nextflow
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`launch_nextflow` does not handle properly the spaces in java path
Bug report
Expected behavior and actual behavior
Cannot run nextflow CLI
Steps to reproduce the problem
Just run nextflow CLI script
Program output
We are having:
/opt/homebrew/bin/nextflow: line 177: /Library/Internet: No such file or directory
/opt/homebrew/bin/nextflow: line 177: exec: /Library/Internet: cannot execute: No such file or directory
apparently the code in launch_nextflow does not handle properly spaces. For the record, here is the contents of ${launcher[@]}:
"/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java" "-XX:+TieredCompilation" "-XX:TieredStopAtLevel=1" "-Djava.io.tmpdir=/var/folders/jm/hc1mgp813kb_9x8z1kdwvqjc0000gn/T/" "-Djava.library.path=/Users/asl/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java" "-Dfile.encoding=UTF-8" "-Dcapsule.app=nextflow_21.04.1" "-Djava.awt.headless=true" "-Dcapsule.jar=/Users/asl/.nextflow/framework/21.04.1/nextflow-21.04.1-one.jar" "-classpath" "/Users/asl/.nextflow/framework/21.04.1/nextflow-21.04.1-one.jar:/Users/asl/.nextflow/capsule/deps/io/nextflow/nextflow/21.04.1/nextflow-21.04.1.jar:/Users/asl/.nextflow/capsule/deps/org/apache/ivy/ivy/2.3.0/ivy-2.3.0.jar:/Users/asl/.nextflow/capsule/deps/io/nextflow/nf-httpfs/21.04.1/nf-httpfs-21.04.1.jar:/Users/asl/.nextflow/capsule/deps/io/nextflow/nf-commons/21.04.1/nf-commons-21.04.1.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-nio/3.0.7/groovy-nio-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-templates/3.0.7/groovy-templates-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-xml/3.0.7/groovy-xml-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy-json/3.0.7/groovy-json-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/groovy/groovy/3.0.7/groovy-3.0.7.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/jul-to-slf4j/1.7.25/jul-to-slf4j-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/log4j-over-slf4j/1.7.25/log4j-over-slf4j-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/ch/qos/logback/logback-classic/1.1.11/logback-classic-1.1.11.jar:/Users/asl/.nextflow/capsule/deps/ch/qos/logback/logback-core/1.1.11/logback-core-1.1.11.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.jar:/Users/asl/.nextflow/capsule/deps/ch/grengine/grengine/1.3.0/grengine-1.3.0.jar:/Users/asl/.nextflow/capsule/deps/commons-lang/commons-lang/2.6/commons-lang-2.6.jar:/Users/asl/.nextflow/capsule/deps/org/pf4j/pf4j-update/2.3.0/pf4j-update-2.3.0.jar:/Users/asl/.nextflow/capsule/deps/commons-codec/commons-codec/1.10/commons-codec-1.10.jar:/Users/asl/.nextflow/capsule/deps/com/beust/jcommander/1.35/jcommander-1.35.jar:/Users/asl/.nextflow/capsule/deps/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar:/Users/asl/.nextflow/capsule/deps/org/iq80/leveldb/leveldb/0.12/leveldb-0.12.jar:/Users/asl/.nextflow/capsule/deps/org/eclipse/jgit/org.eclipse.jgit/5.2.1.201812262042-r/org.eclipse.jgit-5.2.1.201812262042-r.jar:/Users/asl/.nextflow/capsule/deps/javax/mail/mail/1.4.7/mail-1.4.7.jar:/Users/asl/.nextflow/capsule/deps/javax/activation/activation/1.1.1/activation-1.1.1.jar:/Users/asl/.nextflow/capsule/deps/org/yaml/snakeyaml/1.18/snakeyaml-1.18.jar:/Users/asl/.nextflow/capsule/deps/org/jsoup/jsoup/1.11.2/jsoup-1.11.2.jar:/Users/asl/.nextflow/capsule/deps/jline/jline/2.9/jline-2.9.jar:/Users/asl/.nextflow/capsule/deps/org/pf4j/pf4j/3.4.1/pf4j-3.4.1.jar:/Users/asl/.nextflow/capsule/deps/com/google/guava/guava/24.1.1-jre/guava-24.1.1-jre.jar:/Users/asl/.nextflow/capsule/deps/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar:/Users/asl/.nextflow/capsule/deps/org/multiverse/multiverse-core/0.7.0/multiverse-core-0.7.0.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/jsr166-mirror/jsr166y/1.7.0/jsr166y-1.7.0.jar:/Users/asl/.nextflow/capsule/deps/org/objenesis/objenesis/2.1/objenesis-2.1.jar:/Users/asl/.nextflow/capsule/deps/org/iq80/leveldb/leveldb-api/0.12/leveldb-api-0.12.jar:/Users/asl/.nextflow/capsule/deps/com/jcraft/jsch/0.1.54/jsch-0.1.54.jar:/Users/asl/.nextflow/capsule/deps/com/jcraft/jzlib/1.1.1/jzlib-1.1.1.jar:/Users/asl/.nextflow/capsule/deps/com/googlecode/javaewah/JavaEWAH/1.1.6/JavaEWAH-1.1.6.jar:/Users/asl/.nextflow/capsule/deps/com/github/zafarkhaja/java-semver/0.9.0/java-semver-0.9.0.jar:/Users/asl/.nextflow/capsule/deps/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar:/Users/asl/.nextflow/capsule/deps/org/checkerframework/checker-compat-qual/2.0.0/checker-compat-qual-2.0.0.jar:/Users/asl/.nextflow/capsule/deps/com/google/errorprone/error_prone_annotations/2.1.3/error_prone_annotations-2.1.3.jar:/Users/asl/.nextflow/capsule/deps/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar:/Users/asl/.nextflow/capsule/deps/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14.jar:/Users/asl/.nextflow/capsule/deps/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar" "nextflow.cli.Launcher"
Environment
- Nextflow version: [?]
- Java version: 1.8.0_261
- Operating system: macOS
- Bash version: (use the command
$SHELL --version):
GNU bash, version 3.2.57(1)-release (arm64-apple-darwin21)
Copyright (C) 2007 Free Software Foundation, Inc.
(note that $SHELL reports current shell which might be not bash)