The shotgun metagenomics pipeline deploys and runs individual software components developed at the PennCHOP Microbiome program.
The deployment scripts assume that python 2.7 and pip are already installed.
To deploy the pipeline on a fresh computer:
source deploy_virtualenv.sh
./deploy.shThe first script will set up and activate a new virtual environment
named shotgun-pipeline. Please see the notes inside the file
deploy_virtualenv.sh for help with setting up virtual environment in
future sessions.
The second script will then download and unzip the software and data files necessary to run the pipeline.
To test the pipeline, run the command:
./test/test_qsub.shThis will run the pipeline on a small dataset, and should complete in a few minutes.
The pipeline expects a work directory to be set up with three files.
The first file, containing the forward reads in FASTQ format, must end
in _R1.fastq. The second file should contain the reverse reads in
FASTQ format, and end with _R2.fastq. The third file should contain
the sample names and barcode sequences, one per line, in tab-separated
format. Rules for the barcode file are specified in the decontam
software.
The pipeline is run by a submission script, which takes two arguments:
a job ID and the work directory. For example, to run the pipeline on
a dataset stored in the folder /home/norf/MyData, run the command:
/pipeline-qsub/submit.sh job1 /home/norf/MyDataJobs submitted to the queue will then be prefixed by "job1-".
To run jobs without a queuing system, you may set the environment
variable NO_QSUB to 1. See the file ./test/test_qsub.sh for an
example.