Installation and Usage

If you have paired-end umi-tagged fastqs, you can run the ACCESS fastq to bam workflow with the following steps

Step 1: Create a virtual environment.

Option (A) - if using cwltool

If you are using cwltool only, please proceed using python 3.9 as done below:

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

python3-conda-virtualenv

conda create --name my_project python=3.9
conda activate my_project

Option (B) - recommended for Juno HPC cluster

If you are using toil, python 3 is required. Please install using Python 3.9 as done below:

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

python3-conda-virtaulenv

conda create --name my_project python=3.9
conda activate my_project

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

bash-prompt-example

(my_project)[server]$

Step 2: Clone the repository

git-clone-with-submodule

git clone --recursive --branch 3.0.4 https://github.com/msk-access/nucleo.git

Note: Change 3.0.4 to the latest stable release of the pipeline

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

#python3
cd nucleo
pip3 install -r requirements.txt

Step 4: Check if you have singularity and nodejs for HPC

For HPC normally singularity is used for containers. Thus please make sure that is installed. For JUNO, you can do the following:

load-singularity-on-juno

module load singularity

We also need to make sure nodejs is installed, this can be installed using conda:

conda-install-nodejs

conda install -c conda-forge nodejs

Step 5: Generate an inputs file

Next, you must generate a proper input file in either json or yaml format.

For details on how to create this file, please follow this example (there is a minimal example of what needs to be filled in at the end of the page):

Inputs Description

It's also possible to create and fill in a "template" inputs file using this command:

$ cwltool --make-template nucleo.cwl > inputs.yaml

This may or may not work. We are not exactly sure why. But you can always use Rabix to generate the template input

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

Once we have successfully installed the requirements we can now run the workflow using cwltool/toil .

Step 6: Run the workflow

Using cwltool

Here we show how to use cwltool to run the workflow on a single machine, such as a laptop

Run the workflow with a given set of input using cwltool on single machine

cwltool-execution

cwltool nucleo.cwl inputs.yaml

Using toil-cwl-runner locally

Here we show how to run the workflow using toil-cwl-runner 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 json or yaml format. Please look at Inputs Description for more details.

Run the workflow with a given set of input using toil on single machine

toil-local-execution

toil-cwl-runner nucleo.cwl inputs.yaml

Using toil-cwl-runner on JUNO

Here we show how to run the workflow using toil-cwl-runner on MSKCC internal compute cluster called JUNO which has IBM LSF as a scheduler.

Note the use of --singularityto convert Docker containers into singularity containers, the TMPDIR environment variable to avoid writing temporary files to shared disk space, the _JAVA_OPTIONS environment variable to specify java temporary directory to /scratch, using SINGULARITY_BINDPATH environment variable to bind the /scratch when running singularity containers and TOIl_LSF_ARGS to specify any additional arguments to bsubcommands that the jobs should have (in this case, setting a max wall-time of 6 hours).

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

toil-lsf-execution

TMPDIR=$PWD
TOIL_LSF_ARGS='-W 3600 -P test_nucleo -app anyOS -R select[type==CentOS7]'
_JAVA_OPTIONS='-Djava.io.tmpdir=/scratch/'
SINGULARITY_BINDPATH='/scratch:/scratch:rw'
toil-cwl-runner \
       --singularity \
       --logFile ./example.log  \
       --jobStore ./example_jobStore \
       --batchSystem lsf \
       --workDir ./example_working_directory/ \
       --outdir $PWD \
       --writeLogs ./example_log_folder/ \
       --logLevel DEBUG \
       --stats \
       --retryCount 2 \
       --disableCaching \
       --disableChaining \
       --preserve-environment TOIL_LSF_ARGS TMPDIR \
       --maxLogFileSize 20000000000 \
       --cleanWorkDir onSuccess \
       nucleo.cwl \
       inputs.yaml \
       > toil.stdout \
       2> toil.stderr &

Your workflow should now be running on the specified batch system. See outputs for a description of the resulting files when is it completed.