwd`
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
-INSTALL_DIR=`dirname $DIR`
+INSTALL_DIR=$(dirname $DIR)
 SOURCE_PATH=$INSTALL_DIR/src
 DIST_PATH=$INSTALL_DIR/dist
 
@@ -97,20 +97,20 @@ curl --silent -L \
     "https://github.com/awslabs/amazon-ebs-autoscale/archive/${EBS_AUTOSCALE_VERSION}.tar.gz" \
     -o ./amazon-ebs-autoscale.tar.gz 
 
-echo "copying `tar -tzf ./amazon-ebs-autoscale.tar.gz | wc -l` files from ebs-autoscale $EBS_AUTOSCALE_VERSION into tmp/amazon-ebs-autoscale/"
+echo "copying $(tar -tzf ./amazon-ebs-autoscale.tar.gz | wc -l) files from ebs-autoscale $EBS_AUTOSCALE_VERSION into tmp/amazon-ebs-autoscale/"
 tar $VERBOSE -xzf ./amazon-ebs-autoscale.tar.gz
 mv ./amazon-ebs-autoscale*/ ./amazon-ebs-autoscale
 echo $EBS_AUTOSCALE_VERSION > ./amazon-ebs-autoscale/VERSION
 
-echo "copying src/ebs-autoscale with `find $SOURCE_PATH/ebs-autoscale/ -type f | wc -l` files to tmp/"
+echo "copying src/ebs-autoscale with $(find $SOURCE_PATH/ebs-autoscale/ -type f | wc -l) files to tmp/"
 cp $VERBOSE -Rf $SOURCE_PATH/ebs-autoscale .
-echo "copying `find amazon-ebs-autoscale -type f | wc -l` files from tmp/amazon-ebs-autoscale/ to tmp/ebs-autoscale/"
+echo "copying $(find amazon-ebs-autoscale -type f | wc -l) files from tmp/amazon-ebs-autoscale/ to tmp/ebs-autoscale/"
 cp $VERBOSE -Rf ./amazon-ebs-autoscale/* ./ebs-autoscale/
-echo "creating artifacts/aws-ebs-autoscale.tgz with `find ./ebs-autoscale/ -type f | wc -l` files from tmp/ebs-autoscale/"
+echo "creating artifacts/aws-ebs-autoscale.tgz with $(find ./ebs-autoscale/ -type f | wc -l) files from tmp/ebs-autoscale/"
 tar $VERBOSE -czf $ARTIFACT_PATH/aws-ebs-autoscale.tgz ./ebs-autoscale/
 
 # add a copy of the release tarball for naming consistency
-echo "creating artifacts/amazon-ebs-autoscale.tgz with `find ./amazon-ebs-autoscale/ -type f | wc -l` files from tmp/amazon-ebs-autoscale/"
+echo "creating artifacts/amazon-ebs-autoscale.tgz with $(find ./amazon-ebs-autoscale/ -type f | wc -l) files from tmp/amazon-ebs-autoscale/"
 tar $VERBOSE -czf $ARTIFACT_PATH/amazon-ebs-autoscale.tgz ./amazon-ebs-autoscale
 
 # add a retrieval script
@@ -126,7 +126,7 @@ for fn in `ls .`; do
     cd $TEMP_PATH/lambda/$fn
     [ -z $VERBOSE ] && P_QUIET='--quiet' || P_QUIET=''
     pip $P_QUIET install -t . -r requirements.txt
-    echo "creating artifacts/lambda-${fn}.zip with `find . -type f | wc -l` files"
+    echo "creating artifacts/lambda-${fn}.zip with $(find . -type f | wc -l) files"
     [ -z $VERBOSE ] && Z_QUIET='-q' || Z_QUIET=''
     zip $Z_QUIET -r $ARTIFACT_PATH/lambda-$fn.zip .
 done
@@ -151,13 +151,13 @@ zip $Z_QUIET -r $ARTIFACT_PATH/aws-ecs-additions.zip ./*
 
 
 # package container code
-echo "packaging container definitions with `find $SOURCE_PATH/containers -type f | wc -l` files"
+echo "packaging container definitions with $(find $SOURCE_PATH/containers -type f | wc -l) files"
 cd $SOURCE_PATH/containers
 zip $Z_QUIET -r $ARTIFACT_PATH/containers.zip ./*
 
 
 # add templates to dist
-echo "copying `find $SOURCE_PATH/templates/ -type f | wc -l` cloudformation templates"
+echo "copying $(find $SOURCE_PATH/templates/ -type f | wc -l) cloudformation templates"
 cp $VERBOSE -R $SOURCE_PATH/templates/. $TEMPLATES_PATH
 
 

From e1a1cc6cec7aab14fbf4ef069fa8ef65fd8855e3 Mon Sep 17 00:00:00 2001
From: Andrew Crabb <crabba@amazon.com>
Date: Mon, 22 Mar 2021 11:57:30 -0400
Subject: [PATCH 3/5] Use --verbose when calling deploy.sh from travis

---
 .travis.yml        | 4 ++--
 _scripts/deploy.sh | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3a29c5928..94add2e5c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,14 +28,14 @@ before_deploy:
 
 deploy:
   - provider: script
-    script: bash _scripts/deploy.sh production
+    script: bash _scripts/deploy.sh --verbose production
     skip_cleanup: true
     on:
       repo: aws-samples/aws-genomics-workflows
       branch: release
       tags: true
   - provider: script
-    script: bash _scripts/deploy.sh test
+    script: bash _scripts/deploy.sh --verbose test
     skip_cleanup: true
     on:
       repo: aws-samples/aws-genomics-workflows
diff --git a/_scripts/deploy.sh b/_scripts/deploy.sh
index e03003e45..4e40237c6 100755
--- a/_scripts/deploy.sh
+++ b/_scripts/deploy.sh
@@ -77,6 +77,7 @@ function s3_sync() {
     cmd="aws s3 sync \
         --profile $ASSET_PROFILE \
         --region $DEPLOY_REGION \
+        --acl public-read \
         --delete \
         --metadata commit=$(git rev-parse HEAD) \
         $source \

From 679e202ac7e6f2a33f48ffb0902d9893bfd58877 Mon Sep 17 00:00:00 2001
From: Andrew Crabb <crabba@amazon.com>
Date: Mon, 22 Mar 2021 19:59:11 -0400
Subject: [PATCH 4/5] Add option to deploy to public buckets. Add clobber
 option to configure-deploy

---
 .travis.yml                  |  6 ++---
 _scripts/configure-deploy.sh | 50 ++++++++++++++++++++++++++++++++++++
 _scripts/deploy.sh           | 31 +++++++++++++++++++---
 _scripts/make-dist.sh        |  7 ++++-
 4 files changed, 87 insertions(+), 7 deletions(-)
 mode change 100644 => 100755 _scripts/configure-deploy.sh

diff --git a/.travis.yml b/.travis.yml
index 94add2e5c..240c76254 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,18 +24,18 @@ script:
 before_deploy:
 
   - pip install awscli --upgrade
-  - bash _scripts/configure-deploy.sh
+  - bash _scripts/configure-deploy.sh --clobber
 
 deploy:
   - provider: script
-    script: bash _scripts/deploy.sh --verbose production
+    script: bash _scripts/deploy.sh --public --verbose production
     skip_cleanup: true
     on:
       repo: aws-samples/aws-genomics-workflows
       branch: release
       tags: true
   - provider: script
-    script: bash _scripts/deploy.sh --verbose test
+    script: bash _scripts/deploy.sh --public --verbose test
     skip_cleanup: true
     on:
       repo: aws-samples/aws-genomics-workflows
diff --git a/_scripts/configure-deploy.sh b/_scripts/configure-deploy.sh
old mode 100644
new mode 100755
index 309192f25..1fe6dcccc
--- a/_scripts/configure-deploy.sh
+++ b/_scripts/configure-deploy.sh
@@ -1,10 +1,60 @@
 #!/bin/bash
 
+# Create a default ~/.aws/configure file for Travis testing
+
 set -e
 
 # This script expects the following environment variable(s)
 # ASSET_ROLE_ARN: the AWS role ARN that is used to publish assets
 
+usage() {
+    cat <<EOM
+    Usage:
+    $(basename $0) [--clobber]
+
+    --clobber  Overwrite ~/.aws/configure file without asking
+EOM
+}
+
+CLOBBER=''
+PARAMS=""
+while (( "$#" )); do
+    case "$1" in
+        --clobber)
+            CLOBBER=1
+            shift
+            ;;
+        --help)
+            usage
+            exit 0
+            ;;
+        --) # end optional argument parsing
+            shift
+            break
+            ;;
+        -*|--*=)
+            echo "Error: unsupported argument $1" >&2
+            exit 1
+            ;;
+        *) # positional agruments
+            PARAMS="$PARAMS $1"
+            shift
+            ;;
+    esac
+done
+eval set -- "$PARAMS"
+
+if [ -z $CLOBBER ]; then
+    while true; do
+        read -p "Overwrite ~/.aws/config file [y/n]? " yn
+        case $yn in
+            [Yy]* ) CLOBBER=1; break;;
+            [Nn]* ) echo "Exiting"; exit;;
+            * ) echo "Please answer yes or no.";;
+        esac
+    done
+fi
+
 mkdir -p $HOME/.aws
 cat << EOF > $HOME/.aws/config
 [default]
diff --git a/_scripts/deploy.sh b/_scripts/deploy.sh
index 4e40237c6..dc30d0225 100755
--- a/_scripts/deploy.sh
+++ b/_scripts/deploy.sh
@@ -10,6 +10,21 @@ ASSET_STAGE=test
 ASSET_PROFILE=asset-publisher
 DEPLOY_REGION=us-east-1
 
+usage() {
+    cat <<EOM
+    Usage:
+    $(basename $0) [--site-bucket BUCKET] [--asset-bucket BUCKET] [--asset-profile PROFILE] [--deploy-region REGION] [--public] [--verbose]
+
+    --site-bucket BUCKET        Deploy documentation site to BUCKET
+    --asset-bucket BUCKET       Deploy assets to BUCKET
+    --asset-profile PROFILE     Use PROFILE for AWS CLI commands
+    --deploy-region REGION      Deploy in region REGION
+    --public                    Deploy to public bucket with '--acl public-read' (Default false)
+    --verbose                   Display more output
+EOM
+}
+
+ACL_PUBLIC_READ=''
 VERBOSE=''
 PARAMS=""
 while (( "$#" )); do
@@ -30,6 +45,14 @@ while (( "$#" )); do
             DEPLOY_REGION=$2
             shift 2
             ;;
+        --help)
+            usage
+            exit 0
+            ;;
+        --public)
+            ACL_PUBLIC_READ='--acl public-read'
+            shift
+            ;;
         --verbose)
             VERBOSE='--verbose'
             shift
@@ -77,7 +100,7 @@ function s3_sync() {
     cmd="aws s3 sync \
         --profile $ASSET_PROFILE \
         --region $DEPLOY_REGION \
-        --acl public-read \
+        $ACL_PUBLIC_READ \
         --delete \
         --metadata commit=$(git rev-parse HEAD) \
         $source \
@@ -164,12 +187,14 @@ function site() {
         echo "requirement mkdocs not found. aborting"
         exit 1
     fi
-    mkdocs build
+    [ -z $VERBOSE ] && QUIET='-q' || QUIET=''
+    mkdocs build $QUIET
 
     echo "publishing site"
     aws s3 sync \
+        --profile $ASSET_PROFILE \
         --region $DEPLOY_REGION \
-        --acl public-read \
+        $ACL_PUBLIC_READ \
         --delete \
         --metadata commit=$(git rev-parse HEAD) \
         ./site \
diff --git a/_scripts/make-dist.sh b/_scripts/make-dist.sh
index d871adb82..c9d2d85e3 100755
--- a/_scripts/make-dist.sh
+++ b/_scripts/make-dist.sh
@@ -92,7 +92,12 @@ done
 echo "packaging amazon-ebs-autoscale"
 cd $TEMP_PATH
 
-EBS_AUTOSCALE_VERSION=$(curl --silent "https://api.github.com/repos/awslabs/amazon-ebs-autoscale/releases/latest" | jq -r .tag_name)
+RESPONSE=$(curl --silent "https://api.github.com/repos/awslabs/amazon-ebs-autoscale/releases/latest")
+EBS_AUTOSCALE_VERSION=$(echo $RESPONSE | jq -r .tag_name)
+if [[ $EBS_AUTOSCALE_VERSION = 'null' ]]; then
+    echo "ERROR: $RESPONSE"
+    exit 1
+fi
 curl --silent -L \
     "https://github.com/awslabs/amazon-ebs-autoscale/archive/${EBS_AUTOSCALE_VERSION}.tar.gz" \
     -o ./amazon-ebs-autoscale.tar.gz 

From 5ad4e8e8a76ab71b91de4fab9342e7f14a8c41a0 Mon Sep 17 00:00:00 2001
From: Andrew Crabb <crabba@amazon.com>
Date: Tue, 23 Mar 2021 16:22:42 -0400
Subject: [PATCH 5/5] Source nextflow container image from ECR Public

---
 _scripts/deploy.sh                 | 6 +++---
 src/containers/nextflow/Dockerfile | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/_scripts/deploy.sh b/_scripts/deploy.sh
index dc30d0225..e00ab7aae 100755
--- a/_scripts/deploy.sh
+++ b/_scripts/deploy.sh
@@ -107,7 +107,6 @@ function s3_sync() {
         $destination"
     echo $cmd
     eval $cmd
-    exit
 }
 
 function publish() {
@@ -158,11 +157,12 @@ function pin_version() {
     local version=$1
     local asset=$2
     local folder=$3
-
+    
     echo "PINNING VERSIONS"
     for file in `grep -irl "$asset  # dist: pin_version" $folder`; do
         echo "pinning '$asset' as '$version/$asset' in '$file'"
-        sed -i'' -e "s|$asset  # dist: pin_version|$version/$asset  #|g" $file
+        sed -e "s|$asset  # dist: pin_version|$version/$asset  #|g" $file > $file.tmp
+        mv $file.tmp $file
     done
 }
 
diff --git a/src/containers/nextflow/Dockerfile b/src/containers/nextflow/Dockerfile
index 920e7ab06..249ffdd16 100644
--- a/src/containers/nextflow/Dockerfile
+++ b/src/containers/nextflow/Dockerfile
@@ -1,5 +1,5 @@
 ARG VERSION=latest
-FROM nextflow/nextflow:${VERSION} AS build
+FROM public.ecr.aws/seqera-labs/nextflow:${VERSION} AS build
 
 # The upstream nextflow containers are based on alpine
 # which are not compatible with the aws cli