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ava_mem = (double) (Runtime.getRuntime().freeMemory()) ava_cpu = Runtime.getRuntime().availableProcessors()
Hello here :-)
By any luck, would anyone have a circle-ci version 2 config to share (instead of travis)?
I can't get it to work with containerized processes...
.circleci/config.yml looks like this:
version: 2 jobs: build: docker: - image: circleci/openjdk:8-jdk-stretch-node-browsers working_directory: ~/repo steps: - checkout - run: name: Install nextflow command: | cd /tmp wget -qO- https://get.nextflow.io | bash chmod 777 nextflow sudo ln -s /tmp/nextflow /usr/local/bin/nextflow - setup_remote_docker: docker_layer_caching: true - run: name: Testing nextflow command: | chmod 775 ~/repo cd ~/repo nextflow -dockerize run -w ~/repo hello
and the failure message from circle-ci :
ERROR ~ .nextflow/history.lock (No such file or directory)
("project" at https://github.com/huguesfontenelle/nextflow-circleci )
-w ~/repois a great idea either. Not sure what that will do. Any reason why you can't leave that as the default? (will end up being
-d, -dockerize Launch nextflow via Docker (experimental)
OK I got it:
It's not possible to use volume mounting with the docker executor, but using the machine executor it's possible to mount local directories to your running Docker containers. You can learn more about the machine executor here on our docs page.
singularity pull --name nf-core-deepvariant.simg docker://nfcore/deepvariant
Thanks for addressing,
the "problem" with building it, is that it takes cpu, so locally is not always a possibility. and if you are working on "GDPR proof " cluster you dont have that option.
of course it is easy to get around this by having an open cluster somewhere, but that means another layer for someone to set up.