Files for CWL testing

tests/awe-cwl-submitter-wrapper.sh

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+#!/bin/bash
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+${DIR}/awe-submitter --pack --wait \
+        --shockurl=${SHOCK_SERVER} \
+        --serverurl=${AWE_SERVER} --download_files=true $@

tests/setup-env.sh

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+
+build=$1
+echo Setup build in ${build}
+cd $1
+
+export TAG=CWL
+
+git clone https://github.com/MG-RAST/Skyport2.git
+git clone https://github.com/MG-RAST/AWE.git
+git clone https://github.com/common-workflow-language/common-workflow-language.git
+git clone https://github.com/common-workflow-language/cwltest.git
+
+# Build cwltest
+cd cwltest/
+mkdir install
+export PYTHONPATH=$PATHONPATH:`pwd`/install//lib/python2.7/site-packages/
+export PATH=$PATH:`pwd`/install/bin/
+python setup.py install --prefix `pwd`/install/
+cd .. 
+
+### Build ne AWE container
+
+#git clone https://github.com/MG-RAST/Skyport2.git
+### Build ne AWE container
+export TAG=CWL
+cd AWE
+docker build -t mgrast/awe:${TAG} -f Dockerfile .
+docker build -t mgrast/awe-worker:${TAG} -f Dockerfile_worker .
+docker build -t mgrast/awe-submitter:${TAG} -f Dockerfile_submitter .
+
+### Copy submitter
+docker create --name submitter mgrast/awe-submitter:${TAG}
+docker cp submitter:/go/bin/awe-submitter awe-submitter
+docker rm submitter 
+
+### Start stack
+cd ../Skyport2	
+./init.sh
+. ./skyport2.env
+# skyport2.env overwrites TAG - set back
+export TAG=CWL
+docker-compose down
+docker-compose -f Docker/Compose/skyport-awe-jenkins.yaml up -d
+sleep 60
+
+# Execute tests
+cd ../common-workflow-language/
+./run_test.sh RUNNER=`pwd`/../AWE/tests/awe-cwl-submitter-wrapper.sh
+
+# Shut down
+cd ../Skyport2
+docker-compose -f Docker/Compose/skyport-awe-jenkins.yaml  down
+## TEST COMES HERE