Merge pull request #126 from henriqueribeiro/add_cromwell_tools

Add cromwell tools

Author: wleepang

README.md

@@ -43,13 +43,15 @@ TEMPLATE_ROOT_URL=https://<dist-bucketname>.s3-<region>.amazonaws.com/test/templ
 aws cloudformation create-stack \
     --region <region> \
     --stack-name <stackname> \
-    --template-url $TEMPLATE_ROOT_URL/gwfcore-root.template.yaml \
+    --template-url $TEMPLATE_ROOT_URL/gwfcore/gwfcore-root.template.yaml \
     --capabilities CAPABILITY_IAM CAPABILITY_AUTO_EXPAND \
     --parameters \
         ParameterKey=VpcId,ParameterValue=<vpc-id> \
         ParameterKey=SubnetIds,ParameterValue=\"<subnet-id-1>,<subnet-id-2>,...\" \
         ParameterKey=ArtifactBucketName,ParameterValue=<dist-bucketname> \
-        ParameterKey=TemplateRootUrl,ParameterValue=$TEMPLATE_ROOT_URL
+        ParameterKey=TemplateRootUrl,ParameterValue=$TEMPLATE_ROOT_URL \
+        ParameterKey=S3BucketName,ParameterValue=<store-buketname> \
+        ParameterKey=ExistingBucket,ParameterValue=false
 
 ```
 

docs/orchestration/cromwell/cromwell-overview.md

@@ -210,7 +210,9 @@ This value can also be supplied as a Java command line variable.
 
 ### Accessing the Cromwell server
 
-The Cromwell EC2 instance may be accessed using the [AWS Session Manager](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/session-manager.html). Please note that by default this will log you in as user `ec2-user` in the directory `/usr/bin`. You may prefer to become the ec2-user with the command `sudo su - ec2-user` which will switch you to that user's home directory.
+The Cromwell EC2 instance may be accessed using the [AWS Session Manager](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/session-manager.html) via console or in the terminal with the command `aws ssm start-session --target <instance-id>`.
+
+Please note that by default this will log you in as user `ec2-user` in the directory `/usr/bin`. You may prefer to become the ec2-user with the command `sudo su - ec2-user` which will switch you to that user's home directory.
 
 ### Stop / Start / Restart the Cromwell service
 

src/templates/cromwell/cromwell-resources.template.yaml

@@ -382,6 +382,20 @@ Resources:
               owner: "ec2-user"
               group: "ec2-user"
 
+            "/home/ec2-user/get_cromwell_tools.sh":
+              content: |
+                #!/bin/bash
+                url=$(curl --silent --retry 5 --retry-connrefused https://api.github.com/repos/broadinstitute/cromwell/releases/latest | jq -r .assets[1].browser_download_url)
+                curl --retry 5 --retry-connrefused -LO $url
+
+                curl --retry 5 --retry-connrefused -LO https://raw.githubusercontent.com/broadinstitute/cromshell/master/cromshell
+                chmod +x cromshell
+                sudo mv cromshell /usr/local/bin/
+
+              mode: "000755"
+              owner: "ec2-user"
+              group: "ec2-user"
+
             "/home/ec2-user/cromwell.conf":
               content: !Sub
                 - |
@@ -605,6 +619,16 @@ Resources:
             02_start_cromwell:
               cwd: "/home/ec2-user"
               command: "sudo -u ec2-user /usr/local/bin/supervisord"
+
+        config4:
+          commands:
+            00_get_cromwell_tools:
+              cwd: "/home/ec2-user/"
+              command: "./get_cromwell_tools.sh"
+            
+            01_chown_womtool:
+              cwd: "/home/ec2-user/"
+              command: "chown ec2-user:ec2-user womtool*.jar"
 
     Properties:
       ImageId: !Ref LatestAmazonLinuxAMI
@@ -623,7 +647,7 @@ Resources:
           #!/bin/bash -x
           yum -y update
           yum install -y aws-cfn-bootstrap
-          yum install -y jq awslogs python3 java
+          yum install -y jq awslogs python3 java mailx
 
           amazon-linux-extras install -y nginx1
           pip3 install supervisor