Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Blocker
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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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Story Points:2
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Epic Link:
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Sprint:Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul
Description
Recently a researcher asked about these quickload instructions from the User's Guide:
He wrote:
Is this method still the easiest way to upload BAM/BED files to IGB Quickload?
The last edit to this page was in Jan 2016. The content may be out of date.
Before we answer the question, we should check that the content is still correct.
To do this, try to follow the instructions to set up a satellite Quickload site on your computer, using the latest tomato genome currently available in IGB. Make note of any problems you encounter. Your test QL site should include a BED and a BAM file, since this is what the researcher asked about. You can get examples from the RNA-Seq quickload site.
Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions.
If you run into problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Include it in the current sprint.
Attachments
Issue Links
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2424 [ 18604 ] |
| Rank | Ranked higher |
| Description |
Recently a researcher who is new to using IGB sent us a question about these quickload instructions from the User's Guide:
* https://wiki.transvar.org/display/igbman/Create+a+satellite+IGB+QuickLoad+site+for+genomes+that+are+already+supported+in+the+main+IGB+QuickLoad+site He wrote: {quote} Is this method still the easiest way to upload BAM/BED files to IGB Quickload? {quote} The last edit to this page was in Jan 2016, so it is possible that the content is out of date. To check that the content is still correct, let's walk through the instructions. Our goal is to make sure that if someone follows the instructions, they can set up their own "satellite" quickload site. For this task, try to set up your own satellite quickload site using the latest tomato genome as a test case. Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions. If there are any problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Included it in the current sprint. |
Recently a researcher who is new to using IGB about about these quickload instructions from the User's Guide:
* https://wiki.transvar.org/display/igbman/Create+a+satellite+IGB+QuickLoad+site+for+genomes+that+are+already+supported+in+the+main+IGB+QuickLoad+site He wrote: {quote} Is this method still the easiest way to upload BAM/BED files to IGB Quickload? {quote} The last edit to this page was in Jan 2016, so it is possible that the content is out of date. To check that the content is still correct, let's walk through the instructions. Our goal is to make sure that if someone follows the instructions, they can set up their own "satellite" quickload site. For this task, try to set up your own satellite quickload site using the latest tomato genome as a test case. Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions. If there are any problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Included it in the current sprint. |
| Description |
Recently a researcher who is new to using IGB about about these quickload instructions from the User's Guide:
* https://wiki.transvar.org/display/igbman/Create+a+satellite+IGB+QuickLoad+site+for+genomes+that+are+already+supported+in+the+main+IGB+QuickLoad+site He wrote: {quote} Is this method still the easiest way to upload BAM/BED files to IGB Quickload? {quote} The last edit to this page was in Jan 2016, so it is possible that the content is out of date. To check that the content is still correct, let's walk through the instructions. Our goal is to make sure that if someone follows the instructions, they can set up their own "satellite" quickload site. For this task, try to set up your own satellite quickload site using the latest tomato genome as a test case. Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions. If there are any problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Included it in the current sprint. |
Recently a researcher asked about these quickload instructions from the User's Guide:
* https://wiki.transvar.org/display/igbman/Create+a+satellite+IGB+QuickLoad+site+for+genomes+that+are+already+supported+in+the+main+IGB+QuickLoad+site He wrote: {quote} Is this method still the easiest way to upload BAM/BED files to IGB Quickload? {quote} The last edit to this page was in Jan 2016. The content may be out of date. Before we answer the question, we should check that the content is still correct. To do this, try to follow the instructions to set up a satellite Quickload site on your computer, using the latest tomato genome currently available in IGB. Make note of any problems you encounter. Your test QL site should include a BED and a BAM file, since this is what the researcher asked about. You can get examples from the RNA-Seq quickload site. Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions. If you run into problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Included it in the current sprint. |
| Labels | Beginner Intern |
| Description |
Recently a researcher asked about these quickload instructions from the User's Guide:
* https://wiki.transvar.org/display/igbman/Create+a+satellite+IGB+QuickLoad+site+for+genomes+that+are+already+supported+in+the+main+IGB+QuickLoad+site He wrote: {quote} Is this method still the easiest way to upload BAM/BED files to IGB Quickload? {quote} The last edit to this page was in Jan 2016. The content may be out of date. Before we answer the question, we should check that the content is still correct. To do this, try to follow the instructions to set up a satellite Quickload site on your computer, using the latest tomato genome currently available in IGB. Make note of any problems you encounter. Your test QL site should include a BED and a BAM file, since this is what the researcher asked about. You can get examples from the RNA-Seq quickload site. Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions. If you run into problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Included it in the current sprint. |
Recently a researcher asked about these quickload instructions from the User's Guide:
* https://wiki.transvar.org/display/igbman/Create+a+satellite+IGB+QuickLoad+site+for+genomes+that+are+already+supported+in+the+main+IGB+QuickLoad+site He wrote: {quote} Is this method still the easiest way to upload BAM/BED files to IGB Quickload? {quote} The last edit to this page was in Jan 2016. The content may be out of date. Before we answer the question, we should check that the content is still correct. To do this, try to follow the instructions to set up a satellite Quickload site on your computer, using the latest tomato genome currently available in IGB. Make note of any problems you encounter. Your test QL site should include a BED and a BAM file, since this is what the researcher asked about. You can get examples from the RNA-Seq quickload site. Make notes in this ticket about any changes or problems you notice as you do the walk-through. Hopefully everything will work properly! But it not, your observations will help us think of some potential solutions. If you run into problems, please make a new Jira ticket in the "Teach people to use IGB" epic and link it to this one. Include it in the current sprint. |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Story Points | 0.5 | 1 |
| Story Points | 1 | 2 |
| Sprint | Summer 1: 8 Jun - 19 Jun [ 96 ] | Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 July [ 96, 97 ] |
| Rank | Ranked higher |
| Summary | Check that quickload instructions | Check quickload instructions |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Comment | [ Do we want to investigate the http://www.igbquickload.org/quickload/ large-file download problem? ] |
| 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 ] |