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I am trying to run nextflow in a singularity container and further use this for running other pipelines that are made for nextflow. This will help us bypass installation of nextflow in our servers. I am running this on a Linux server.
I am able to run nextflow on a singularity container
I am also able to run the singularity container that contains the workflow on a separate server that has nextflow installed. I also made a config file for nextflow
WARN: Inferring genetic sex of sample as params.sex was not provided.
Pulling Singularity image docker://ontresearch/wf-common:sha338caea0a2532dc0ea8f46638ccc322bb8f9af48 [cache /home/ontresearch-wf-common-sha338caea0a2532dc0ea8f46638ccc322bb8f9af48.img]
Pulling Singularity image docker://ontresearch/wf-human-variation-str:shaa2f49ce57886426516eadd4048b6fdf9c22c7437 [cache /home/ontresearch-wf-human-variation-str-shaa2f49ce57886426516eadd4048b6fdf9c22c7437.img]
Pulling Singularity image docker://ontresearch/spectre:sha5a2890023dc7a7899f47585103b4f5762fb9d1b3 [cache /home/ontresearch-spectre-sha5a2890023dc7a7899f47585103b4f5762fb9d1b3.img]
Pulling Singularity image docker://ontresearch/wf-human-variation-snp:sha17e686336bf6305f9c90b36bc52ff9dd1fa73ee9 [cache /home/ontresearch-wf-human-variation-snp-sha17e686336bf6305f9c90b36bc52ff9dd1fa73ee9.img]
ERROR ~ Error executing process > 'str:getVersions'
Caused by:
Failed to pull singularity image
command: singularity pull --name ontresearch-wf-human-variation-str-shaa2f49ce57886426516eadd4048b6fdf9c22c7437.img.pulling.1720615544417 docker://ontresearch/wf-human-variation-str:shaa2f49ce57886426516eadd4048b6fdf9c22c7437 > /dev/null
status : 127
message:
bash: line 1: singularity: command not found
I could add the .nextflow.log report as well if it is useful. I have tried multiple ways that the local singularity container is recognised but it isnt working. Is there something within my script I should add so that the other singularity image is also recognised? am I missing something?
Thanks for your help
The text was updated successfully, but these errors were encountered:
Hello,
I am trying to run nextflow in a singularity container and further use this for running other pipelines that are made for nextflow. This will help us bypass installation of nextflow in our servers. I am running this on a Linux server.
I am able to run nextflow on a singularity container
I am also able to run the singularity container that contains the workflow on a separate server that has nextflow installed. I also made a config file for nextflow
I tried to launch the script like this:
I get the following error
I could add the .nextflow.log report as well if it is useful. I have tried multiple ways that the local singularity container is recognised but it isnt working. Is there something within my script I should add so that the other singularity image is also recognised? am I missing something?
Thanks for your help
The text was updated successfully, but these errors were encountered: