fraunhofer-izi / uap

Universal Analysis Pipeline - A python tool for controlled and coordinated data analysis

uap -- Universal Analysis Pipeline

Authors

Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor, Jörg Hackermüller

uap: reproducible and robust HTS data analysis. BMC Bioinformatics 20, 664 (2019)

Introduction

The uap package is a framework to configure, run, and control large data multi-step analyses. Its main focus is on the analysis of high-throughput sequencing data.

The aim of this data processing pipeline is to enable robust and straightforward bioinformatics data evaluation. It is implemented in Python, runs under GNU/Linux and can be controlled from the command-line interface. Although the primary focus is the evaluation of sequencing data, its design allows for a variety of other applications.

About this Repository

This repository contains the development status of uap at Fraunhofer IZI. It is based on the uap repository as published in Kämpf, C., Specht, M.,Scholz, A. et al. uap: reproducible and robust HTS data analysis. BMC Bioinformatics 20, 664 (2019), which is located here.

This version v2.0.0rc2 contains the following changes (for a complete list see the CHANGELOG):

• code conversion from Python2 to Python3
• improved user interaction
• enhanced error detection for configuration
• validation of existing results by using annotation as configuration and recalculation of SHA256
• status --details completely lists errors or changes caused by adaptation of the configuration
• enhanced detection of changes (software version, output files, sha256 of results (optional))
• improved error-management
• removed checksum suffix in output directories
• extended backward-compatible connection-management
• Source_controller step to check input data
• no need to configure uap internal scripts, GNU coreutils and lmod
• improved job-execution (signal handling, array jobs, enhanced logging, changes to configuration do not impact running jobs)
• processes are executed in temporary directories
• error fixing and code improvement

Please note, the version v2.0.0rc2 of uap requires Python >= 3.5 and is only tested on SLURM.

Documentation

Find the documentation here.

Contacts

• Christoph Kämpf, [email protected]
• Kristin Reiche, [email protected]
• Jana Schor, [email protected]
• Jörg Hackermüller, [email protected]

Helmholtz Centre for Environmental Research - UFZ
Permoserstr. 15, 04318 Leipzig, Germany

Fraunhofer Institute for Cell Therapy and Immunology (IZI)
Perlickstraße 1, 04103 Leipzig, Germany

Main contributors:

• Christoph Kämpf
• Dominik Otto
• Michael Specht
• Alexander Scholz
• Sven-Holger Puppel
• Gero Doose
• Kristin Reiche
• Jana Schor
• Jörg Hackermüller

Copyright Notice

Copyright (C) 2011 - 2020, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ and Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V. acting on behalf of its Fraunhofer Institute for Cell Therapy and Immunology (IZI). All rights reserved.

The code is a property of:

Helmholtz-Zentrum für Umweltforschung GmbH – UFZ
Registered Office: Leipzig
Registration Office: Amtsgericht Leipzig
Trade Register Nr. B 4703
Chairman of the Supervisory Board: MinDirig'in Oda Keppler
Scientific Director: Prof. Dr. Georg Teutsch
Administrative Director: Dr. Sabine König

and

Fraunhofer-Gesellschaft zur Foerderung der angewandten Forschung e.V.
Hansastraße 27c, 80686 München
acting on behalf of its
Fraunhofer Institute for Cell Therapy and Immunology (IZI)
Perlickstraße 1, 04103 Leipzig

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, it can be found at the end of this document or see at https://www.gnu.org/licenses/gpl-3.0.de.html.

Redistribution

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, the list of conditions for redistribution and modification as well as the GNU General Public License.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions, the GNU General Public License and the modification conditions in the documentation and/or other materials provided with the distribution.
• Neither the name of Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, the name of the Fraunhofer Institute for Cell Therapy and Immunology (IZI) nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

Modification

If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from Helmholtz-Zentrum für Umweltforschung GmbH – UFZ or Fraunhofer Institute for Cell Therapy and Immunology (IZI).