Web-based file browser that allows for easy access to GDM files
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Bundle ownCloud with GDM as a
separate container (preferred)
Configure ownCloud to user-authentication - same as used by GDM
Configure ownCloud with the following folder structure, for each crop:
Crops [/data/gobii_bundle/crops]
<cropname>
extractor
done
inprogress
instructions
output
files
hdf5
loader
digest
done
inprogress
instructions
qc
notices
confidentiality.txt
logs - should be at same level as crops
Configure ownCloud so there is no ability to "File/Folder Delete"
file types we need to be able to view:
.txt
.genotype
.log
.file
.json
digest. files
digest.dataset_marker
digest.dataset_dnarun
digest.dnarun
digest.dnasample
digest.germplasm
digest.marker
digest.marker_linkage_group
digest.linkage_group
Marker Tools Portal
A portal that will consolidate all GOBii related tools in one view, which also allows users to add/link their own tools to the portal.
To be able to see all web-based tools in one space, as well as desktop tools to download, and web-sites of interest
read more...
Tabs: Default Applications to be shipped out with MarkerPortal
tab for web based tools
GDM - one for each crop
KDCompute
ownCloud
TimeScope
EIB Galaxy Demo
tab for desktop tools to download
GDM Loader
Flapjack
TASSEL 5
tab for web sites of interest
GOBii Project
EIB Platform
Allow sys-admins to register more tools by directly modifying MPortal's configuration file
Each application should allow for specification of documentation link
GDM -
User Manual
Technical Documentation
APIs
TimeScope
KDC - Data QC
EIB Galaxy Demo
EIB Galaxy
Galaxy
Flapjack
TASSEL 5
Import GDM dataset into Flapjack
BrAPI implementation to view GOBII datasets directly in Flapjack, without having to use the GOBii extractor UI.
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The user will be able to use the FlapJack *Import Data* tool to specify the url of a GOBII server and do the following:
Select a "Study" (which is the same as a GOBii project);
Select a "Marrix" (a GOBii dataset, concatenated with the experiment name, from within the project);
View the resutlting dataset in FlapJack.
The data should conform to several criteria:
The list of studies (projects) should be filtered to those for which there exist datasets that have been loaded into the system;
The list of matrices (datasets) should also be filtered in this way;
The names of the matrices should include the number of alleles in the matrix. This number can be derived, in theory, by multiplying the number of markers by the number samples in the dataset.
Matrices with a large number of alleles will be flagged as a high risk for processing and download delay. It will be up to FlapJack to determine the threshold for this warning.
When the extract results in error, the error condition should be reported to the user in a graceful way. An example of this error, as reported by email, is attached. Ideally, the error reported should be similar to what you get in an email notification.
Portainer
A container designed for System Administrators to monitor local and remote container environments.
Extract by marker or sample into hapmap or FJ format incorrectly reports as failed if one of the datasets containing the marker or sample is not available - but the ouput file has errors
Extract By Sample sets Project Id to '0' in Instruction file if a Project name is selected and then user selects 'All Projects', resulting in a failed extract