SYNOPSIS

The programm palantir-processor links NGS data from the Queue API of the Next Generation Sequencing Facility of the Vienna Biocenter Core Facilities to your local filesystem. It runs basic quantification operations (e.g. counting) which act as basis for the import in the Palantir database.

USAGE

Help for each of the commands of palantir-processor can be obtained by calling it with -h

query

Given a valid Queue account with required permissions to access group data, you would start with getting an overview of the available experiments:

palantir-processor query -g group -u user -p password

palantir-processor will list all available experiments for the given group

Available data for group:

ChIP-Seq
RNA-Seq

prepare

Now that you made up your mind of which data to import, a directory tree can be build and the raw data is linked into it.

palantir-processor prepare [-f] -r ROOT -g GROUP -u USER -p PASSWORD experiments [experiments ...]

Below is the help message describing usage & options:

positional arguments:
  experiments           Experiment(s)

optional arguments:
  -h, --help            show this help message and exit
  -r ROOT, --rootDirectory ROOT
                        Root directory for data preparation prepare data to
  -g GROUP, --group GROUP
                        Group to retrieve data from
  -u USER, --user USER  Username
  -p PASSWORD, --password PASSWORD
                        Password
  -f, --force           Force directory creation (updating current data
                        otherwise)

You will have to choose the root directory where the directory tree is created and the respective experiments from palantir-processor query you want to link. The directory tree can be either forced (deleting old contents) or updated (only linking new samples).

count

This module counts read data given a reference using featureCounts from WEHI.

palantir-processor count [-h] -r ROOT -a REFERENCE [-t THREADS] [-f] [-d] experiments [experiments ...]

Below is the help message describing usage & options:

positional arguments:
  experiments           Experiment(s)

optional arguments:
  -h, --help            show this help message and exit
  -r ROOT, --rootDirectory ROOT
                        Root directory for data preparation prepare data to
  -a REFERENCE, --reference REFERENCE
                        Reference to use for counting
  -t THREADS, --threads THREADS
                        Threads to use
  -f, --force           Force counting (running on new samples only otherwise)
  -d, --dryrun          Dry run

A reference has to be selected for counting (described TODO) which will be automatically only used on compatible genome builds. Again, counting can be forced (overwriting old files) or updated.

INSTALLATION

The installation process currently consists of simply checking the projects out from GitHub.

Just do the following:

git clone https://github.com/t-neumann/palantir-processor.git
cd palantir-processor
./bin/palantir-processor

NOTES

This has been successfully run on Debian GNU/Linux 3.2.0 workstations (both 32-bit and 64-bit machines).

AUTHORS

Tobias Neumann (tobias.neumann@imp.ac.at)

ACKNOWLEDGEMENTS

This software was developed at The Research Center for Molecular Pathology, Vienna, Austria.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

March 18, 2016