changed 2 years ago  
Published Linked with GitHub

https://liulab-dfci.github.io/RIMA/index.html
https://github.com/liulab-dfci/RIMA_pipeline

Container definition file: https://github.com/pmitev/UPPMAX-Singularity/tree/main/RIMA

The pipeline setup is installed in a Singularity/Apptainer container with all required tools to run the complete workflow.

  1. Transfer the Singularity container that is currently stored on Rackham1 at rackham1.uppmax.uu.se:/tmp/RIMA.sif to Bianca in the project folder /crex/proj/PROJECT/RIMA or so.

The container contains the git repository as well. To extract the repository outside the container run

# adapt the destination folder
singularity exec RIMA.sif cp -av /installs/RIMA_pipeline /crex/proj/PROJECT/RIMA/

Small fix for the renamed program that is still called from modules/microbiome/microbiome_cohort.snakefile:44: " && {params.path}; Rscript src/microbiome/mic_plot.R --input {output.merged_file}

cd RIMA_pipeline/src/microbiome
ln -s microbiome_plot.R mic_plot.R
  1. Start an interactive job with at least 8 CPUs (to reserve at least 64GB as mentioned in the manual).
interactive -A sensXXXXX -n 16 -t 5-00:00

On the allocated node…

# adapt the location
cd /crex/proj/PROJECT/RIMA/RIMA_pipeline
singularity shell ../RIMA.sif
Singularity> source activate RIMA
(RIMA) Singularity> snakemake -s RIMA.snakefile -np
...

To run non interactively (example)

singularity exec RIMA.sif bash -c "source activate RIMA; snakemake -v; python -V "
5.5.4
Python 3.6.10 :: Anaconda, Inc.

Singularity container definition file (for reference only)

https://github.com/pmitev/UPPMAX-Singularity/tree/main/RIMA

Bootstrap: docker
From: condaforge/mambaforge

%environment
  export LC_ALL=C
  export PYTHONNOUSERSITE=True

%files

%post
  export LC_ALL=C
  export PYTHONNOUSERSITE=True
  export CONDA_PKGS_DIRS=/tmp/mamba_pkgs_dir
  mkdir -p ${CONDA_PKGS_DIRS}

  apt-get update &&  apt-get install -y git libfontconfig1 libxrender1 libffi7
  ln -s /usr/lib/x86_64-linux-gnu/libffi.so.7 /usr/lib/x86_64-linux-gnu/libffi.so.6

  mkdir -p /installs 

  cd /installs
  git clone https://github.com/liulab-dfci/RIMA_pipeline.git
  cd RIMA_pipeline
  echo "    - markdown==3.3.7"  >> static/environment/GCP/rna.yml
  echo "    - requests==2.27.1" >> static/environment/GCP/rna.yml
  echo "    - Cython"           >> static/environment/GCP/rna.yml
  bash ./RIMA_environment.sh -p GCP

  conda env list
  
  # No need to clean = packages are kept otside in $CONDA_PKGS_DIRS
  #conda clean --all --yes

%runscript
  /bin/bash "$@"

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