ARGOSQC Usage Tutorial - Revision history

Miaowang: /* Batch Mode Parameter breakdown: */

2025-09-22T15:07:49Z

Batch Mode Parameter breakdown:

← Older revision		Revision as of 15:07, 22 September 2025
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	[[File:Batcheg2.png\|none\|thumb\|500px]]		[[File:Batcheg2.png\|none\|thumb\|500px]]

			The following colorful and highlighted example displays the syntax for grouping inputs.

			<br>They would be grouped for computations like this:

	Assembly 1:		Assembly 1:

Miaowang: /* Batch Mode Parameter breakdown: */

2025-09-22T03:56:54Z

Batch Mode Parameter breakdown:

← Older revision		Revision as of 03:56, 22 September 2025
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	The following colorful and highlighted example displays the syntax for grouping inputs.		The following colorful and highlighted example displays the syntax for grouping inputs.

	They would be grouped for computations like this:		<br>They would be grouped for computations like this:

	Assembly 1:		Assembly 1:

Miaowang: /* Batch Mode Parameter breakdown: */

2025-09-22T03:56:40Z

Batch Mode Parameter breakdown:

← Older revision		Revision as of 03:56, 22 September 2025
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	== ''Batch Mode Parameter breakdown:'' ==		== ''Batch Mode Parameter breakdown:'' ==
	~~The following colorful and highlighted example displays the syntax for grouping inputs.~~[[File:Batcheg1.png\|none\|thumb\|500px]]		[[File:Batcheg1.png\|none\|thumb\|500px]]

			The following colorful and highlighted example displays the syntax for grouping inputs.

	They would be grouped for computations like this:		They would be grouped for computations like this:

Miaowang: /* Batch Mode Computation */

2025-09-22T03:21:44Z

Batch Mode Computation

← Older revision		Revision as of 03:21, 22 September 2025
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	SAMN110654323, SAMN110654324		SAMN110654323, SAMN110654324

	To separate between batches, use a semicolon “;” in between the IDs. A comma denotes separate IDs but semicolons as separate batches. These will be inputted in the General tab of the pipeline, same as single computation. Within each field, this is how the above example would look like in batch mode:		<br>To separate between batches, use a semicolon “;” in between the IDs. A comma denotes separate IDs but semicolons as separate batches. These will be inputted in the General tab of the pipeline, same as single computation. Within each field, this is how the above example would look like in batch mode:

	<u>SRR IDS:</u> SRR0123456, SRR0123457, SRR0123458, SRR0123459<mark>;</mark> SRR0123451, SRR0123452, SRR0123453, SRR0123454		<u>SRR IDS:</u> SRR0123456, SRR0123457, SRR0123458, SRR0123459<mark>;</mark> SRR0123451, SRR0123452, SRR0123453, SRR0123454

Miaowang: /* Batch Mode Computation */

2025-09-22T03:21:09Z

Batch Mode Computation

← Older revision		Revision as of 03:21, 22 September 2025
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	SRR IDS: SRR0123456,SRR0123457,SRR0123458,SRR0123459''';'''SRR0123451,SRR0123452,SRR0123453,SRR0123454		SRR IDS: SRR0123456,SRR0123457,SRR0123458,SRR0123459''';'''SRR0123451,SRR0123452,SRR0123453,SRR0123454

	'''Step 1:''' Navigate to the tab title Batch, Figure 10. This can be found on the ARGOS input settings page, Figure 1., next to the General tab.		<br>'''Step 1:''' Navigate to the tab title Batch, Figure 10. This can be found on the ARGOS input settings page, Figure 1., next to the General tab.

	'''Step 2:''' For the parameter “batch service" at the bottom select, from the dropdown menu batch mode. This will have the pipeline set to Batch Mode rather than single computations.		'''Step 2:''' For the parameter “batch service" at the bottom select, from the dropdown menu batch mode. This will have the pipeline set to Batch Mode rather than single computations.

Miaowang: /* Batch Mode Computation */

2025-09-22T03:20:21Z

Batch Mode Computation

← Older revision		Revision as of 03:20, 22 September 2025
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	<u>BioSample Accessions:</u> SAMN110654321, SAMN110654322<mark>;</mark> SAMN110654323, SAMN110654324		<u>BioSample Accessions:</u> SAMN110654321, SAMN110654322<mark>;</mark> SAMN110654323, SAMN110654324

	Notice the semicolon separation according to the example above. The commas separate the ids, and the semicolon the batch.		<br>Notice the semicolon separation according to the example above. The commas separate the ids, and the semicolon the batch.

	'''Troubleshooting Note:''' If your computation fails or if there is an error, remove the spaces between the , and ; .Previously, this has thrown an error but has been fixed, but worth a shot if your computation fails. It would look like:		'''Troubleshooting Note:''' If your computation fails or if there is an error, remove the spaces between the , and ; .Previously, this has thrown an error but has been fixed, but worth a shot if your computation fails. It would look like:

Miaowang: /* Batch Mode Parameter breakdown: */

2025-09-22T03:17:31Z

Batch Mode Parameter breakdown:

← Older revision		Revision as of 03:17, 22 September 2025
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	== ''Batch Mode Parameter breakdown:'' ==		== ''Batch Mode Parameter breakdown:'' ==
	[[File:Batcheg1.png\|none\|thumb\|500px]]		The following colorful and highlighted example displays the syntax for grouping inputs.[[File:Batcheg1.png\|none\|thumb\|500px]]

			They would be grouped for computations like this:

	Assembly 1:		Assembly 1:

Miaowang: /* Single QC Computation */

2025-09-22T03:04:56Z

Single QC Computation

← Older revision		Revision as of 03:04, 22 September 2025
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	'''Step 5:''' Next, select from the Coding Table dropdown menu the genetic code you would like to use for your computation, if applicable. The default is “human, viral (Standard)”.		'''Step 5:''' Next, select from the Coding Table dropdown menu the genetic code you would like to use for your computation, if applicable. The default is “human, viral (Standard)”.

	'''Step 6:''' Lastly, navigate to the Advanced tab and open the pipeline section. Under the All objects section, select argos-cflow System Application.		'''Step 6:''' Lastly, navigate to the Advanced tab and open the pipeline section as shown in Figure 12. Under the All objects section, select argos-cflow System Application as shown in Figure 13.

	'''~~Step7~~:''' Once all of the information has been inputted correctly, click on the big blue Submit button in the middle, as seen in Figure 8.		'''Step 7:''' Once all of the information has been inputted correctly, click on the big blue Submit button in the middle, as seen in Figure 8.

	'''Step 8:''' Once your computation has been submitted, you can click on the Home tab found in the top left to go back to the homepage and see the workflow.		'''Step 8:''' Once your computation has been submitted, you can click on the Home tab found in the top left to go back to the homepage and see the workflow.

Christie.woodside at 17:10, 19 September 2025

2025-09-19T17:10:02Z

← Older revision		Revision as of 17:10, 19 September 2025
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			Back to [[FDA-ARGOS WIKI\|Home Page]] for FDA-ARGOS

	HIVE3 one-click pipeline tutorial for the FDA HIVE instance. This protocol will guide the user in running single and batch-mode QC computations. HIVE3 is an instance of HIVE not owned by the FDA which can be directly modified by Vahan or others on our team with permissions.		HIVE3 one-click pipeline tutorial for the FDA HIVE instance. This protocol will guide the user in running single and batch-mode QC computations. HIVE3 is an instance of HIVE not owned by the FDA which can be directly modified by Vahan or others on our team with permissions.

Miaowang: /* Batch Mode Computation */

2025-09-17T18:54:45Z

Batch Mode Computation

← Older revision		Revision as of 18:54, 17 September 2025
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	* If the ratio is 1:1:1 then enter the value 1 for each box.		* If the ratio is 1:1:1 then enter the value 1 for each box.
	* One set of SRRs to one assembly to one biosample.		* One set of SRRs to one assembly to one biosample.
	'''Step 5:''' Navigate to the Advanced tab and open the Pipeline section. ~~Click~~ on the dropdown arrow next to Pipeline, and under All Projects, locate argos-cflow System Application. ~~Select~~ argos-cflow System Application by clicking on it, then confirm the selection by clicking Select at the bottom of the window. Leave all other settings in the Advanced section as default.		'''Step 5:''' Navigate to the Advanced tab and open the Pipeline section. As shown in Figure 12, click on the dropdown arrow next to Pipeline, and under All Projects, locate argos-cflow System Application. As shown in FIgure 13, select argos-cflow System Application by clicking on it, then confirm the selection by clicking Select at the bottom of the window. Leave all other settings in the Advanced section as default.
	[[File:Fig12.png\|none\|thumb\|700px\|'''Figure 12.''' Advanced tab showing the Pipeline dropdown menu where the argos-cflow System Application can be selected.]]		[[File:Fig12.png\|none\|thumb\|700px\|'''Figure 12.''' Advanced tab showing the Pipeline dropdown menu where the argos-cflow System Application can be selected.]]
	[[File:Fig13.png\|none\|thumb\|700px\|'''Figure 13.''' All Projects window displaying available workflows. The argos-cflow System Application is highlighted and can be selected by clicking “Select” at the bottom. ]]		[[File:Fig13.png\|none\|thumb\|700px\|'''Figure 13.''' All Projects window displaying available workflows. The argos-cflow System Application is highlighted and can be selected by clicking “Select” at the bottom. ]]