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COSMOS: Python library for massively parallel workflows.
Gafni, Erik; Luquette, Lovelace J; Lancaster, Alex K; Hawkins, Jared B; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P; Tonellato, Peter J.
Afiliação
  • Gafni E; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
  • Luquette LJ; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
  • Lancaster AK; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
  • Hawkins JB; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
  • Jung JY; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
  • Souilmi Y; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
  • Wall DP; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
  • Tonellato PJ; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP,
Bioinformatics ; 30(20): 2956-8, 2014 Oct 15.
Article em En | MEDLINE | ID: mdl-24982428
ABSTRACT

SUMMARY:

Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. AVAILABILITY AND IMPLEMENTATION Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http//lpm.hms.harvard.edu and http//wall-lab.stanford.edu. CONTACT dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Linguagens de Programação / Genômica / Sequenciamento de Nucleotídeos em Larga Escala Idioma: En Ano de publicação: 2014 Tipo de documento: Article
Texto completo
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XML
PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Linguagens de Programação / Genômica / Sequenciamento de Nucleotídeos em Larga Escala Idioma: En Ano de publicação: 2014 Tipo de documento: Article