Adding a module cycleassembler?

Hello,

I need to use : cycleassembler GitHub - ntoda03/cycleassembler
is it possible to install this module?

Thanks!

Hi @cmaridakis, you can use this nextflow pipeline directly with nextflow.

Load the nextflow module: module load nextflow/24.04.1 and then get the pipeline: nextflow pull ntoda03/cycleassembler -r master.

See documentation here: Nextflow - IFB Core Cluster Documentation, we have a profile for the cluster as well: nf-core/configs: ifb_core

Let us know if you encounter a technical difficulty running the pipeline

Thank you!

Hi! I have tried using the pipeline (we are both interested in it with @cmaridakis ), and I’m stuck with the dependencies.
The author of the pipeline recommends using Docker for dependencies, but I figure the IFB cluster doesn’t have it. I thus created a conda environment with all dependencies, but once I activate the environment, I don’t have access to nextflow anymore and I can’t start the pipeline at all.
How can I approach this?

I ended up solving the environment problem!
The logic was to use the Dockerfile included in the cycleassembler repository, create the image using docker on my local machine, then upload this image to the cluster and convert the docker image into a singularity image.
I followed this tutorial: Converting Docker Images to Singularity for Use on Pleiades - HECC Knowledge Base
On local machine:

  • download the Dockerfile
  • install docker
  • build image from Dockerfile (will take a while)
  • copy the image on the cluster
  • convert the image to .sif
    Then, you have to add to your nextflow command "-with-apptainer <your_singularity_file>.sif" and everything runs perfect (for now at least).
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