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#244 --------- Co-authored-by: Dr. Ernie Prabhakar <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -93,8 +93,8 @@ From the command-line, do, e.g.: | |
| ```bash | ||
| # export NXF_VER=23.04.3 | ||
| export LOG4J_DEBUG=true # for verbose logging | ||
| export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.6/nf-quilt-0.8.6-meta.json | ||
| nextflow run main.nf -plugins [email protected].6 | ||
| export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.7/nf-quilt-0.8.7-meta.json | ||
| nextflow run main.nf -plugins [email protected].7 | ||
| ``` | ||
|
|
||
| For Tower, you can use the "Pre-run script" to set the environment variables. | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,49 +1,49 @@ | ||
| gradle.projectsLoaded { | ||
| rootProject { | ||
| afterEvaluate { project -> | ||
| if (!project.repositories.any{it.name == 'MavenRepo'}) { | ||
| project.repositories { | ||
| // To be able to load org.codehaus.groovy:groovy-groovysh | ||
| mavenCentral() | ||
| } | ||
| } | ||
|
|
||
| project.configurations { | ||
| groovyshdependencies | ||
| } | ||
|
|
||
| project.dependencies { | ||
| groovyshdependencies("org.codehaus.groovy:groovy-groovysh:${GroovySystem.version}") { | ||
| exclude group: 'org.codehaus.groovy' | ||
| } | ||
| } | ||
|
|
||
| project.tasks.register('groovysh') { | ||
| group 'debug' | ||
| description 'Runs an interactive shell in the context of the project.' | ||
| doLast { | ||
| URLClassLoader groovyObjectClassLoader = GroovyObject.class.classLoader | ||
| def groovyshClass | ||
| def groovyShell | ||
|
|
||
| // Add dependency jars to classloader | ||
| configurations.groovyshdependencies.each {File file -> | ||
| groovyObjectClassLoader.addURL(file.toURL()) | ||
| } | ||
| Class.forName('jline.console.history.FileHistory', true, groovyObjectClassLoader) | ||
| groovyshClass = Class.forName('org.codehaus.groovy.tools.shell.Groovysh', true, groovyObjectClassLoader) | ||
|
|
||
| if (groovyshClass) { | ||
| groovyShell = groovyshClass.newInstance() | ||
| } | ||
| if (groovyShell) { | ||
| groovyShell.interp.context.variables.put("gradle", gradle) | ||
| groovyShell.interp.context.variables.put("settings", gradle.settings) | ||
| groovyShell.interp.context.variables.put("project", project) | ||
| groovyShell.run('') | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| gradle.projectsLoaded { | ||
| rootProject { | ||
| afterEvaluate { project -> | ||
| if (!project.repositories.any { it.name == 'MavenRepo' }) { | ||
| project.repositories { | ||
| // To be able to load org.codehaus.groovy:groovy-groovysh | ||
| mavenCentral() | ||
| } | ||
| } | ||
|
|
||
| project.configurations { | ||
| groovyshdependencies | ||
| } | ||
|
|
||
| project.dependencies { | ||
| groovyshdependencies("org.codehaus.groovy:groovy-groovysh:${GroovySystem.version}") { | ||
| exclude group: 'org.codehaus.groovy' | ||
| } | ||
| } | ||
|
|
||
| project.tasks.register('groovysh') { | ||
| group 'debug' | ||
| description 'Runs an interactive shell in the context of the project.' | ||
| doLast { | ||
| URLClassLoader groovyObjectClassLoader = GroovyObject.classLoader | ||
| def groovyshClass | ||
| def groovyShell | ||
|
|
||
| // Add dependency jars to classloader | ||
| configurations.groovyshdependencies.each { File file -> | ||
| groovyObjectClassLoader.addURL(file.toURL()) | ||
| } | ||
| Class.forName('jline.console.history.FileHistory', true, groovyObjectClassLoader) | ||
| groovyshClass = Class.forName('org.codehaus.groovy.tools.shell.Groovysh', true, groovyObjectClassLoader) | ||
|
|
||
| if (groovyshClass) { | ||
| groovyShell = groovyshClass.newInstance() | ||
| } | ||
| if (groovyShell) { | ||
| groovyShell.interp.context.variables.put('gradle', gradle) | ||
| groovyShell.interp.context.variables.put('settings', gradle.settings) | ||
| groovyShell.interp.context.variables.put('project', project) | ||
| groovyShell.run('') | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,52 @@ | ||
| gradle.projectsLoaded { | ||
| rootProject { | ||
| afterEvaluate { project -> | ||
| if (!project.repositories.any{it.name == 'MavenRepo'}) { | ||
| project.repositories { | ||
| // To be able to load org.apache.groovy:groovy-groovysh and dependencies | ||
| mavenCentral { | ||
| content { | ||
| includeGroup 'org.apache.groovy' | ||
| includeGroup 'jline' | ||
| includeGroup 'com.github.javaparser' | ||
| includeGroup 'org.ow2.asm' | ||
| includeGroup 'org.abego.treelayout' | ||
| includeGroup 'org.apache.ivy' | ||
| } | ||
| } | ||
| } | ||
| } | ||
| project.configurations { | ||
| groovyshdependencies | ||
| } | ||
|
|
||
| project.dependencies { | ||
| groovyshdependencies "org.apache.groovy:groovy-groovysh:4.0.23" | ||
| } | ||
|
|
||
| project.tasks.register('groovysh') { | ||
| group 'debug' | ||
| description 'Runs an interactive shell in the context of the project. Use :inspect command to inspect project, gradle, settings or other objects.' | ||
| doLast { | ||
| URLClassLoader groovyshClassLoader = new URLClassLoader(); | ||
| configurations.groovyshdependencies.each {File file -> | ||
| groovyshClassLoader.addURL(file.toURI().toURL()) | ||
| } | ||
|
|
||
| def fileHistoryClass | ||
| def groovyshClass | ||
| def groovyShell | ||
| fileHistoryClass = Class.forName('jline.console.history.FileHistory', true, groovyshClassLoader) | ||
| groovyshClass = Class.forName('org.apache.groovy.groovysh.Groovysh', true, groovyshClassLoader) | ||
| if (groovyshClass) { | ||
| groovyShell = groovyshClass.newInstance() | ||
| if (groovyShell) { | ||
| groovyShell.interp.context.variables.put("gradle", gradle) | ||
| groovyShell.interp.context.variables.put("settings", gradle.settings) | ||
| groovyShell.interp.context.variables.put("project", project) | ||
| groovyShell.run('# Available objects: gradle, settings, project\n# Try :inspect project') | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| gradle.projectsLoaded { | ||
| rootProject { | ||
| afterEvaluate { project -> | ||
| if (!project.repositories.any { it.name == 'MavenRepo' }) { | ||
| project.repositories { | ||
| // To be able to load org.apache.groovy:groovy-groovysh and dependencies | ||
| mavenCentral { | ||
| content { | ||
| includeGroup 'org.apache.groovy' | ||
| includeGroup 'jline' | ||
| includeGroup 'com.github.javaparser' | ||
| includeGroup 'org.ow2.asm' | ||
| includeGroup 'org.abego.treelayout' | ||
| includeGroup 'org.apache.ivy' | ||
| } | ||
| } | ||
| } | ||
| } | ||
| project.configurations { | ||
| groovyshdependencies | ||
| } | ||
|
|
||
| project.dependencies { | ||
| groovyshdependencies 'org.apache.groovy:groovy-groovysh:4.0.23' | ||
| } | ||
|
|
||
| project.tasks.register('groovysh') { | ||
| group 'debug' | ||
| description 'Runs an interactive shell in the context of the project. Use :inspect command to inspect project, gradle, settings or other objects.' | ||
| doLast { | ||
| URLClassLoader groovyshClassLoader = new URLClassLoader() | ||
| configurations.groovyshdependencies.each { File file -> | ||
| groovyshClassLoader.addURL(file.toURI().toURL()) | ||
| } | ||
|
|
||
| def groovyshClass | ||
| def groovyShell | ||
| groovyshClass = Class.forName('org.apache.groovy.groovysh.Groovysh', true, groovyshClassLoader) | ||
| if (groovyshClass) { | ||
| groovyShell = groovyshClass.newInstance() | ||
| if (groovyShell) { | ||
| groovyShell.interp.context.variables.put('gradle', gradle) | ||
| groovyShell.interp.context.variables.put('settings', gradle.settings) | ||
| groovyShell.interp.context.variables.put('project', project) | ||
| groovyShell.run('# Available objects: gradle, settings, project\n# Try :inspect project') | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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