pandora_workflow's Introduction

Pandora workflow

Snakemake pipeline to run pandora with and without denovo enabled.

The version used in the pandora paper review has tag pandora_paper_update_31_03_2021.

The version used in the pandora paper submission has tag pandora_paper_tag1.

Running

Requirements

Dependencies

python 3.6+;
singularity 2.4.1+;

Setting up virtualenv

./setup.sh

Running on the sample example:

Download sample data (TODO: add link);
unzip sample_data.zip
source venv/bin/activate
bash scripts/run_pipeline_local.sh -j8

Running on the paper data:

git checkout pandora_paper_tag1
source venv/bin/activate

If you want to run local:

bash scripts/run_pipeline_local.sh -j <NB_OF_THREADS> --configfile config.pandora_paper_tag1.yaml

If you want to run on an LSF cluster:

bash scripts/submit_lsf.sh --configfile config.pandora_paper_tag1.yaml

Troubleshooting

If you get this error:

Building DAG of jobs...
Pulling singularity image docker://leandroishilima/subsampler:pandora_paper_tag1.
WorkflowError:
Failed to pull singularity image from docker://leandroishilima/subsampler:pandora_paper_tag1:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
ERROR: Image file exists, not overwriting.

  File "/hps/nobackup2/iqbal/leandro/pandora_paper_tag1/subsampler/venv/lib/python3.7/site-packages/snakemake/deployment/singularity.py", line 88, in pull

pass to the running script the default location where singularity images are store. For example, in the EBI cluster, it would be --singularity-prefix /nfs/leia/singularity/leandro/.

pandora_workflow's People

Contributors

Stargazers

Watchers

pandora_workflow's Issues

Original PRG and new PRG dont have the same number of entries

Hello,

Thank you for your wonderful tool. I have been testing it out and I am getting an error at this step:

assert prgs_in_original == prgs_in_new, f"Original PRG ({prgs_in_original}) and new PRG ({prgs_in_new}) dont have the same number of entries!"

I looked the prgs_run_status folder and don't see any issues. I am not sure why I have fewer PRGs in the new (2454) compared to the original (3804). I would appreciate your guidance on this matter.

Best wishes,
Sara