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chore(deps): bump y18n from 3.2… (compare)
Model error: e.requirements.forEach is not a function
I'm on
Version: 1.45.1
Commit: 5763d909d5f12fe19f215cbfdd29a91c0fa9208a
Date: 2020-05-14T08:33:47.663Z (2 wks ago)
Electron: 7.2.4
Chrome: 78.0.3904.130
Node.js: 12.8.1
V8: 7.8.279.23-electron.0
OS: Darwin x64 19.4.0
With Benten VS Code version 2019.12.3
Hi all!
I am experimenting with the composer and had an issue. The example I am running through says to use the following:
requirements:
- class: DockerRequirement
dockerPull: biocontainers/bwa
but the docker pull fails unless I put the SPECIFIC tag desired in the line dockerPull: biocontainers/bwa:v0.7.17_cv1
I tried using dockerPull: biocontainers/bwa:latest
as well and that failed. Is the tutorial outdated or is it a Docker issue or something else? I know I heard that Docker is changing things up...
quay.io/biocontainers/bwa:0.7.8--hed695b0_5
instead
[2020-12-01 08:33:25.051] [DEBUG] Pulling docker image
[2020-12-01 08:33:25.051] [INFO] Pulling docker image biocontainers/bwa:latest
[2020-12-01 08:33:25.052] [DEBUG] Using configfile: /Users/hadley/.docker/config.json
[2020-12-01 08:33:25.063] [WARN] Could not find auth field for https://index.docker.io/v1/
[2020-12-01 08:33:26.451] [INFO] Failed to pull docker image. Retrying in 30 seconds
[2020-12-01 08:33:26.451] [INFO] Composer: {"status": "DOCKER_PULL_FAILED", "retry": 30, "image": "biocontainers/bwa:latest","message": "Request error: POST unix://localhost:80/images/create?fromImage=biocontainers/bwa&tag=latest: 404"}
[2020-12-01 08:33:26.456] [ERROR] Method invocation failed. Method public synchronized void org.rabix.executor.container.impl.DockerContainerHandler$DockerClientLockDecorator.pull(java.lang.String,com.spotify.docker.client.messages.AuthConfig) throws com.spotify.docker.client.exceptions.DockerException,java.lang.InterruptedException
java.util.concurrent.ExecutionException: java.lang.Exception: com.spotify.docker.client.exceptions.DockerRequestException: Request error: POST unix://localhost:80/images/create?fromImage=biocontainers/bwa&tag=latest: 404
at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[na:1.8.0_191]
Failed to pull docker image. Retrying in 30 seconds
I was given a CWL workflow with over 16,000 lines (after removing the sbg:*
fields and collapsing long JS expressions to single lines), and I would like to visualize it. Its size is mostly because it's nested, i.e. sub-workflows are defined within the CWL file rather than using external references. I tried using Rabix Composer to visualize the workflow, but I can't seem to inspect the sub-workflows.
Does anyone here have suggestions on how to visualize a nested workflow in either Rabix Composer or another tool? Thanks in advance!
I tried using the "Benten: CWL preview" feature in the VS Code extension, but I ran into the following error:
Command 'Benten: CWL preview' resulted in an error (command 'cwl.show_graph' not found)
If folks here can confirm that they expect this cwl.show_graph
command to work on nested workflows, then I can dig deeper to resolve this issue. Any pointers would be appreciated!
heya Rabix folks... I'm trying out Composer 1.5.0 ... but when I open a workflow it does not seem to use the namespaces I provided. I.e. I have
$namespaces:
bio-cwl-tools: https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/
edam: http://edamontology.org/
iana: https://www.iana.org/assignments/media-types/
lukasa: https://raw.githubusercontent.com/pvanheus/lukasa/main/tools/
s: http://schema.org/
but it wants to find lukasa:BLAH.cwl
in my working directory. Is there a way to switch on HTTP/S link resolution?