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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| #!/bin/bash | ||
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| : ${PLANEMO_TARGET:="planemo==0.50.1"} | ||
| : ${PLANEMO_OPTIONS:="--verbose"} | ||
| : ${PLANEMO_PROFILE_NAME:="wxflowtest"} | ||
| : ${PLANEMO_SERVE_PORT:="9019"} | ||
| : ${PLANEMO_TEST_STYLE:="serve_and_test"} # profile_serve_and_test, serve_and_test, docker_serve_and_test, test, docker_test | ||
| : ${PLANEMO_SERVE_DATABASE_TYPE:="postgres"} # used if not using Docker with PLANEMO_TEST_STYLE | ||
| : ${PLANEMO_DOCKER_GALAXY_IMAGE:="quay.io/bgruening/galaxy:18.01"} # used if used Docker with PLANEMO_TEST_STYLE | ||
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| GALAXY_URL="http://localhost:$PLANEMO_SERVE_PORT" | ||
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| # Ensure Planemo is installed. | ||
| if [ ! -d .venv ]; then | ||
| virtualenv .venv | ||
| . .venv/bin/activate | ||
| pip install -U pip | ||
| # Intentionally expand wildcards in PLANEMO_TARGET. | ||
| shopt -s extglob | ||
| pip install ${PLANEMO_TARGET} | ||
| fi | ||
| . .venv/bin/activate | ||
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| # Run test. | ||
| # This example shows off a bunch of different ways one could test with Planemo, | ||
| # but for actual workflow testing projects - probably best just to take one of the last | ||
| # two very easy invocations to simplify things. | ||
| if [ "$PLANEMO_TEST_STYLE" = "profile_serve_and_test" ]; then | ||
| planemo $PLANEMO_OPTIONS profile_create \ | ||
| --database_type "$PLANEMO_SERVE_DATABASE_TYPE" \ | ||
| "$PLANEMO_PROFILE_NAME" | ||
| planemo $PLANEMO_OPTIONS serve \ | ||
| --daemon \ | ||
| --profile "$PLANEMO_PROFILE_NAME" \ | ||
| --port "$PLANEMO_SERVE_PORT" \ | ||
| "$1" | ||
| planemo $PLANEMO_OPTIONS test \ | ||
| --galaxy_url "$GALAXY_URL" \ | ||
| --engine external_galaxy \ | ||
| "$1" | ||
| elif [ "$PLANEMO_TEST_STYLE" = "serve_and_test" ]; then | ||
| planemo $PLANEMO_OPTIONS serve \ | ||
| --daemon \ | ||
| --database_type "$PLANEMO_SERVE_DATABASE_TYPE" \ | ||
| --port "$PLANEMO_SERVE_PORT" \ | ||
| "$1" | ||
| planemo $PLANEMO_OPTIONS test \ | ||
| --galaxy_url "$GALAXY_URL" \ | ||
| --engine external_galaxy \ | ||
| "$1" | ||
| elif [ "$PLANEMO_TEST_STYLE" = "docker_serve_and_test" ]; then | ||
| docker pull "${PLANEMO_DOCKER_GALAXY_IMAGE}" | ||
| planemo $PLANEMO_OPTIONS serve \ | ||
| --daemon \ | ||
| --engine docker_galaxy \ | ||
| --docker_galaxy_image "${PLANEMO_DOCKER_GALAXY_IMAGE}" \ | ||
| --docker_extra_volume . \ | ||
| --port "$PLANEMO_SERVE_PORT" \ | ||
| "$1" | ||
| planemo $PLANEMO_OPTIONS test \ | ||
| --galaxy_url "$GALAXY_URL" \ | ||
| --engine external_galaxy \ | ||
| "$1" | ||
| elif [ "$PLANEMO_TEST_STYLE" = "test" ]; then | ||
| planemo $PLANEMO_OPTIONS test \ | ||
| --database_type "$PLANEMO_SERVE_DATABASE_TYPE" \ | ||
| "$1" | ||
| elif [ "$PLANEMO_TEST_STYLE" = "docker_test" ]; then | ||
| docker pull "${PLANEMO_DOCKER_GALAXY_IMAGE}" | ||
| planemo $PLANEMO_OPTIONS test \ | ||
| --engine docker_galaxy \ | ||
| --docker_galaxy_image "${PLANEMO_DOCKER_GALAXY_IMAGE}" \ | ||
| --docker_extra_volume . \ | ||
| "$1" > /dev/null | ||
| else | ||
| echo "Unknown test style ${PLANEMO_TEST_STYLE}" | ||
| exit 1 | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| #!/bin/bash | ||
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| # Ensure working directory is planemo project. | ||
| SCRIPTS_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" | ||
| PROJECT_DIRECTORY="${SCRIPTS_DIRECTORY}/.." | ||
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| TEMP_DIRECTORY=`mktemp -d 2>/dev/null || mktemp -d -t 'planemowftest'` | ||
| cp "$SCRIPTS_DIRECTORY/run_workflow_tests.sh" "$TEMP_DIRECTORY" | ||
| cp "$PROJECT_DIRECTORY/tests/data/"wf4* "$TEMP_DIRECTORY" | ||
| cp "$PROJECT_DIRECTORY/tests/data/1.bed" "$TEMP_DIRECTORY" | ||
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| cd $PROJECT_DIRECTORY | ||
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| # Build Planemo wheel. | ||
| make dist | ||
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| # Test against wheel. | ||
| export PLANEMO_TARGET="$PROJECT_DIRECTORY/dist/planemo*whl" | ||
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| cd $TEMP_DIRECTORY | ||
| bash run_workflow_tests.sh "wf4-distro-tools.gxwf.yml" |
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