Is it possible to run Snakemake pipelines on DNAnexus? I'm trying to use DROP () but having many issues running it, any previous code example on Snakemake that works on DNAnexus?

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  Former User of DNAx Community_100

  • 09 August 2023 16:25

  DROP: https://gagneurlab-drop.readthedocs.io/en/latest/

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  Ondrej Klempir DNAnexus Team

  • 10 August 2023 11:57

  Can you elaborate more about the issues you observed and how you try to run the tool?

   

  I have tried to install the tool you mentioned on RAP and it was successful. I used the ttyd app (interactive session) with multicore instance type.

   

  First, I had to install Mamba:

   

  wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"

  bash Mambaforge-$(uname)-$(uname -m).sh

   

  Second, I explored the mamba installation, changed directory to mamba and created an env for drop:

  cd /home/dnanexus/mambaforge

  ./mamba create -n drop -c conda-forge -c bioconda drop

   

  Third, activate the drop env:

  mamba activate drop

   

  Tested commands such as:

  drop

  drop demo

  snakemake

  snakemake --cores 1 -n

   

  It seems to me that all went well, but I am pretty new to snakemake so I might be wrong.

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