Re: [mart-dev] Command Based marteditor
Hi! You might be interested in MartScript, http://github.com/joejimbo/MartScript, which can be used to automatically create Ensembl (and related) marts. I do not know your database structure, but perhaps it would work for you with some minor modifications as well. The major downside of using MartScript right now is obvious: I have been too lazy to document it properly yet. If you have a go at it, please let me know and perhaps we can figure out to get it working together. Are you around at Genome Informatics next week? We could have a chat about it too. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Command Based marteditor
Hi, On 8 September 2010 11:51, a.has...@har.mrc.ac.uk wrote: File = Naive File = import File = update all File = export Do you reckon that MartScript will help us? 'Naive' is not supported as such, but you could have a look at the Java code and implement it yourself. It is fairly straightforward, because I just call MartEditor code from within MartScript when mimicking MartBuilder/MartEditor functionality. The other steps would work though. I am going to IMGC, Crete, Greece in October. Please let me know if you will be there then we can discuss this further. Thanks. Unfortunately, I am not going there. Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Command Based marteditor
Hi, Just out of interest - is your data changing that rapidly between releases that you need to reconfigure/rebuild the MartEditor XMLs each build? We automatically rebuild our biomarts nightly, all we do is just re-run the SQL generated by MartBuilder (incorporating your new data) and reconfigure/restart your webserver.* If you want some more info i'd be happy to show you some of our build code. Thanks, Daz * This is a slightly simplified version. As our mart build takes a few hours, (and we don't want our mart to be offline for that long), we run the MartBuilder SQL into a slave/redundant database and then when we reconfigure/restart the webserver we point it at the new database, so we get the minimum amount of downtime we can running off a single apache instance. On 8 Sep 2010, at 12:14, Richard Holland wrote: Word of warning - MartEditor will (highly likely) be replaced in BioMart 0.8, with entirely new source code producing an entirely new mart XML format. cheers, Richard On 8 Sep 2010, at 12:05, Joachim Baran wrote: Hi, On 8 September 2010 11:51, a.has...@har.mrc.ac.uk wrote: File = Naive File = import File = update all File = export Do you reckon that MartScript will help us? 'Naive' is not supported as such, but you could have a look at the Java code and implement it yourself. It is fairly straightforward, because I just call MartEditor code from within MartScript when mimicking MartBuilder/MartEditor functionality. The other steps would work though. I am going to IMGC, Crete, Greece in October. Please let me know if you will be there then we can discuss this further. Thanks. Unfortunately, I am not going there. Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/ -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
Re: [mart-dev] Command Based marteditor
Hiya Darren It's not really the data build that's the problem it's when we use the actual data in the build to auto-populate a drop down in the filters section of the biomart. When we build the next one the only way we've found of resetting those filter dropdowns is to recreate them by hand using the gui rather than scripted - If you don't have any drop downs populated from the data you'll probably never run into this problem but in case we are doing something daft any advice is welcome :-) We may have to just lose the drop downs ?? Cheers Andy On 08/09/2010 13:52, Darren Oakley wrote: Hi, Just out of interest - is your data changing that rapidly between releases that you need to reconfigure/rebuild the MartEditor XMLs each build? We automatically rebuild our biomarts nightly, all we do is just re-run the SQL generated by MartBuilder (incorporating your new data) and reconfigure/restart your webserver.* If you want some more info i'd be happy to show you some of our build code. Thanks, Daz * This is a slightly simplified version. As our mart build takes a few hours, (and we don't want our mart to be offline for that long), we run the MartBuilder SQL into a slave/redundant database and then when we reconfigure/restart the webserver we point it at the new database, so we get the minimum amount of downtime we can running off a single apache instance. On 8 Sep 2010, at 12:14, Richard Holland wrote: Word of warning - MartEditor will (highly likely) be replaced in BioMart 0.8, with entirely new source code producing an entirely new mart XML format. cheers, Richard On 8 Sep 2010, at 12:05, Joachim Baran wrote: Hi, On 8 September 2010 11:51,a.has...@har.mrc.ac.uk wrote: File = Naive File = import File = update all File = export Do you reckon that MartScript will help us? 'Naive' is not supported as such, but you could have a look at the Java code and implement it yourself. It is fairly straightforward, because I just call MartEditor code from within MartScript when mimicking MartBuilder/MartEditor functionality. The other steps would work though. I am going to IMGC, Crete, Greece in October. Please let me know if you will be there then we can discuss this further. Thanks. Unfortunately, I am not going there. Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/ This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
Re: [mart-dev] Command Based marteditor
Hi Hassan, There has been a number of similar requests in the past. We are planning to properly expose the update API in the 0.8. a On 08/09/10 6:51 AM, a.has...@har.mrc.ac.uk a.has...@har.mrc.ac.uk wrote: Hi, Everytime we have a new data from medical clinics, we do the following steps from MartEditor GUI in order to update biomart: File = Naive File = import File = update all File = export Just because of this manual step, we cannot script/automate our whole data upload process. It will be great if we can script the above functionality. Do you reckon that MartScript will help us? I am going to IMGC, Crete, Greece in October. Please let me know if you will be there then we can discuss this further. Thanks. Best Regards, Hassan http://cern.ch/ahmadh/portfolio Hi! You might be interested in MartScript, http://github.com/joejimbo/MartScript, which can be used to automatically create Ensembl (and related) marts. I do not know your database structure, but perhaps it would work for you with some minor modifications as well. The major downside of using MartScript right now is obvious: I have been too lazy to document it properly yet. If you have a go at it, please let me know and perhaps we can figure out to get it working together. Are you around at Genome Informatics next week? We could have a chat about it too. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm Arek Kasprzyk Director, Bioinformatics Operations and Principal Investigator Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel:416-673-8559 Toll-free: 1-866-678-6427 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
