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Re: [Gmod-ajax] URL help
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From: Scott C. <sc...@sc...> - 2022-10-13 04:21:39
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Hi Olivia, I wrote a bunch of stuff below, but then went back and reread your email, so maybe I can ask more useful questions. I'll keep the other stuff below a line so you can read it if you want :-) So you have some BAM and BAI files on a Microsoft One Drive and want to use the data on that to load into JBrowse. I've never used one drive. Is it mounted locally so that it "looks like" a local drive, or is it a cloud drive that you have to use some other mechanism to access the data (for example, can you/do you want to access the data via a URL)? If it's a mounted drive and you can load it like it's a local file, I would expect that would work. If you've tried that and it doesn't work, please open the browser's developer tools/javascript console to see if there are any errors and send them to us. If you have to access the data on one drive via a URL, it gets a little trickier. It would make life easier if the data were accessible publicly (meaning you don't need a password or other credential to get it), but that might be possible to work around. Additionally, binary data like BAM have to be accessed via http using a web server that supports range requests, and I have no idea whether one drive does. If you want to give us access to the data, we can try to see if we can sort it out. Again, if you try it and nothing happens, look in the javascript console for error messages. Networking technology aside, do these files load correctly if the files are local on your computer? Things like naming chromosomes the same as your reference sequence frequently trips people up, since "1" is not the same as "chr1" which is also not the same as "Chr1". Just something to look into. Anyway, that's a lot of stuff to get started with. Let us know where to go from here. Scott ------------------------ Maybe you can tell us a little more about what you want to do. As Colin wrote this morning, JBrowse doesn't really "upload" any data at all. If you load local data into the jbrowse instance, it stays on your computer and the web browser just accesses the data locally. If you need to upload something (like so one person can share a view with someone else of data they have on their computer), you have to sort out some way outside of JBrowse to make that happen. If the users are all local to one another, that could be as easy as a shared network drive where the data are placed, or if the users aren't all on the same local network, you could put the data in a cloud resource like AWS S3 (if this is for a student project, you might be able to get a grant from Amazon to supply you with some S3 space). But this is all hand-waving until we really know what you want to do. Scott On Wed, Oct 12, 2022 at 12:14 PM Rasmussen, Olivia < Oli...@st...> wrote: > Hello, > Yes I am. Sorry I sent both! It’s probably easier via email if that’s > alright. I’m just wondering if it’s possible to upload the links directly > to jbrowse via a url or if it’s not possible and the data set just needs to > be downloaded. I've tried and nothing happens. Uploading the downloaded set > from my computer works fine but because the files are large it's not > sustainable for the type of project I'm trying to accomplish. > > Olivia > > Get Outlook for iOS <https://aka.ms/o0ukef> > ------------------------------ > *From:* Scott Cain <sc...@sc...> > *Sent:* Wednesday, October 12, 2022 3:06:58 PM > *To:* Rasmussen, Olivia <Oli...@st...> > *Cc:* gmo...@li... <gmo...@li...> > *Subject:* Re: [Gmod-ajax] URL help > > You don't often get email from sc...@sc.... Learn why this is > important <https://aka.ms/LearnAboutSenderIdentification> > Hi Olivia, > > I'm wondering if you are the same person who asked a similar question on > gitter. Either is fine with me; you're welcome to have the discussion > anywhere you want :-) > > Scott > > > On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia < > Oli...@st...> wrote: > > Hello, > My name is Olivia and I am a student at Umass Lowell, currently working on > a research project which involves teaching high school students how to use > Jbrowse. > I am wondering gif there is a way to upload data directly from a URL? > Currently the data is on a one drive account and I have tried many times to > upload the links into the new track box but nothing ever works. We are > using BAM and BAI links. Wondering if you have any insight. > > Thanks, > Olivia > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335030060%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hPRlitPKF41f6x7ZD9n21TtiIIjGQeXhEaxyn%2BPC8%2Bw%3D&reserved=0> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8qdJOemrYrxjj2LTDuxdowLsqCgyHNf%2FSlWs9xus2uM%3D&reserved=0>) > 216-392-3087 > WormBase Developer (http://wormbase.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jgKfndwNjtWPytb4psTSsGzSvuBzJyAlfQiutq4XrIo%3D&reserved=0> > ) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEE1xDPHnFX9AU3jAYMqQ1o07DdG9eqfGV%2BKGbToDYc%3D&reserved=0> > ) > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NnJNItf5mJ0VzsmQIdSjH9dJO5YVmcK%2FvHF0uRr42g4%3D&reserved=0> > ) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C35ea5e2a7763468bdceb08daac84f785%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638011984335186283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=T0YcMeGE3ghiJt2xjIlgv5QI8FKtXzMGN7%2FVIA9zS6o%3D&reserved=0> > ) > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
