Mercurial > repos > eschen42 > w4mclassfilter
annotate run_test.sh @ 0:bab3a658f74e draft
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
author | eschen42 |
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date | Tue, 09 May 2017 18:34:35 -0400 |
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bab3a658f74e
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
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1 #!/bin/bash |
bab3a658f74e
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
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2 |
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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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3 # purge old output files |
bab3a658f74e
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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4 if [ -f test_log.txt ]; then rm test_log.txt; fi |
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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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5 if [ -f tool_test_output.html ]; then rm tool_test_output.html; fi |
bab3a658f74e
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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6 if [ -f tool_test_output.json ]; then rm tool_test_output.json; fi |
bab3a658f74e
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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7 |
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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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8 # run test and write new output files, showing progress to command line output |
bab3a658f74e
planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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9 planemo conda_install . |
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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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10 planemo test --conda_dependency_resolution w4mclassfilter.xml 2>&1 | grep -v -i observer | tee test_log.txt |
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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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11 |
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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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12 # summarize warnings and errors to command line output |
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planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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13 grep -E "(ERROR)|(WARNING)" test_log.txt | grep -v samtools | grep -v "Dynamic Display Application links" | grep -v "twobit.loc" |