KNIME Labelfree Quantification Experiments

This is the KNIME Labelfree Quantification workflow. We have extended the original Docker image to be compatible with RED and Curious Containers.

Execute from Reproducible Experiment Description (RED)

# install CC-FAICE
pip3 install --user pipx
pipx install cc-faice==8.*


# prepare
cd knime-labelfree-quantification

# execute
faice exec knime-labelfree-quantification.red.yml

# check outputs
ls outputs/*

Alternative: Execute from Common Workflow Language (CWL)

# install CWLTool
pip3 install --user pipx
pipx install cwltool

# prepare
cd knime-labelfree-quantification
curl -fOL https://s3.denbi.uni-tuebingen.de/fb-test/demo_container/cibi_user_meeting_2018/labelfree_example.tar.gz
mkdir labelfree_example
tar -zxvf labelfree_example.tar.gz -C labelfree_example

# execute
cwltool knime-labelfree-quantification.cwl.yml job.yml

# check outputs
ls *.csv *.log

Resources

• Docker Build Directory