Nextflow - have just used it on our HPC cluster and liked it
Hello,
I must admit that I am rather impressed - a series of images were auto-downloaded to function together with singularity and this then worked on a test data collection of the workflow. So, with singularity (or docker) in Debian, and nextflow, we would have an immediate sync with what upstream offers.
I had a look at the table in Google docs and found that the one dependency that was once missing to get nextflow through its autotests, i.e. capsule-nextflow is in the archive now. So I thought to give the main package of nextflow another look. I am impressed by all work that Pierre already invested into the packaging. @Pierre, where does that work stand? I only saw that kryo5 is listed as a dependency that is not in the archive.
Best,
Steffen
A "debian/rules binary" got this far:
Starting process 'Gradle Worker Daemon 1'. Working directory: ..../Salsa/Med/nextflow/.gradle/workers Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java @/tmp/gradle-worker-classpath9650940302470954557txt -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Worker Daemon 1'
Successfully started process 'Gradle Worker Daemon 1'
Started Gradle worker daemon (3.129 secs) with fork options DaemonForkOptions{executable=/usr/lib/jvm/java-17-openjdk-amd64/bin/java, minHeapSize=null, maxHeapSize=null, jvmArgs=[], classpath=[/usr/share/maven-repo/org/codehaus/groovy/groovy-ant/debian/groovy-ant-debian.jar, /usr/share/maven-repo/org/codehaus/groovy/groovy-groovydoc/debian/groovy-groovydoc-debian.jar, /usr/share/maven-repo/org/codehaus/groovy/groovy-templates/debian/groovy-templates-debian.jar, /usr/share/maven-repo/org/codehaus/groovy/groovy-xml/debian/groovy-xml-debian.jar, /usr/share/maven-repo/org/codehaus/groovy/groovy/debian/groovy-debian.jar, /usr/share/maven-repo/org/apache/ant/ant-junit/debian/ant-junit-debian.jar, /usr/share/maven-repo/org/apache/ant/ant/debian/ant-debian.jar, /usr/share/maven-repo/org/apache/ant/ant-launcher/debian/ant-launcher-debian.jar, /usr/share/maven-repo/org/apache/ant/ant-antlr/debian/ant-antlr-debian.jar, /usr/share/java/ant-1.10.13.jar, /usr/share/java/ant-launcher-1.10.13.jar], keepAliveMode=SESSION}.
This JVM does not support getting OS memory, so no OS memory status updates will be broadcast
Initialized native services in: .../Salsa/Med/nextflow/.gradle/native
Compiling with JDK Java compiler API.
warning: [options] bootstrap class path not set in conjunction with -source 8
Note: org.pf4j.processor.ExtensionAnnotationProcessor init
Note: Options {}
Note: Processing @org.pf4j.Extension
warning: Implicitly compiled files were not subject to annotation processing.
Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation.
2 warnings
startup failed:
.../Salsa/Med/nextflow/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy: 68: [Static type checking] - Cannot find matching method org.pf4j.SingletonExtensionFactory#<init>(). Please check if the declared type is correct and if the method exists.
@ line 68, column 16.
return new SingletonExtensionFactory()
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