Build Project Land from your own OmicSoft Project.pdf

From Array Suite Wiki

Jump to: navigation, search

OmicSoft 'Project Lands' are a new, lighter-weight way to manage and access 'Omics data projects using the Land metadata framework, without reprocessing the data.

This new technology is used in OmicSoft’s 'Single Cell Project Lands', which enables Land subscribers to download highly-curated scRNAseq projects, processed using the OmicSoft single cell analysis pipeline from our cloud repository.

These projects include full quantification, tSNE projections and clustering, and differentially-expressed genes.

Users can identify projects of interest in Lands by exploring the curated metadata, and choose to download selected projects to the analysis tab.

Using the same technology, your OmicSoft Server administrator can build your own “Project Lands” to store and organize internal projects.

This requires an onsite OmicSoft Server installation with Server Cloud support, and at least one project to store. These steps should be performed by an OmicSoft Server administrator.

Tips.pngBuilding your own "Project Lands" requires the Server Cloud add-on, to enable storage of projects on an S3 bucket.

Steps to create a Project Land

  1. Create a 'Project Land'
  2. Package up some OmicSoft Studio projects (.osprj files + matching folder) into a .zip file
  3. Upload to an S3 bucket
  4. Add metadata that matches your project names

Steps to enable downloading of Single Cell Projects for a land

  1. Create a “Project Land”
    1. Create a new Land
      • Name it whatever you like, e.g. InternalProjectLand
      • In your land.cfg or land.cfg2 file, include the parameter "EnableCloudProjectDownload=True"
    2. Map a Cloud folder called CloudLandProjects to a folder in the S3 bucket where your Land projects will be uploaded
      • e.g. s3://east.cloudLandLocation.CompanyName
    3. Create a subfolder matching your new Project Land name
      • e.g. s3://east.cloudLandLocation.CompanyName/InternalProjectLand
  2. Package up some OmicSoft projects
    1. For each project to upload, include the .osprj file (e.g. “MyRNAseqAnalysis.osprj”) and the associated subfolder (also named “MyRNAseqAnalysis”) in a .zip file, in the pattern
      • ProjectName can be whatever you want
      • Platform is usually the NCBI GPL number, by convention, e.g. GPL670
  3. Upload the .zip file to your cloud location mapped to CloudLandProjects
  4. Create metadata for your new Lands
    1. You’ll need sample metadata and project metadata
    2. Project Lands find your zipped project by the following logic
      • Look in the mapped CloudLandProjects folder
      • Find a subfolder matching your open Project Land Name
      • Look for a file named for the project you selected from the project metadata.
    3. Sample metadata will need to include a “ProjectName” column, matching the zipped project’s ProjectName
    4. Project metadata will need both ProjectName and Platform columns.