Merge pull request #346 from 4dn-dcic/ecr

Ecr

awsf3-docker/run.sh

@@ -54,7 +54,7 @@ export LOCAL_WF_TMPDIR_CWL=$MOUNT_DIR_PREFIX$LOCAL_WF_TMPDIR
 
 # function that executes a command and collecting log
 exl(){ $@ >> $LOGFILE 2>> $LOGFILE; handle_error $?; } ## usage: exl command  ## ERRCODE has the error code for the command. if something is wrong, send error to s3.
-exlj(){ $@ >> $LOGJSONFILE 2>> $LOGFILE; $ERRCODE=$?; cat $LOGJSONFILE >> $LOGFILE; handle_error $ERRCODE; } ## usage: exl command  ## ERRCODE has the error code for the command. if something is wrong, send error to s3. This one separates stdout to json as well.
+exlj(){ $@ >> $LOGJSONFILE 2>> $LOGFILE; ERRCODE=$?; cat $LOGJSONFILE >> $LOGFILE; handle_error $ERRCODE; } ## usage: exl command  ## ERRCODE has the error code for the command. if something is wrong, send error to s3. This one separates stdout to json as well.
 exle(){ $@ >> /dev/null 2>> $LOGFILE; handle_error $?; } ## usage: exle command  ## ERRCODE has the error code for the command. if something is wrong, send error to s3. This one eats stdout. Useful for downloading/uploading files to/from s3, because it writes progress to stdout.
 exlo(){ $@ 2>> /dev/null >> $LOGFILE; handle_error $?; } ## usage: exlo command  ## ERRCODE has the error code for the command. if something is wrong, send error to s3. This one eats stderr. Useful for hiding long errors or credentials.
 

awsf3/aws_run_workflow_generic.sh

@@ -47,10 +47,12 @@ export LOGFILE2=$LOCAL_OUTDIR/$JOBID.log
 export STATUS=0
 export ERRFILE=$LOCAL_OUTDIR/$JOBID.error  # if this is found on s3, that means something went wrong.
 export INSTANCE_REGION=$(ec2metadata --availability-zone | sed 's/[a-z]$//')
+export AWS_ACCOUNT_ID=$(aws sts get-caller-identity| grep Account | sed 's/[^0-9]//g')
 
 
 # function that executes a command and collecting log
 exl(){ $@ >> $LOGFILE 2>> $LOGFILE; handle_error $?; } ## usage: exl command  ## ERRCODE has the error code for the command. if something is wrong, send error to s3.
+exlo(){ $@ 2>> /dev/null >> $LOGFILE; handle_error $?; } ## usage: exlo command  ## ERRCODE has the error code for the command. if something is wrong, send error to s3. This one eats stderr. Useful for hiding long errors or credentials.
 
 # function that sends log to s3 (it requires LOGBUCKET to be defined, which is done by sourcing $ENV_FILE.)
 send_log(){  aws s3 cp $LOGFILE s3://$LOGBUCKET &>/dev/null; }  ## usage: send_log (no argument)
@@ -159,12 +161,21 @@ if [ ! -z $ACCESS_KEY -a ! -z $SECRET_KEY -a ! -z $REGION ]; then
   echo -ne "$ACCESS_KEY\n$SECRET_KEY\n$REGION\njson" | aws configure --profile user1
 fi
 
+### log into ECR if necessary
+exl echo
+exl echo "## Logging into ECR"
+exl echo "Logging into ECR $AWS_ACCOUNT_ID.dkr.ecr.$INSTANCE_REGION.amazonaws.com..."
+exlo docker login --username AWS --password $(aws ecr get-login-password --region $INSTANCE_REGION) $AWS_ACCOUNT_ID.dkr.ecr.$INSTANCE_REGION.amazonaws.com;
+send_log
+
 # send log before starting docker
 exl echo
 exl echo "## Running dockerized awsf scripts"
 send_log
 
 # run dockerized awsf scripts
+exl docker pull $AWSF_IMAGE
+send_log
 docker run --privileged --net host -v /home/ubuntu/:/home/ubuntu/:rw -v /mnt/:/mnt/:rw $AWSF_IMAGE run.sh -i $JOBID -l $LOGBUCKET -f $EBS_DEVICE -S $STATUS $SINGULARITY_OPTION_TO_PASS
 handle_error $?
 

tibanna/_version.py

@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ = "1.4.1"
+__version__ = "1.5.0"