May 1, 2019, Wednesday

• -d for updating both description and metadata

  • curl -X POST -sk -H "user: lwang" -H "Authorization: Bearer $AGAVETOKEN" -H "Content-Type: application/json" https://de.sciapps.org/workflow/3be623ed-c3ce-473a-9ffe-5aa30a731f60/update -d '{"workflow_desc": "ems", "metadata": {"avus":[{"attr":"SciApps_id","value":"af72ea64-2126-41ce-ac00-cdc5d69a1c7f","unit":""},{"attr":"sra_project_id","value":"PRJNA438108","unit":""},{"attr":"cultivar","value":"B73","unit":""},{"attr":"organism","value":"Zea mays","unit":""}],"irods-avus":[]}}'

• To update metadata only, omit the description

  • curl -X POST -sk -H "user: lwang" -H "Authorization: Bearer $AGAVETOKEN" -H "Content-Type: application/json" https://de.sciapps.org/workflow/3be623ed-c3ce-473a-9ffe-5aa30a731f60/update -d '{"metadata": {"avus":[{"attr":"SciApps_id","value":"af72ea64-2126-41ce-ac00-cdc5d69a1c7f","unit":""},{"attr":"sra_project_id","value":"PRJNA438108","unit":""},{"attr":"cultivar","value":"B73","unit":""},{"attr":"organism","value":"Zea mays","unit":""}],"irods-avus":[]}}'

• After login, use ils to check if sci_data folder exists, if not, give a warning, pop up window.

• EMS filter app

  • Move DP filtering from bcf_call to ems_filter
  • From the filtered VCF file, get DP4:n1,n2,n3,n4 get a ratio, (n3+n4)/(n1+n2+n3+n4)
  • Generate an additional file, hetero_plot.view.tgz: chr, pos, ratio
  • This file will be used for an interactive plot