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:4
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Epic Link:
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Sprint:Winter 1, Spring 1, Summer 4
Description
Situation: We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
Task:
- Clone the Galaxy repo and deploy it on a local machine for development and testing.
- Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml".
- Submit a pull request with that new file to the latest Galaxy release branch.
- Determine how to test that the new capability is working as expected.
- Once finished with testing, next steps will be to make a new ticket for adding a CRAM file to the "Open Galaxy Files in Integrated Genome Browser" History (https://usegalaxy.org/published/history?id=4d6cb5a8a3640b22). I'd suggest maybe using the one that was subsetted to a smaller size as part of
IGBF-3841.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1880 [ 17970 ] |
| Link | This issue relates to IGBF-2160 [ IGBF-2160 ] |
| Description |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. See linked tickets as well as |
| Description |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. See linked tickets as well as |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. |
| Description |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. * Once finished with testing, make sure to update the release documentation linked above. |
| Description |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. * Once finished with testing, make sure to update the release documentation linked above. |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. * Once finished with testing, next steps will be to add a CRAM file to the "Open Galaxy Files in Integrated Genome Browser" History (https://usegalaxy.org/published/history?id=4d6cb5a8a3640b22). I'd suggest maybe using the one that was subsetted to a smaller size as part of |
| Description |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. * Once finished with testing, next steps will be to add a CRAM file to the "Open Galaxy Files in Integrated Genome Browser" History (https://usegalaxy.org/published/history?id=4d6cb5a8a3640b22). I'd suggest maybe using the one that was subsetted to a smaller size as part of |
*Situation:* We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
*Task:* * Clone the Galaxy repo and deploy it on a local machine for development and testing. * Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml". * Submit a pull request with that new file to the latest Galaxy release branch. * Determine how to test that the new capability is working as expected. * Once finished with testing, next steps will be to make a new ticket for adding a CRAM file to the "Open Galaxy Files in Integrated Genome Browser" History (https://usegalaxy.org/published/history?id=4d6cb5a8a3640b22). I'd suggest maybe using the one that was subsetted to a smaller size as part of |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
| Sprint | Winter 1 [ 209 ] | Winter 1, Spring 1 [ 209, 210 ] |
| Rank | Ranked higher |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Sprint | Winter 1, Spring 1 [ 209, 210 ] | Winter 1, Spring 1, Spring 2 [ 209, 210, 211 ] |
| Rank | Ranked higher |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Sprint | Winter 1, Spring 1, Spring 2 [ 209, 210, 211 ] | Winter 1, Spring 1, Spring 3 [ 209, 210, 212 ] |
| Sprint | Winter 1, Spring 1, Spring 3 [ 209, 210, 212 ] | Winter 1, Spring 1 [ 209, 210 ] |
| Sprint | Winter 1, Spring 1 [ 209, 210 ] | Winter 1, Spring 1, Spring 4 [ 209, 210, 213 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Winter 1, Spring 1, Spring 4 [ 209, 210, 213 ] | Winter 1, Spring 1 [ 209, 210 ] |
| Rank | Ranked higher |
| Sprint | Winter 1, Spring 1 [ 209, 210 ] | Winter 1, Spring 1, Summer 4 [ 209, 210, 221 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Nowlan Freese [ nfreese ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |