Question: How To Download All Sra Samples At Once ?
13

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6.9 years ago by
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Dear Biostars,

As you may know SRA is a repository for all types of sequencing data. I often times have to do manual download by copying links of every SRA dataset by hand and use wget. I am wondering is there any simplest approach than manual copying of links ? Thanx in advance

For ex: How can I download all the data related to SRP026197 ? http://www.ncbi.nlm.nih.gov/sra?term=SRP026197

ADD COMMENT • link • modified 2.6 years ago by Federico Giorgi • 630 • written 6.9 years ago by biorepine • 1.5k
1

Have you tried the SRAdb package from bioconductor? It's been a while, but I think it can be used to do that sort of thing.

ADD REPLY • link written 6.9 years ago by Devon Ryan ♦ 98k

Actually, SRA is the repository for sequence data, not GEO. There are links between the two databases, but your question is actually related to SRA.

ADD REPLY • link written 6.9 years ago by Sean Davis ♦ 26k

oh yeah you are right. I will edit my question. thanx 1942 the pacific air war game download.

ADD REPLY • link written 6.9 years ago by biorepine • 1.5k

here is another solution A: How to download raw sequence data from GEO/SRA

ADD REPLY • link written 6.3 years ago by Istvan Albert ♦♦ 86k

when I run the code on my computer,I have a problem below,what is wrong?

library(SRAdb)

srafile=getSRAdbFile()

trying URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'Content type 'application/x-gzip' length 1308358823 bytes (1247.7 Mb)opened URLdownloaded 1247.7 Mb

Unzipping..

Error in .local(drv, ..) : Could not connect to database:unable to open database file

ADD REPLY • link modified 4.8 years ago • written 4.8 years ago by Ada • 0

Perhaps you ran out of space in /tmp or the equivalent. Anyway, please post things like this as new questions.

ADD REPLY • link modified 4.8 years ago • written 4.8 years ago by Devon Ryan ♦ 98k

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Architecture


Architekturmodelle - Werner, Germany, www.werner-modelle.de
Barkow Leibinger Architekten, Berlin, www.barkowleibinger.com
Della Valle Bernheimer, New York, www.d-bd.com
The Berlage Institute, the Netherlands, www.theberlage.nl
UNStudio, Amsterdam, www.unstudio.com
Zwimpfer Partner, Switzerland, www.ffbk.ch

Arts


Andrew Werby, USA, www.juxtamorph.com
Dennis O. Collier, USA, www.woodsculpture.com
Eja Siepman van den Berg, the Netherlands, www.ejasiepmanvandenberg.nl
Kreysler & Ass., USA (digital sculpture enlargement), www.kreysler.com
Sheldon Brown, Center for Research in Computing and the Arts, USA, crca.ucsd.edu

Ceramics


Escuela de Arte Francisco Alcantara, Spain, www.escueladeceramica.com
European Ceramics Work Centre, the Netherlands, www.ekwc.nl
MaatWerkTegels, the Netherlands (tiles), www.maatwerktegels.com
Royal Goedewaagen, the Netherlands (pottery and Delft Blue), www.goedewaagen.nl

Consumer goods


Barco, Belgium, www.barco.com
Dancohr Technics, the Netherlands, webshop.dancohr.com
GateGroup, Belgium, www.gategroup.com
Fractus, Spain/Korea, www.fractus.com
Garmin International, Inc, USA, www.garmin.com
Hallmark Cards, (Advancing Technologies), USA, www.hallmark.com
Intel Corporation, USA, www.intel.com
Mettler Toledo, Switzerland
Nefit Buderus, the Netherlands, www.nefit.nl
Nilfisk, Denmark, www.nilfisk.com
Pentas Moulding, the Netherlands, www.pentas.nl
Playmobil (Brandstätter GmbH), Germany, www.playmobil.de
Sony Ericsson Telecommunication, Sweden, www.ericsson.com
Texas Instruments, the Netherlands, www.ti.com
Unilever, (Advanced Manufacturing Technology Group), the Netherlands, www.unilever.com
Toto Enpla, Japan, www.toto.com
Vacu Vin, the Netherlands, www.vacuvin.com
White-Rodgers, USA, climate.emerson.com

Education


Anders Ljungstedts Gymnasium, Sweden, www.linkoping.se/alg
Arizona State University, (School of Arts), USA, www.asu.edu
Art Center College of Design, USA, www.artcenter.edu
Cape Technikon, South Africa
Cardiff Metropolitan University, Great Britain, www.cardiffmet.ac.uk
Case Western Reserve University, USA
Clemson University, (Lab Advanced Industrial Prototyping), USA, www.clemson.edu
Delft University of Technology, Dept Industrial Design, the Netherlands, www.tudelft.nl
Dublin Institute of Technology, School of Architecture, Ireland, www.dit.ie
Ecole Nationale Superieure des Arts et Metiers, Angers, France, www.ensam.eu
Ecole Nationale Superieure des Beaux Arts, Paris, France, www.ensba.fr (see press release)
Escuela Superior de Diseño Industrial, (automotive design), Spain
Fachhochschule Wiesbaden, Germany, www.gestaltung.fh-wiesbaden.de
Fontys Hogescholen, the Netherlands, www.fontys.nl
Gerrit Rietveld Academie, Amsterdam, the Netherlands, www.gerritrietveldacademie.nl
Hogeschool West Vlaanderen, Kortrijk, Belgium, www.howest.be
King Saud University, Riyadh, Saudi Arabia, ksu.edu.sa
Lycée Gustave Flaubert, La Marsa, Tunisia, www.erlm.tn/lgf
MIT, Center for Bits and Atoms, USA, www.cba.mit.edu
NTNU, Dept of Product Design Engineering, Norway, www.ntnu.no
PennState Erie, Behrend College, USA, www.psu.edu
Politecnico di Bari, Italy, www.poliba.it
Royal College of Art, London, Great Britain, www.rca.ac.uk
Seoul National University, Korea, www.snu.ac.kr
Smithsonian Institution, Washington DC, USA, www.si.edu
Technicon Free State, South Africa
Temasek Polytechnic, Singapore
Thomas More College, Belgium, www.thomasmore.be
Tokyo University of Technology, Japan, www.teu.ac.jp
Turku Polytechnic, Dept of Naval Architecture, Finland, www.turkuamk.fi
University of Southern California, USA

Private Downloadsdrako Students


Food and sweets



Cake concepts, the Netherlands, www.cakeconcepts.cc
Chupa Chups (Confipack), Spain, www.chupachups.com
Deltavorm, the Netherlands, www.deltavorm.com
Leaf Holland, the Netherlands, www.cloetta.com
Robèrt's Chocoladewerken, the Netherlands, www.roberts-chocolade.nl

Private Downloadsdrako Student


Jewelry


Bijouterie Bouchard, France, www.gilles-bouchard.com
Diamond Design Co, USA, www.diamonddesignco.com
Edelsmederij Turmali, the Netherlands, www.goudsmidbreda.nl
Catherine Rudacille, USA, www.catherinethejeweler.com
Gary Swank Jewelers (OR), USA, www.garyswank.com
Goldschmiede Wittel, Germany, www.goldschmiede-wittel.de
MWM Jewelers Services, Concord (MA), USA, www.mwmjewelry.com
Rhudy's Jewelry, USA,www.rjmrp.com

Medical


BORGinsole, Belgium (custom insoles) www.borginsole.com
Coloplast, Denmark, (ostomy care) www.coloplast.com
Cranial Technologies, USA, (plagiocephaly treatment) www.cranialtech.com
Diapedia, USA, (diabetic foot care) www.diapedia.com
Klaveness, Norway, (footwear) www.klaveness.no
Maden, Mexico, (teeth) www.maden.com.mx
Nordic Ortopedica, Sweden (orthopaedic products) www.nordicortopedica.se
Orthopodolab, the Netherlands, (custom insoles) www.orthopodolab.com
Otto Bock, various countries, (mobility aids) www.ottobock.com
Royal Perth Hospital, Australia, www.health.wa.gov.au

Model Making


1A100, Italy, www.1a100.it
Amalgam Modelmaking Ltd, Great Britain, www.amalgam-models.co.uk
Castor.es, Spain, www.castor.es
Crawley Creatures, Great Britain, www.crawley-creatures.com
EpokeModeller, Denmark, www.epokemodeller.dk
Flex / the workshop, the Netherlands, www.flex.nl
Jorge Queipo Prototipos, Spain
HCH Model, Spain, www.hchmodel.es
Inchausti Parinelli, Argentina, www.inchaustiparinelli.com
Modellbau Heidenreich, Germany, www.modellbau-heidenreich.de
Model Engineering, the Netherlands, www.modelengineering.nl
PD Models, Great Britain, www.pdmodels.co.uk
PROTOway, Italy, www.protoway.com
Scopulus Relief Objekte, Germany, www.scopulus.de
Weta Workshop, New Zealand, www.wetanz.com

Musical Instruments


Butch Hall Flutes, USA, www.butchhallflutes.com
Guitar Mill, USA, www.guitarmill.com
Hanson Musical Instruments (guitars), USA. www.hansonguitars.com

Packaging


Avon cosmetics, New York, USA, www.avon.com
Campina, the Netherlands, www.campina.nl
HSV Packaging, the Netherlands, www.hsv.nl
Lancome, Paris, France, www.lancome.fr

Product Design


Private Downloadsdrako Studios

Brandes en Meurs, the Netherlands, www.brandesenmeurs.nl
D3O Lab, Great Britain, www.d3o.com
Eclipse Product Development, USA, www.eclipsepd.com
Enthoven Associates, Belgium, www.eadc.be
Flex Development, the Netherlands, www.flex.nl
Katana-Design, Germany, www.katana-design.de
Lemmens Company, the Netherlands, www.lemmenscompany.nl
PI Global, Great Britain, www.piglobal.com
Simonis Voogd Design, Netherlands & South Africa, www.simonis-voogd.com
Structural Composites, USA, www.structuralcomposites.com
WAACS Design, the Netherlands, www.waacs.com

Research


BIBA, Germany, www.biba.uni-bremen.de
Delft University of Technology, Dept Marine Technology, the Netherlands, www.tudelft.nl
Gintic Inst of Mfg Technology, (Rapid Prototyping Development Centre), Singapore
NASA, Langley Research Center, USA, www.larc.nasa.gov
NERC, National Energy Research Council, Amman, Jordan, www.nerc.gov.jo
Vattenfall R&D (hydraulic testing models), Sweden www.vattenfall.com

Scale Models


Anderboat Models, USA (RC submarines)
Busch Models, Germany (cars) www.busch-model.info
EpokeModeller, Denmark (trains) www.www.epokemodeller.dk
Hartvigson Studios, USA (action figures and more) www.hartvigsonstudios.com
Into Things, USA (boats) www.intothings.com
LaHeli, Czech Republic (RC helicopters) www.laheli.com
PST Jets, Thailand (RC airplanes) www.pstjets.com
RBC Kits, the Netherlands (RC airplanes) www.rbckits.com
Robbe Modellsport, Austria (various models) www.robbe.de
Schuebeler jet-modell-systeme, Germany (RC airplanes) www.schuebeler-jets.de
ZN Line, Belgium (RC airplanes) www.znline.com

Signmaking


Arquiletras, Brasil, www.arquiletras.com
Shoreline Sign & Awning, USA, www.shorelinesign.com

(Rapid) Toolmaking



Albright Technologies, Inc, USA, www.albrightsilicone.com
Domas Systems, the Netherlands, www.domas.nl
WAA Venlo, the Netherlands, www.waagroep.nl

Transportation


Escuela Superior de Diseño Industrial, (automotive design), Spain
Volkswagen AG, Wolfsburg, Germany

Various


Private Downloadsdrako Studio

Ultilabs (3D Printers), the Netherlands, www.ultimaker.com
CNC-Service Herget (rudders), Germany, cnc-herget.de

Woodworking


CarveTech, USA, www.carvetech.com
Sculptures Sonia, Italy, www.sculpturessonia.it
South Coast Woodworks, Australia, www.southcoastwoodworks.com.au
ロア木工 Atelier Roy, Japan, www.roymokkou.com

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