Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Minor
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:2
-
Epic Link:
-
Sprint:Spring 10, Summer 1
Description
The goal here is to test both Trinity and the Blat scripts from our reference free alignment pipeline.
There are 4 Trinity jobs.
There are 4 blat jobs.
To test this, Brandon will tackle running these scripts to see if he can recreate the results.
Need to decide a test area.
The scripts reside on the cluster at the following location:
/projects/tomato_genome/fnb/dataprocessing/trinity
Script names:
trinity-hei.slurm
trinity-mal.slurm
trinity-nag.slurm
trinity-tam.slurm
blat-hei.slurm
blat-mal.slurm
blat-nag.slurm
blat-tam.slurm
These scripts also need to be cleaned up as well. Remove line comments that are no longer relevant, etc.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
The goal here is to test both Trinity and the Blat scripts from our reference free alignment pipeline. Details to come in comments. |
The goal here is to test both Trinity and the Blat scripts from our reference free alignment pipeline.
There are 4 Trinity jobs. There are 4 blat jobs. To test this, Brandon will tackle running these scripts to see if he can recreate the results. Need to decide a test area. The scripts reside on the cluster at the following location: /projects/tomato_genome/fnb/dataprocessing/trinity *Script names:* trinity-hei.slurm trinity-mal.slurm trinity-nag.slurm trinity-tam.slurm blat-hei.slurm blat-mal.slurm blat-nag.slurm blat-tam.slurm These scripts also need to be cleaned up as well. Remove line comments that are no longer relevant, etc. |
| Assignee | Robert Reid [ robertreid ] | Brandon Benkick [ bbendick ] |
| Sprint | Spring 10 [ 194 ] | Spring 10, Summer 1 [ 194, 195 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |