singularity guide

[Tcvalenzuela]

Hi the tool looks amazing!.

I'm trying to use it, maybe is my lack of experience with singularity but after downloading and run it as :

singularity shell -B /srv/public:/srv/public graffite_latest.sif

I face the problem that I don't know where are the programs.

I tried: ` Singularity> run GraffiTE bash: run: command not found

Singularity> nextflow run cgroza/GraffiTE
bash: nextflow: command not found

` Can you add some translation of the documentation for Nextflow?

Thanks!

[clemgoub]

Hi there!

You actually don't need to use the singularity container by yourself, Nextflow will take care of it for you =)

• 1. Make sure you have Nextflow installed
• 2. To use GraffiTE, make sure Nextflow and Singularity are in the path (or loaded as module on the HPC) and run GraffiTE with the command:

nextflow run cgroza/GraffiTE \
   --assemblies assemblies.csv \
   --TE_library library.fa \
   --reference reference.fa \
   --reads reads.csv

It should download and cache the pipeline and the singularity container. It may take a while do download everything at the first time, but then it will be cached and available on the spot.

If for some reasons (for example your compute nodes don't have access to internet, or else,...) you can

1. Clone the github repos git clone https://github.com/cgroza/GraffiTE.git
2. Pull the singularity image (as you did) singularity pull --arch amd64 graffite_latest.sif library://clemgoub/graffite/graffite:latest
3. Use the pipeline with this command:

nextflow run <path-to-install>/GraffiTE/main.nf \
   --assemblies assemblies.csv \
   --TE_library library.fa \
   --reference reference.fa \
   --reads reads.csv \
   -with-singularity <your-path>/graffite_latest.sif

-with-singularity need to be given with a single -, because it is a Nextflow override command. You can also set the path to the singularity image in <your-path>/GraffiTE/nextflow.config in order to skip this command when you run the pipeline.

Let me know if you need further help!

Cheers,

Clément