Expanding the Galaxy's reference data

Nagampalli Vijaykrishna; Jayadev Joshi; Nate Coraor; Jennifer Hillman-Jackson; Dave Bouvier; Marius Van Den Beek; Ignacio Eguinoa; Frederik Coppens; John Davis; Michał Stolarczyk; Nathan C. Sheffield; Simon Gladman; Gianmauro Cuccuru; Björn Grüning; Nicola Soranzo; Helena Rasche; Bradley W. Langhorst; Matthias Bernt; Dan Fornika; David Anderson De Lima Morais; Michel Barrette; Peter Van Heusden; Mauro Petrillo; Antonio Puertas-Gallardo; Alex Patak; Hans Rudolf Hotz; Daniel Blankenberg

doi:10.1093/bioadv/vbac030

Expanding the Galaxy's reference data

Nagampalli Vijaykrishna, Jayadev Joshi, Nate Coraor, Jennifer Hillman-Jackson, Dave Bouvier, Marius Van Den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michał Stolarczyk, Nathan C. Sheffield, Simon Gladman, Gianmauro Cuccuru, Björn Grüning, Nicola Soranzo, Helena Rasche, Bradley W. Langhorst, Matthias Bernt, Dan Fornika, David Anderson De Lima MoraisMichel Barrette, Peter Van Heusden, Mauro Petrillo, Antonio Puertas-Gallardo, Alex Patak, Hans Rudolf Hotz, Daniel Blankenberg^*

^*Corresponding author for this work

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Abstract

Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.

Original language	English
Article number	vbac030
Journal	Bioinformatics Advances
Volume	2
Issue number	1
DOIs	https://doi.org/10.1093/bioadv/vbac030
Publication status	Published - 29 Apr 2022

Bibliographical note

Funding
This work was supported by funds provided by the Cleveland Clinic; the National Institutes of Health [U24HG006620, U24CA231877]; the Biotechnology and Biological Sciences Research Council, part of UK Research and Innovation [BB/CCG1720/1 to N.S., BBS/E/T/000PR9814 to N.S.]; the Novartis Research Foundation [to H.-R.H.]; the South African Research
Chairs Initiatives of the Department of Science and Technology and National Research Foundation of South Africa [64751 to P.V.H.]; the Research Foundation—Flanders [I002819N]; and the European Union’s Horizon 2020 programme [824087].

Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press.

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vbac030Final published version, 738 KBLicence: CC BY

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Vijaykrishna, N., Joshi, J., Coraor, N., Hillman-Jackson, J., Bouvier, D., Van Den Beek, M., Eguinoa, I., Coppens, F., Davis, J., Stolarczyk, M., Sheffield, N. C., Gladman, S., Cuccuru, G., Grüning, B., Soranzo, N., Rasche, H., Langhorst, B. W., Bernt, M., Fornika, D., ... Blankenberg, D. (2022). Expanding the Galaxy's reference data. Bioinformatics Advances, 2(1), [vbac030]. https://doi.org/10.1093/bioadv/vbac030

@article{90eddbf66013459e982a38b7a33e1c8e,

title = "Expanding the Galaxy's reference data",

abstract = "Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.",

author = "Nagampalli Vijaykrishna and Jayadev Joshi and Nate Coraor and Jennifer Hillman-Jackson and Dave Bouvier and {Van Den Beek}, Marius and Ignacio Eguinoa and Frederik Coppens and John Davis and Micha{\l} Stolarczyk and Sheffield, {Nathan C.} and Simon Gladman and Gianmauro Cuccuru and Bj{\"o}rn Gr{\"u}ning and Nicola Soranzo and Helena Rasche and Langhorst, {Bradley W.} and Matthias Bernt and Dan Fornika and {De Lima Morais}, {David Anderson} and Michel Barrette and {Van Heusden}, Peter and Mauro Petrillo and Antonio Puertas-Gallardo and Alex Patak and Hotz, {Hans Rudolf} and Daniel Blankenberg",

note = "Funding This work was supported by funds provided by the Cleveland Clinic; the National Institutes of Health [U24HG006620, U24CA231877]; the Biotechnology and Biological Sciences Research Council, part of UK Research and Innovation [BB/CCG1720/1 to N.S., BBS/E/T/000PR9814 to N.S.]; the Novartis Research Foundation [to H.-R.H.]; the South African Research Chairs Initiatives of the Department of Science and Technology and National Research Foundation of South Africa [64751 to P.V.H.]; the Research Foundation—Flanders [I002819N]; and the European Union{\textquoteright}s Horizon 2020 programme [824087]. Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press.",

year = "2022",

month = apr,

day = "29",

doi = "10.1093/bioadv/vbac030",

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Vijaykrishna, N, Joshi, J, Coraor, N, Hillman-Jackson, J, Bouvier, D, Van Den Beek, M, Eguinoa, I, Coppens, F, Davis, J, Stolarczyk, M, Sheffield, NC, Gladman, S, Cuccuru, G, Grüning, B, Soranzo, N, Rasche, H, Langhorst, BW, Bernt, M, Fornika, D, De Lima Morais, DA, Barrette, M, Van Heusden, P, Petrillo, M, Puertas-Gallardo, A, Patak, A, Hotz, HR & Blankenberg, D 2022, 'Expanding the Galaxy's reference data', Bioinformatics Advances, vol. 2, no. 1, vbac030. https://doi.org/10.1093/bioadv/vbac030

TY - JOUR

T1 - Expanding the Galaxy's reference data

AU - Vijaykrishna, Nagampalli

AU - Joshi, Jayadev

AU - Coraor, Nate

AU - Hillman-Jackson, Jennifer

AU - Bouvier, Dave

AU - Van Den Beek, Marius

AU - Eguinoa, Ignacio

AU - Coppens, Frederik

AU - Davis, John

AU - Stolarczyk, Michał

AU - Sheffield, Nathan C.

AU - Gladman, Simon

AU - Cuccuru, Gianmauro

AU - Grüning, Björn

AU - Soranzo, Nicola

AU - Rasche, Helena

AU - Langhorst, Bradley W.

AU - Bernt, Matthias

AU - Fornika, Dan

AU - De Lima Morais, David Anderson

AU - Barrette, Michel

AU - Van Heusden, Peter

AU - Petrillo, Mauro

AU - Puertas-Gallardo, Antonio

AU - Patak, Alex

AU - Hotz, Hans Rudolf

AU - Blankenberg, Daniel

N1 - Funding This work was supported by funds provided by the Cleveland Clinic; the National Institutes of Health [U24HG006620, U24CA231877]; the Biotechnology and Biological Sciences Research Council, part of UK Research and Innovation [BB/CCG1720/1 to N.S., BBS/E/T/000PR9814 to N.S.]; the Novartis Research Foundation [to H.-R.H.]; the South African Research Chairs Initiatives of the Department of Science and Technology and National Research Foundation of South Africa [64751 to P.V.H.]; the Research Foundation—Flanders [I002819N]; and the European Union’s Horizon 2020 programme [824087]. Publisher Copyright: © 2022 The Author(s). Published by Oxford University Press.

PY - 2022/4/29

Y1 - 2022/4/29

N2 - Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.

AB - Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.

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DO - 10.1093/bioadv/vbac030

M3 - Article

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VL - 2

IS - 1

M1 - vbac030

ER -

Expanding the Galaxy's reference data

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