Uncollapsed Bam Generation
1.0.0
1.0.0
  • Introduction
  • Requirements
  • Installation and Usage
  • Tools Used
  • Inputs Description
  • Outputs Description
Powered by GitBook
On this page
  • Step 1: Create a virtual environment.
  • Step 1: For cwltool/toil, please install using python 3.6 as done below:
  • Step 2: Clone the repository
  • Step 3: Install requirements using pip
  • Step 4: Run the workflow with a given set of input using cwltool on single machine
  • Step 4: Run the workflow with a given set of input using toil on single machine
  • Step 4: Run the workflow with a given set of input using toil on JUNO (MSKCC Research Cluster)

Was this helpful?

Installation and Usage

How to install and run the workflow

PreviousRequirementsNextTools Used

Last updated 4 years ago

Was this helpful?

Step 1: Create a virtual environment.

Step 1: For cwltool/toil, please install using python 3.6 as done below:

Here we can use either or . Here we will use virtualenv.

pip3 install virtualenv
python3 -m venv my_project
source my_project/bin/activate

Once you execute the above command you will see your bash prompt something on these lines:

(my_project)[server]$

Step 2: Clone the repository

git-clone-with-submodule
git clone --recursive https://github.com/msk-access/uncollapsed_bam_generation.git
cd standard_bam_processing
git submodule update --recursive --remote

Step 3: Install requirements using pip

We have already specified the version of cwltool and other packages in the requirements.txt file. Please use this to install.

python-package-installation-using-pip
#python2
pip install -r requirements.txt
#python3
pip3 install -r requirements.txt

To see help for the inputs for cwl workflow you can use: cwltool uncollapsed_bam_generation.cwl --help

To see help for the inputs for cwl workflow you can use: toil-cwl-runner uncollapsed_bam_generation.cwl --help

cwltool-execution
cwltool uncollapsed_bam_generation.cwl inputs.yaml
toil-local-execution
toil-cwl-runner uncollapsed_bam_generation.cwl inputs.yaml
TMPDIR=$PWD
TOIL_LSF_ARGS='-W 3600'
toil-cwl-runner \
       --singularity \
       --logFile /path/to/toil_log/cwltoil.log  \
       --jobStore /path/to/jobStore \
       --batchSystem lsf \
       --workDir /path/to/toil_log \
       --outdir $PWD \
       --writeLogs /path/to/toil_log \
       --logLevel DEBUG \
       --stats \
       --retryCount 2 
       --disableCaching \
       --disableChaining \
       --maxLogFileSize 20000000000 \
       --cleanWorkDir onSuccess
       --preserve-environment TOIL_LSF_ARGS TMPDIR \
       /path/to/uncollapsed_bam_generation.cwl \
       /path/to/inputs.yaml \
       > toil.stdout \
       2> toil.stderr &

You should now be running the workflow on the specified batch system

Once we have successfully installed the requirements we can now run the workflow using cwltool/toil if you have proper input file generated either in or format. Please look at for more details.

Here we show how to use to run the workflow on single machine

Step 4: Run the workflow with a given set of input using on single machine

Here we show how to run the workflow using using single machine interface.

Once we have successfully installed the requirements we can now run the workflow using cwltool if you have proper input file generated either in or format. Please look at for more details.

Step 4: Run the workflow with a given set of input using on single machine

Here we show how to run the workflow using on MSKCC internal compute cluster called JUNO which has as a scheduler.

Step 4: Run the workflow with a given set of input using on JUNO (MSKCC Research Cluster)

virtualenv
conda
json
yaml
Inputs Description
cwltool
cwltool
toil-cwl-runner
json
yaml
Inputs Description
toil
toil-cwl-runner
IBM LSF
toil