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:Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11
Description
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using a tool from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file.
This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file).
Create a Cyverse analyses app that does two things:
- creates a scaled coverage graph using bamCoverage (from the deepTools suite)
- sorts and tabix-indexes the resulting bedgraph file (the output from bamCoverage)
References:
bamCoverage documentation
How to index a bedgraph
tabix and bgzip in Samtools
Deploying apps in CyVerse
Tool integration in DE
Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2376 [ 18533 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Create a Cyverse analyses app to index Bedgraph.
[How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] |
| Description |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
| Description |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
| Description |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 9 2021 Dec 13 - Dec 24 [ 135 ] | Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14 [ 135, 136 ] |
| Rank | Ranked higher |
| Link | This issue relates to IGBF-2971 [ IGBF-2971 ] |
| Summary | Create Cyverse App to Index Bedgraph | Create Cyverse App to create and index Bedgraph |
| Description |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app to index Bedgraph. [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app to index Bedgraph. [How to create a scaled coverage graph (bedgraph) file - bamCoverage |documentation|https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.htm] [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
| Description |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app to index Bedgraph. [How to create a scaled coverage graph (bedgraph) file - bamCoverage |documentation|https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.htm] [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app to index Bedgraph. [bamCoverage documentation|https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.htm] [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
| Description |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app to index Bedgraph. [bamCoverage documentation|https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.htm] [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app that does two things: * creates a scaled coverage graph using bamCoverage (from the deepTools suite) * sorts and tabix-indexes the resulting bedgraph file (the output from bamCoverage) References: [bamCoverage documentation|https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.htm] [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
| Comment | [ Also, please see linked issue: IGBF-2971 ] |
| Sprint | Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14 [ 135, 136 ] | Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 135, 136, 137 ] |
| Rank | Ranked higher |
| Story Points | 2 | 4 |
| Sprint | Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 135, 136, 137 ] | Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11 [ 135, 136, 137, 138 ] |
| Rank | Ranked higher |
| Description |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using genomeCov from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app that does two things: * creates a scaled coverage graph using bamCoverage (from the deepTools suite) * sorts and tabix-indexes the resulting bedgraph file (the output from bamCoverage) References: [bamCoverage documentation|https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.htm] [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
Use case scenario:
A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using a tool from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file. This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file). Create a Cyverse analyses app that does two things: * creates a scaled coverage graph using bamCoverage (from the deepTools suite) * sorts and tabix-indexes the resulting bedgraph file (the output from bamCoverage) References: [bamCoverage documentation|https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.htm] [How to index a bedgraph | https://www.biostars.org/p/121967/] [tabix and bgzip in Samtools | http://www.htslib.org/doc/tabix.html] [Deploying apps in CyVerse | https://learning.cyverse.org/projects/container_camp_workshop_2019/en/latest/cyverse/de_docker.html] [Tool integration in DE | https://learning.cyverse.org/projects/Container-camp-2020/en/latest/cyverse/tool_integration_app_building_DE.html] Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts. |
| Assignee | Karthik Raveendran [ karthik ] |
| 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 ] | To-Do [ 10305 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |