Sync job file template with galaxy

.github/workflows/galaxy_framework.yaml

@@ -8,11 +8,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
         galaxy-branch: ['dev', 'master']
         metadata-strategy: ['directory']
         include:
-          - python-version: '3.7'
+          - python-version: '3.8'
             galaxy-branch: 'dev'
             metadata-strategy: 'extended'
     services:

.github/workflows/pulsar.yaml

@@ -51,8 +51,6 @@ jobs:
           python: 3.11
         - tox-env: py311-test-unit
           python: 3.11
-        - tox-env: py39-install_wheel-no_conda
-          python: 3.9
         - tox-env: py37-install_wheel
           python: 3.7
     services:

Makefile

@@ -84,14 +84,11 @@ tests:
 	$(IN_VENV) nosetests $(NOSE_TESTS)
 
 test-install-pypi:
-	bash install_test/test_install.bash
+	bash install_test/test_install_conda.bash
 
 test-install-wheel: dist
 	PULSAR_INSTALL_TARGET=$(wildcard $(shell pwd)/dist/pulsar_app*.whl)[web] bash install_test/test_install_conda.bash
 
-test-install-wheel-no-conda: dist
-	PULSAR_INSTALL_TARGET=$(wildcard $(shell pwd)/dist/pulsar_app*.whl)[web] bash install_test/test_install.bash
-
 coverage:
 	coverage run --source $(SOURCE_DIR) setup.py $(TEST_DIR)
 	coverage report -m

install_test/common_functions.bash

@@ -107,6 +107,7 @@ run_planemo() {
     then
         galaxy_root_args="--galaxy_root $GALAXY_ROOT"
     fi
-    planemo --verbose test $galaxy_root_args "$@"
+    MARKDOWN_OUTPUT="${GITHUB_STEP_SUMMARY:-tool_test_output.md}"
+    planemo --verbose test --test_output_markdown "$MARKDOWN_OUTPUT" $galaxy_root_args "$@"
     echo "Tests complete."
 }

install_test/test_install_conda.bash

@@ -17,8 +17,8 @@ cd ..
 
 check_pulsar
 
-init_planemo "conda_testing"
+init_planemo "seqtk_complete"
 
-run_planemo --job_config_file "$SCRIPT_DIR/galaxy_job_conf.xml" test_tools/bwa.xml
+run_planemo --job_config_file "$SCRIPT_DIR/galaxy_job_conf.xml" test_tools/seqtk_seq.xml
 
 stop_pulsar

pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh

@@ -35,6 +35,20 @@ GALAXY_LIB="$galaxy_lib"
 _galaxy_setup_environment "$PRESERVE_GALAXY_ENVIRONMENT"
 export _GALAXY_JOB_HOME_DIR
 export _GALAXY_JOB_TMP_DIR
+
+TEMP="${TEMP:-$TMP}"
+TMPDIR="${TMPDIR:-$TMP}"
+
+TMP="${TMP:-$TEMP}"
+TMPDIR="${TMPDIR:-$TEMP}"
+
+TMP="${TMP:-$TMPDIR}"
+TEMP="${TEMP:-$TMPDIR}"
+
+TMP="${TMP:-$_GALAXY_JOB_TMP_DIR}"
+TEMP="${TEMP:-$_GALAXY_JOB_TMP_DIR}"
+TMPDIR="${TMPDIR:-$_GALAXY_JOB_TMP_DIR}"
+
 GALAXY_PYTHON=`command -v python`
 cd $working_directory
 $memory_statement

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = lint, docs, dist, test-unit, test, install_wheel, install_wheel-no_conda
+envlist = lint, docs, dist, test-unit, test, install_wheel
 toxworkdir={env:TOX_WORK_DIR:.tox}
 source_dir = pulsar
 test_dir = test
@@ -11,8 +11,7 @@ commands =
     lint: flake8 --ignore W504 {[tox]source_dir} {[tox]test_dir}
     dist: make lint-dist
     docs: make lint-docs
-    install_wheel-!no_conda: make test-install-wheel
-    install_wheel-no_conda: make test-install-wheel-no-conda
+    install_wheel: make test-install-wheel
     mypy: mypy {[tox]source_dir} {[tox]test_dir}
 
 deps =
@@ -38,6 +37,7 @@ passenv =
     HOME
     USER
     DRMAA_LIBRARY_PATH
+    GITHUB_STEP_SUMMARY
 
 skip_install =
     lint,dist,install_wheel: True