These are chat archives for nextflow-io/nextflow
$ sudo apt-get install default-jre
wget -qO- get.nextflow.io | bash
$ ./nextflow run helloworld Picked up _JAVA_OPTIONS: -Xint Picked up _JAVA_OPTIONS: -Xint N E X T F L O W ~ version 0.22.0 Pulling nextflow-io/helloworld ... downloaded from https://github.com/nextflow-io/hello.git Launching `nextflow-io/helloworld` [tiny_feynman] - revision: 6b9515aba6 [master] [warm up] executor > local [5f/e40692] Submitted process > sayHello (2) [be/b563cd] Submitted process > sayHello (4) [54/51232c] Submitted process > sayHello (3) [c0/90c9d8] Submitted process > sayHello (1) Hola world! Bonjour world! Hello world! Ciao world!
-Xintfix. Hopefuly it will be fixed in a future update.
wget https://get.docker.com/builds/Linux/x86_64/docker-1.12.0.tgz tar -xzvf docker-1.12.0.tgz mkdir ~/bin mv docker/docker ~/bin mv nextflow ~/bin export PATH=$PATH:~/bin export DOCKER_HOST=localhost:2375
docker run -i -v c:/Users/m_fol/AppData/Local/Lxss/home/mfoll/work/01/3649c747b2ea81505e2e8d86207363:/home/mfoll/work/01/3649c747b2ea81505e2e8d86207363 -w "$PWD" --entrypoint /bin/bash nextflow/examples -c "/bin/bash -ue /home/mfoll/work/01/3649c747b2ea81505e2e8d86207363/.command.sh”
c:/Users/m_fol/AppData/Local/Lxssbefore mounting the volume in my case
TraceRecordas a string where the string is just what was being logged before. I've got two concerns with the approach. First, the inputHashesTrace string is being produced every time the TaskProcessor.createTaskHashKey is called, something that was previously only happening when
-tracewas enabled. I don't have a good sense of whether there might be performance concerns with this. Second, the inputHashesTrace string adds a bunch of newlines, which will mess up the log or trace output. The output actually looks OK as it is, it's just not nicely tab delimited. Maybe this is OK since the input_hashes is an optional field, but maybe not? Apart from that, I think this would make debugging caching issues really helpful. Obviously, no rush on this!