ydeng/autoBIGS.galaxy
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base: ydeng:d2dfbb9464ca56c3b737e5bcc5cd9eeeedaa9bea
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ydeng:develop
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compare: ydeng:aaeb02853e68b12858803f3fd38ba6b55fce3ccc
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ydeng:main
ydeng:develop

No commits in common. "d2dfbb9464ca56c3b737e5bcc5cd9eeeedaa9bea" and "aaeb02853e68b12858803f3fd38ba6b55fce3ccc" have entirely different histories.
d2dfbb9464 ... aaeb02853e

2 changed files with 3 additions and 5 deletions
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6
Jenkinsfile vendored
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@ -10,11 +10,9 @@ pipeline {
stages { stages {
stage ("install") { stage ("install") {
steps { steps {
sh 'useradd galaxy -m'
sh 'apt update'
sh 'apt install sudo -y'
sh 'pip install -r requirements.txt' sh 'pip install -r requirements.txt'
sh 'pip install standard-imghdr' sh 'pip install standard-imghdr'
sh 'useradd galaxy -m'
} }
} }
stage ("lint") { stage ("lint") {
@ -25,7 +23,7 @@ pipeline {
stage ("test") { stage ("test") {
steps { steps {
sh 'mkdir test_results' sh 'mkdir test_results'
sh "sudo -u galaxy planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html" sh "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html"
xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)] xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)]
} }
} }

2
autobigs-cli.xml
View File

@ -59,7 +59,7 @@
<data name="info_db_out" label="${tool.name} supported Databases" format="csv"> <data name="info_db_out" label="${tool.name} supported Databases" format="csv">
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter> <filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter>
</data> </data>
<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv"> <data name="info_schemes_out" label="${tool.name} supported Databases" format="csv">
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'schemes'</filter> <filter>mode['operation'] == "info" and select_info['retrieved'] == 'schemes'</filter>
</data> </data>
</outputs> </outputs>