struckma / vre_segmentation

VRE Sample Tool

A simple example tool that is ready to run a workflow

Requirements

• Install the dependencies used by the Wrapper.

sudo apt update
sudo apt install git
sudo apt install docker-ce

Remember to add your username to the docker group.

sudo usermod -a -G docker $USER

• Install the Wrapper dependencies.

  • Python 3.6 or +
  • Python3.6-dev and Python3.6-venv or +
  • mg-tool-api: https://github.com/Multiscale-Genomics/mg-tool-api.git
  • cwltool: https://github.com/common-workflow-language/cwltool.git

Installation

Directly from GitHub:

cd $HOME

git clone https://github.com/lrodrin/vre_sample_tool.git

cd vre_sample_tool

Create the Python environment

python3 -m venv $HOME/vre_sample_tool/venv
source venv/bin/activate
pip install -r requirements.txt

Configuration

Add your ${USER} in tests/basic/config.json:

"arguments": [
  {
      "name": "execution",
      "value": "/home/${USER}/vre_sample_tool/tests/basic/run000"
  }
],
"output_files": [
  {
      "name": "bam_file",
      "required": true,
      "allow_multiple": false,
      "file": {
          "file_path": "/home/${USER}/vre_sample_tool/tests/basic/run000/A.bam"
      }
   }
]

and tests/basic/in_metadata.json:

{
    "_id": "unique_file_id_5e14abe0a37012.29503907",
    "file_path": "/home/${USER}/vre_sample_tool/tests/basic/NA12878.bam"
},
{
    "_id": "unique_file_id_5e14abe0a37012.29503908",
    "file_path": "/home/${USER}/vre_sample_tool/tests/basic/hg38.fa"
{

and /test/basic/input_basic_example.yml:

  input_reads: 
    class: File
    location: /home/{USER}/vre_sample_tool/tests/basic/NA12878.bam
  biospecimen_name: "hg38"
  output_basename: "mytest"
  indexed_reference_fasta:
    class: File 
    location: /home/{USER}/vre_sample_tool/tests/basic/hg38.fa

Run the example

./tests/basic/test_VRE_CWL_RUNNER.sh