Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24
Description
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
For this task, we need to:
- Get familiar with the UNC Charlotte compute cluster environment and job schedular
- Understand how various software packages are configured and installed - how can we get Nextflow onto the cluster
- Communicate with support personnnel to ask for new software to be installed, as required
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Sprint | Fall 1 2021 Aug 16 - Aug 27 [ 127 ] | Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Aug 10 [ 127, 128 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Summary | Deploy rice salt stress and strain data to RNA-Seq quickload | Deploy rice salt stress and strain data |
| Summary | Deploy rice salt stress and strain data | Re-align rice salt stress RNA-Seq data using hisat |
| Summary | Re-align rice salt stress RNA-Seq data using hisat | Determine if we can use Nextflow to align RNA-Seq data on cluster |
| Description |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. |
| Description |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schelular * Understand how various software packages are configured and installed * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for alignment RNA-seq data onto a reference genome |
| Description |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schelular * Understand how various software packages are configured and installed * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for alignment RNA-seq data onto a reference genome |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schedular * Understand how various software packages are configured and installed * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for alignment RNA-seq data onto a reference genome |
| Summary | Determine if we can use Nextflow to align RNA-Seq data on cluster | Determine if and how we can use Nextflow to align RNA-Seq data on cluster |
| Description |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schedular * Understand how various software packages are configured and installed * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for alignment RNA-seq data onto a reference genome |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schedular * Understand how various software packages are configured and installed - how can we get Nextflow onto the cluster * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for alignment RNA-seq data onto a reference genome |
| Description |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schedular * Understand how various software packages are configured and installed - how can we get Nextflow onto the cluster * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for alignment RNA-seq data onto a reference genome |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schedular * Understand how various software packages are configured and installed - how can we get Nextflow onto the cluster * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for aligning RNA-seq data onto a reference genome |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Link | This issue relates to IGBF-2935 [ IGBF-2935 ] |
| Comment |
[ Nextflow scripts can run in lots of different environments, using diverse schedulers. I ran a script on the UNCC HPC queue "Orion" by creating a file named "nextflow.config" in the same directory as my nextflow script.
nextflow.config: {code} process { executor='slurm' queue = 'Orion' time = '5m' } {code} I first tried it without the time parameter, but I got an error message. I think you can specify the time variable in the Nextflow script itself. ] |
| Sprint | Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10 [ 127, 128 ] | Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021Sep 13 - Sep 24 [ 127, 128, 129 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
| Description |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
If the environment does not support it for some reason, we can use AWS instead. For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schedular * Understand how various software packages are configured and installed - how can we get Nextflow onto the cluster * Communicate with support personnnel to ask for new software to be installed, as required * Investigate Nextflow workflows others have published for aligning RNA-seq data onto a reference genome |
Determine if we can use Nextflow workflow management software on the UNC Charlotte compute cluster.
For this task, we need to: * Get familiar with the UNC Charlotte compute cluster environment and job schedular * Understand how various software packages are configured and installed - how can we get Nextflow onto the cluster * Communicate with support personnnel to ask for new software to be installed, as required |
| Summary | Determine if and how we can use Nextflow to align RNA-Seq data on cluster | Determine if and how we can use Nextflow on UNCC HPC cluster |
| 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 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |