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Hi Paul,biomaRt R package pulls the data from ensembl installation of biomart 0.7. You would need to install biomart-perl software and the download the relevant mart databases from ensembl. You are downloading biomart software v0.9 which is not what you want if your target is to point biomaRt R api to talk to a local biomart server.On a different note, I wonder if it is necessary to setup all this for one user - is it because they send many queries or because queries expect very large amount of data and hence getting a slow response/timeouts?Best,Syed
Just to make sure I am not barking up the wrong tree - the only reason I'm trying to install this, is that one of our bioinformaticians is using the R package biomaRt, which connects remotely to the ensembl biomart database on the interwebs. I'm being tasked with downloading the relevant hg38 ensembl data into a local mysql database, and having the user point her biomaRt to that instead. So using https://github.com/biomart/BioMart seemed like the way to go, but maybe there is a better way?--On Wednesday, October 7, 2020 at 1:03:15 PM UTC-5 Paul Schilling wrote:Hi All,I am trying to locally install biomart and am following the github instructions at https://github.com/biomart/BioMartAt the ant compile step, it throws an error at the beginning:[javac] /bioinfo/userhome/pschilling/biomart/BioMart/src/org/biomart/api/soap/PortalServiceImpl.java:8: error: package javax.jws does not existGoogling the error, it becomes apparent that these java dependencies are no longer valid:import javax.jws.WebMethod; import javax.jws.WebParam; import javax.jws.WebService; import javax.jws.soap.SOAPBinding;However the only solution that is presented involves adding a dependency block to a maven .pom file...but maven is not used at all in the github instructions for biomart.Can anyone here help, or point me to someone who can?Thanks!
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