Comments (1)
Hi @Ramakant701 thank you for bringing this to our attention! We are currently deprecating the Docker Hub repository and have moved the newest images to Quay.io — these images should have support for the linux/arm64/v8 platform.
Image Source
Quay.io ✅
https://quay.io/repository/ohsu-comp-bio/funnel?tab=tags
Docker Hub ❌
https://hub.docker.com/r/ohsucompbio/funnel
Running Nextflow (Default)
When running the command you listed we encountered a "unable to start container process: exec: "/bin/bash": stat /bin/bash: no such file or directory" error, which may be due to a slight difference in local configuration.
Changing the Docker image to from Alpine to Ubuntu resolved this error, and when run against nf-canary returned successfully results:
nextflow run main.nf -profile test,docker -with-docker ubuntu -plugins nf-ga4gh,nf-tower --outdir local
N E X T F L O W ~ version 23.08.0-edge
Launching `main.nf` [mad_perlman] DSL2 - revision: c4fee08c84
WARN: Access to undefined parameter `remoteFile` -- Initialise it to a default value eg. `params.remoteFile = some_value`
executor > local (12)
[52/f784bc] process > NF_CANARY:TEST_SUCCESS [100%] 1 of 1 ✔
[cb/85ce31] process > NF_CANARY:TEST_CREATE_FILE [100%] 1 of 1 ✔
[85/7cb95a] process > NF_CANARY:TEST_CREATE_FOLDER [100%] 1 of 1 ✔
[d1/9db76e] process > NF_CANARY:TEST_INPUT (1) [100%] 1 of 1 ✔
[87/c97e42] process > NF_CANARY:TEST_BIN_SCRIPT [100%] 1 of 1 ✔
[- ] process > NF_CANARY:TEST_STAGE_REMOTE -
[f1/efb431] process > NF_CANARY:TEST_PASS_FILE [100%] 1 of 1 ✔
[77/6972ab] process > NF_CANARY:TEST_PASS_FOLDER [100%] 1 of 1 ✔
[e2/6270eb] process > NF_CANARY:TEST_PUBLISH_FILE [100%] 1 of 1 ✔
[5c/721c09] process > NF_CANARY:TEST_PUBLISH_FOLDER [100%] 1 of 1 ✔
[5f/e88a92] process > NF_CANARY:TEST_IGNORED_FAIL [100%] 1 of 1, failed: 1 ✔
[24/0e48ec] process > NF_CANARY:TEST_MV_FILE [100%] 1 of 1 ✔
[0e/0c349d] process > NF_CANARY:TEST_MV_FOLDER_CONTENTS [100%] 1 of 1 ✔
[5f/e88a92] NOTE: Process `NF_CANARY:TEST_IGNORED_FAIL` terminated with an error exit status (1) -- Error is ignored
Running Nextflow with Funnel
This local test script demonstrates how to connect Funnel (or any TES executor) to Nextflow:
Haven't tested against Colima but can try that and update here. Also happy to help take a look at the Nextflow or Funnel configs that you are working with to see what the cause of the issue may be!
from funnel.
Related Issues (20)
- TES v1.1: Create task with ignore_error flag
- TES: List task with next page token
- Failing lint job in tests
- github.com/golang/protobuf deprecation
- Homebrew formula returns "wrong number of arguments" error
- funnel binary not found during Slurm tests HOT 1
- Configuration for replacing path prefixes
- Boltdb deprecation HOT 2
- Task ID returned before database doc is created
- Feature Request: Add support for native K8s Executor
- Add Snakemake workflow tests to Funnel
- Funnel Tasks Fail when used as a TES Executor for Nextflow HOT 2
- Allow Funnel to run tasks against custom domain socket HOT 1
- Add option to connect to Gen3 systems
- Expose backend parameter to run container with additional permissions HOT 1
- Funnel does not detect terminated instances on AWS
- Authentication failure connecting to mongodb HOT 1
- funnel 0.11 problems with mongodb
- funnel 0.11 error with AWS batch reconciler
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from funnel.