Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Summer 2019 Sprint 11, Summer 2019 Sprint 12
Description
Task: Investigate how we could automate quickloads, how quickloads currently format data via annots.xml, where can we store quickloads or the data (google drive, dropbox, cyverse).
Attachments
Activity
1. We plan to host quickload host website (say quickload.bioviz.org) which will require authentication from a service.
2. For each user we intend to create a folder under which their multiple quickload related files will be stored. (annots.xml, contents.txt etc)
3. We plan to store all genome.txts in one place and create symbolic links to each of those files in quickload sites folders referring to that genome.
Refer image attached.
https://stackoverflow.com/questions/18116152/how-do-i-get-a-file-list-for-a-google-drive-public-hosted-folder
This link seems to be helpful as it talks about accessing children list of files/folders of a public google drive folder link.
A thought:
Our server could generate the meta-data files "on the fly" as REST endpoints.
The twoBitInfo source code can be downloaded from the UCSC store (free for academic users) as part of the Genome Browser source code.
There is a python package called twobitreader for accessing twobit files, and includes a method for getting the chromosomes and their sizes.
Was previously possible to store quickload in Dropbox . However,
IGBF-1138states that it may no longer be possible (this should be looked into, the issue is still open). UPDATE - It is no longer possible to host a Quickload in Dropbox.It is possible to create a public link to data in Dropbox that will work in IGB (including byte range requests).
For example: https://dl.dropboxusercontent.com/s/7ida9n2p61lrtsa/Dm_genome_v1.0.bed