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December 18, 2018, Tuesday
Liya Wang edited this page Jan 22, 2019
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- MaizeCode metadata example for B73LongRampage
- PRJNA438108
- BioProject_PRJNA438108 (sra_project_id: PRJNA438108) --> LongRampage
- BioSample1 (cultivar: B73; tissue: endosperm; replicate: 1) --> endosperm_rep1
- BioSample1Library1 (assay: Long RNA-Seq (LG)) --> RNAseq
-
Long RNA-Seq of Maize: B73 Endosperm Rep 1
- 300282_S1_R1_001.fastq.gz --> endo_rep1_R1.fq.gz
- 300282_S1_R2_001.fastq.gz --> endo_rep1_R2.fq.gz
- BioSample1Library2 (assay: RAMPAGE (RM)) --> RAMPAGE
- BioSample1 (cultivar: B73; tissue: endosperm; replicate: 1) --> endosperm_rep1
- Goal to combine metadata to one
- Query SRA database with Sample name and BioProject ID to get SRR number?
- Add SRR number to the metadata so that we can pull the data from NCBI
- Modifications to the public site
- Change 'Load a workflow' page to handle loading multiple workflows
- So that we can load multiple workflows and perform 'combinational' downstream analysis
- Steps for running through API
- tok="Authorization: Bearer 77f32c7173ebe6578df669ca449b0"
- curl -X POST -sk -H "user: lwang" -H "$tok" https://de.sciapps.org/workflowJob/new?runWorkflowJob=1 -F "[email protected]" > testw.json
- {
- "wf_step_0:trait": "agave://data.iplantcollaborative.org/lwang/sci_data/height.txt",
- "_derived_from": "5fb15c8f-0d38-4ec3-9b0e-392b59f08883"
- }
- To get workflow_id returned
- jq '.data.workflow_id' testw.json
- To get cleaned workflow json
- jq -c '.data.workflow' testw.json
- Create my.sql file
- insert into workflow (workflow_id, name, description, json) values("0a958127-55fc-48ea-8574-9e6b8185a65d", "testmaizecode", "test", 'workflow_json_output_from_above')
- mysql -u sciapps -p$PWD sciapps < my.sql (on halcott)
- Jobs are missing on the public site unless the job json file is grabbed after jobs are submitted to Agave, which won't take more than 5 minutes since MCrna app is simplified, ideally we will add API to the public site
- curl -X GET -sk -H "user: lwang" -H "$tok" https://de.sciapps.org/workflow/0a958127-55fc-48ea-8574-9e6b8185a65d > testw.json
- jq -c '.data' testw.json
- Create my.sql file
- insert into workflow (workflow_id, name, description, json) values("0a958127-55fc-48ea-8574-9e6b8185a65d", "testmaizecode", "test", 'workflow_json_output_from_above')
- mysql -u sciapps -p$PWD sciapps -e'delete from workflow where workflow_id="0a958127-55fc-48ea-8574-9e6b8185a65d"'
- mysql -u sciapps -p$PWD sciapps < my.sql (on halcott)
-
https://www.sciapps.org/?wf_id=0a958127-55fc-48ea-8574-9e6b8185a65d
- Need to share the job with maizecode, unless the job is submitted by maizecode
- Jobs are missing on the public site unless the job json file is grabbed after jobs are submitted to Agave, which won't take more than 5 minutes since MCrna app is simplified, ideally we will add API to the public site