SUMMARY: We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network. AVAILABILITY AND IMPLEMENTATION: Source code is available on GitHub at https://github.com/4dn-dcic/tibanna. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network. AVAILABILITY AND IMPLEMENTATION: Source code is available on GitHub at https://github.com/4dn-dcic/tibanna. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Belinda Giardine; Cathy Riemer; Ross C Hardison; Richard Burhans; Laura Elnitski; Prachi Shah; Yi Zhang; Daniel Blankenberg; Istvan Albert; James Taylor; Webb Miller; W James Kent; Anton Nekrutenko Journal: Genome Res Date: 2005-09-16 Impact factor: 9.043
Authors: Paolo Di Tommaso; Maria Chatzou; Evan W Floden; Pablo Prieto Barja; Emilio Palumbo; Cedric Notredame Journal: Nat Biotechnol Date: 2017-04-11 Impact factor: 54.908
Authors: John Vivian; Arjun Arkal Rao; Frank Austin Nothaft; Christopher Ketchum; Joel Armstrong; Adam Novak; Jacob Pfeil; Jake Narkizian; Alden D Deran; Audrey Musselman-Brown; Hannes Schmidt; Peter Amstutz; Brian Craft; Mary Goldman; Kate Rosenbloom; Melissa Cline; Brian O'Connor; Megan Hanna; Chet Birger; W James Kent; David A Patterson; Anthony D Joseph; Jingchun Zhu; Sasha Zaranek; Gad Getz; David Haussler; Benedict Paten Journal: Nat Biotechnol Date: 2017-04-11 Impact factor: 54.908
Authors: Job Dekker; Andrew S Belmont; Mitchell Guttman; Victor O Leshyk; John T Lis; Stavros Lomvardas; Leonid A Mirny; Clodagh C O'Shea; Peter J Park; Bing Ren; Joan C Ritland Politz; Jay Shendure; Sheng Zhong Journal: Nature Date: 2017-09-13 Impact factor: 49.962
Authors: Sarah B Reiff; Andrew J Schroeder; Koray Kırlı; Andrea Cosolo; Clara Bakker; Soohyun Lee; Alexander D Veit; Alexander K Balashov; Carl Vitzthum; William Ronchetti; Kent M Pitman; Jeremy Johnson; Shannon R Ehmsen; Peter Kerpedjiev; Nezar Abdennur; Maxim Imakaev; Serkan Utku Öztürk; Uğur Çamoğlu; Leonid A Mirny; Nils Gehlenborg; Burak H Alver; Peter J Park Journal: Nat Commun Date: 2022-05-02 Impact factor: 17.694
Authors: Felix Mölder; Kim Philipp Jablonski; Brice Letcher; Michael B Hall; Christopher H Tomkins-Tinch; Vanessa Sochat; Jan Forster; Soohyun Lee; Sven O Twardziok; Alexander Kanitz; Andreas Wilm; Manuel Holtgrewe; Sven Rahmann; Sven Nahnsen; Johannes Köster Journal: F1000Res Date: 2021-01-18