fastp missing from docker image?

[ChristopherBarrington]

https://github.com/open2c/distiller-nf/blob/4236152b1d3a6ce38f82af257fd837833b782a67/docker/conda.list#L29

We had an issue that fastp could not be found when running the pipeline via docker. It looks like fastp is missing from the list of packages to include in the image? We could still run the pipeline by not using the Docker image.

Thanks!

[gspracklin]

Yes. In configs/local.config set docker = false and it should be fine. We'll update the docker image soon.

https://github.com/open2c/distiller-nf/blob/4236152b1d3a6ce38f82af257fd837833b782a67/configs/local.config#L71

[chorzow]

Hello everyone,

I am facing the same issue when try to launch the pipeline using singularity. @ChristopherBarrington could you share how to run distiller without using the Docker image? I am trying to run the test example as described in README but it fails because fastp is missing although it is installed in my conda environment (fastp 0.12.4). Am I missing something?

[ChristopherBarrington]

my usual approach is to put everything I need into a conda environment and set enabled=false in the docker and singularity stanzas of the --custom_config.

a quick fix would be to forgo the trimming by commenting/removing the trim_options from the parameters file, though that might not be your first choice!

[hisakatha]

For your information, I was able to use my local fastp binary from Singularity container by adding the following lines into configs/*.config:

singularity {
    enabled = true
    runOptions = '--env PREPEND_PATH=/path/to/fastp/dir --bind /mount_point_where_fastp_resides'
}

However, I would like to use an updated image by the maintainers for simplicity. I'm wondering whether #180 resolves this issue.

[agalitsyna]

Resolved in the distiller 0.3.4 release https://github.com/open2c/distiller-nf/releases/tag/v0.3.4 Feel free to re-open if any dependency is missing.