charliecloud

First of all makes sure that you have the following $PATH

PATH=/Xnfs/abc/charliecloud_bin/:/Xnfs/abc/nextflow_bin:$PATH

and add this line to your ~/.bashrc or ~/.zshrc file to make the change permanent.

Here are some example of charliecloud usage to replace singularity:

build a container from the DockerHub (where nfcore/tools:2.6 is the container):

ch-image pull -s /Xnfs/abc/charliecloud/ nfcore/tools:2.6

build a container from quay.io (where biocontainers/fastp:0.23.2--h5f740d0_3 is the container):

ch-image pull -s /Xnfs/abc/charliecloud/ quay.io/biocontainers/fastp:0.23.2--h5f740d0_3

Run a container:

Before running a container make sure that there is a /scratch directory at the root of the container image

update_ch_image.sh

LBMC pipelines

If you want to test slurm and charliecloud with nextflow on the PSMN please do the following in your nextflow pipeline folder:

git remote add upstream git@gitbio.ens-lyon.fr:LBMC/nextflow.git
git pull upstream master

To update your pipeline (DSL2) with the last configuration files:

PATH=/Xnfs/abc/charliecloud_bin/:$PATH

and add this line to your ~/.bashrc or ~/.zshrc file to make the change permanent.

Run your pipeline with the -profile psmn

Complain on element, if it’s not working

Voila

nf-core pipeline

edit: you can check this post for an up to date guide

Here is an example on how to run an nf-core pipeline on the PSMN:

Once you added PATH=/Xnfs/abc/charliecloud_bin/:$PATH to your path you can download a pipeline like so (for the rnaseq pipeline):

cd  <your scratch directory>
ch-run -b /scratch:/scratch \
  /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- nf-core \
  download rnaseq -r 3.9 --outdir <your scratch directory>/nf-core-rnaseq -x none -c none

Move to your nf-core-rnaseq folder

cd nf-core-rnaseq

Download the right configuration files for the PSMN:

rm -R configs
git clone https://github.com/l-modolo/nf-core-configs.git configs

Launch the pipeline with the PSMN profile.

Warning

We are currently working on improving the nextflow support for charliecloud. A patched version of nextflow is available on the PSMN here : /Xnfs/abc/nextflow_bin/nextflow. Older version of nextflow are also available for the DSL1 pipelines.

PATH=/Xnfs/abc/nextflow_bin//:$PATH

and add this line to your ~/.bashrc or ~/.zshrc file to make the change permanent.

With this version you can enable the readOnlyInputs input in charliecloud.

You have to update your configs/conf/psmn.config to the following:

charliecloud {
  enabled = true
  cacheDir = "/Xnfs/abc/charliecloud"
  runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
  readOnlyInputs = true
}
}

nextflow run workflow -profile test,psmn --outdir results/

For your own pipeline you can modify the PSMN profile as follow:

psmn {
    charliecloud.enabled = true
    charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
    charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
    charliecloud.readOnlyInputs = true