Re: [Gmod-ajax] URL help

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In addition to other things noted, JBrowse 2 can also load data directly
from Google Drive or Dropbox share links. Basically, you get a URL from
"sharing" a google drive file or dropbox file, and can paste the share URL
into the "Add track" widget. A screenshot is attached showing the buttons
for dropbox and google drive in the "add track" widget in JBrowse 2

This assumes you are using jbrowse 2, the jbrowse 1 app is a bit different
and doesn't have any google drive/dropbox support

-Colin

On Wed, Oct 19, 2022 at 1:29 PM Scott Cain <sc...@sc...> wrote:

> The other thing that just occurred to me is relatively low-tech: get a
> bunch of thumb usb drives (4 or 8 GB ones are pretty cheap) and put the
> data on them and then just hand them out to your students.
>
> On Wed, Oct 19, 2022 at 9:19 AM Scott Cain <sc...@sc...> wrote:
>
>> Hi Olivia,
>>
>> How much control do you have over the students' learning environment? If
>> you have access to the machines to set them up before the students use them
>> and there aren't too many (or you had a good network admin), you could just
>> place the data files on each computer's hard drive, or if the files are too
>> big to do that, you could mount the one drive on each of the computers as a
>> local drive (I googled for directions for how to do that and it looks like
>> it would probably be doable for Windows and Mac at least).
>>
>> If you don't have easy access to the students' machines, then you need to
>> be able to give them a URL to load data. I have had lots of success with
>> Amazon Web Services S3 buckets, where I configured the bucket to allow CORS
>> requests (cross origin resource sharing--required by web servers as a way
>> to protect against malicious websites from getting dangerous things to your
>> computer without you knowing it) and then set the data in the S3 bucket as
>> publicly readable. If you want to go down that route, we can help you with
>> the details, and I suspect since this is a research project involving
>> teaching students, you could probably get some S3 storage space from AWS
>> for free.
>>
>> I know that it is also possible to do all of the above (CORS, public read
>> data, and a URL) with Google Cloud, but I don't know how to do it; I only
>> know it's possible because I have a track in WormBase's JBrowse that pulls
>> data from a researcher who put his data in a public Google Cloud space. And
>> it is possible that you could do all of this with OneDrive, but I don't
>> know how to do that either.
>>
>> The last thing you could do would be to ask the IT staff at UML to set up
>> a small web server for your project where you could put the data or set one
>> up yourself if you're allowed by the university; if you wanted to go down
>> that route, we can help with that too.
>>
>> Good luck with your choice,
>> Scott
>>
>>
>>
>>
>> On Wed, Oct 19, 2022 at 5:45 AM Rasmussen, Olivia <
>> Oli...@st...> wrote:
>>
>>> Hello,
>>> Thanks so much for getting back to me and sorry for the delayed
>>> response. This is helpful information to know. It seems like the problem is
>>> definitely that it is not public. I was wondering if there is any sort of
>>> work around for this? It's okay if not we are just trying to understand the
>>> best way to approach this based on what we are trying to do with the
>>> research. Open to using something that isn't one drive. That just is where
>>> it is stored at the moment
>>>
>>> Olivia
>>>
>>> Get Outlook for iOS <https://aka.ms/o0ukef>
>>> ------------------------------
>>> *From:* Scott Cain <sc...@sc...>
>>> *Sent:* Thursday, October 13, 2022 12:21:13 AM
>>> *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 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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ObNBohaz0uGMCcWmxsmCahCYVqWT1WUgOaAT5cNlQvQ%3D&reserved=0>
>>> ------------------------------
>>> *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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qQ%2FBysXzDTQOgjR9l53q8l1FrvrNvB5AtbGCBbV%2BGBQ%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8U%2F5MVsNSMnlNjFOa6xapvA2%2FYkziLN0va6%2FSz1NCZE%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEWlRGTiBO1%2FKdFHmrdBSBATe1iJkYHYnbcyd8x%2BRIk%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MLajm2JStSdqzyGglrCVDfaLxs9M9vJpTWJXhLCyx70%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ef%2FtxFQca4jWYKOCgl2hqUnx8JcY4T66J0aChae6DUs%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=poog6eHte%2FW3uaKJimk7TjuKm13XNHqP79pnDnoohGQ%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fkfJ2bZy0oLsERzABMAzo1VHJ%2Fi6tb5tIiIhxMTKoSo%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%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%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%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/)
>>
>
>
> --
> ------------------------------------------------------------------------
> 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/)
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>