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Installation problem #3

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coro1c opened this issue Jan 15, 2025 · 2 comments
Closed

Installation problem #3

coro1c opened this issue Jan 15, 2025 · 2 comments

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@coro1c
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coro1c commented Jan 15, 2025

Hi Peter,

Many thanks for your great analysis pipeline.

I tried pulling sequeduct with:
nextflow pull edinburgh-genome-foundry/Sequeduct -r v0.3.2

but I get the following error message:
Checking edinburgh-genome-foundry/Sequeduct ... Cannot find revision v0.3.2-- Make sure that it exists in the remote repositoryhttps://github.com/edinburgh-genome-foundry/Sequeduct``

Do you know what could cause the problem?

I then tried installing the pipeline using the github repo directly, which worked with just 1 warning:

 1 warning found (use docker --debug to expand):
 - LegacyKeyValueFormat: "ENV key=value" should be used instead of legacy "ENV key value" format (line 55)

However, when I try running the NanoFilt, I get the following error:
nextflow run edinburgh-genome-foundry/Sequeduct -r v0.3.1 -entry preview
--fastq_dir='fastq_pass'
--sample_sheet='sample_sheet.csv'
-profile docker

grafik

Do you know how I can resolve the issue?

I am running it under Ubuntu 22.04, Docker version 27.4.0, build bde2b89.

Many thanks in advance for your help.

@veghp
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veghp commented Jan 15, 2025

Hi, thanks for trying this out. There are two separate issues. The codebase wasn't tagged but now nextflow pull edinburgh-genome-foundry/Sequeduct -r v0.3.2 should work.

The other issue is that you have to build the docker image for yourself, using the above v0.3.2 version. I recently updated the software that it installs to make sure it builds. (pulling the image works only "if you have access to EGF's container repo (e.g. EGF staff members)").

See readme for instructions: https://github.com/Edinburgh-Genome-Foundry/Sequeduct?tab=readme-ov-file#build

Note, after that your command then should be as stated in the readme:

nextflow run edinburgh-genome-foundry/Sequeduct -r v0.3.2 -entry preview --fastq_dir='fastq_pass' \
    --reference_dir='genbank' \
    --sample_sheet='sample_sheet.csv' \
    -with-docker sequeduct_local

where sequeduct_local is the name you gave during build.

@coro1c
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coro1c commented Jan 16, 2025

many thanks! this solved the issue. I can now run Sequeduct.

@coro1c coro1c closed this as completed Jan 16, 2025
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