Flankophile-Sapelo2 - Revision history

Shtsai at 00:37, 5 April 2026

2026-04-05T00:37:25Z

Isaiah: Contents of "Description" also changed to sub-heading 1. Corrected back to paragraph

2024-03-18T15:11:20Z

Contents of "Description" also changed to sub-heading 1. Corrected back to paragraph

← Older revision		Revision as of 11:11, 18 March 2024
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	=== Description ===		=== Description ===
			"''Flankophile is a bioinformatics pipeline for gene synteny analysis.''" [https://bitbucket.org/genomicepidemiology/flankophile/src/master/ Bitbucket]
	~~===~~ "''Flankophile is a bioinformatics pipeline for gene synteny analysis.''" [https://bitbucket.org/genomicepidemiology/flankophile/src/master/ Bitbucket] ~~===~~

	=== Running Program ===		=== Running Program ===

Isaiah: Updated "Description" section to be sub-heading 1

2024-03-18T15:10:02Z

Updated "Description" section to be sub-heading 1

← Older revision		Revision as of 11:10, 18 March 2024
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	[https://bitbucket.org/genomicepidemiology/ Genomic Epidemiology]		[https://bitbucket.org/genomicepidemiology/ Genomic Epidemiology]

	Description		=== Description ===

	"''Flankophile is a bioinformatics pipeline for gene synteny analysis.''" [https://bitbucket.org/genomicepidemiology/flankophile/src/master/ Bitbucket]		=== "''Flankophile is a bioinformatics pipeline for gene synteny analysis.''" [https://bitbucket.org/genomicepidemiology/flankophile/src/master/ Bitbucket] ===

	=== Running Program ===		=== Running Program ===

Isaiah: Added the "Running Pipeline Using /lscratch" section.

2024-03-15T20:02:42Z

Added the "Running Pipeline Using /lscratch" section.

Show changes

Isaiah: Removed Flankophile module and removed sections that stated Flankophile was available as a module

2024-03-07T21:50:41Z

Removed Flankophile module and removed sections that stated Flankophile was available as a module

Show changes

Isaiah: Added "load Snakemake module" step to Manual setup section

2024-03-07T20:54:53Z

Added "load Snakemake module" step to Manual setup section

← Older revision		Revision as of 16:54, 7 March 2024
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	# '''Change the working directory to the newly cloned ''flankophile/'' repository'''		# '''Change the working directory to the newly cloned ''flankophile/'' repository'''
	## <code>cd flankophile</code>		## <code>cd flankophile</code>
			# '''Load the Snakemake module.'''
			## <code>module load snakemake/6.9.1-Mamba-4.11.0-4</code>
	# '''Create the conda environments that ''Flankophile'' will use at runtime''' In some tests, creating the conda environments at runtime causes the pipeline to fail due to missing or incompatible dependencies. To avoid this, create the conda environments ahead of time. '''<u>This step will take ~15-25 minutes to complete.</u>'''		# '''Create the conda environments that ''Flankophile'' will use at runtime''' In some tests, creating the conda environments at runtime causes the pipeline to fail due to missing or incompatible dependencies. To avoid this, create the conda environments ahead of time. '''<u>This step will take ~15-25 minutes to complete.</u>'''
	## <code>snakemake --use-conda --conda-create-envs-only --cores 16</code>		## <code>snakemake --use-conda --conda-create-envs-only --cores 16</code>

Isaiah: Changed /source/$USER to /scratch/$USER

2024-03-06T21:12:06Z

Changed /source/$USER to /scratch/$USER

← Older revision		Revision as of 17:12, 6 March 2024
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	## <code>ls .snakemake/conda/</code>		## <code>ls .snakemake/conda/</code>
	# '''Activate the ''Conda'' environment that ''Flankophile'' will use.'''		# '''Activate the ''Conda'' environment that ''Flankophile'' will use.'''
	## <code>source activate /~~source~~/''$USER''/flankophile/.snakemake/conda/50e62e607e6a24bb70ce9a5a50888445</code>		##<code>source activate /scratch/''$USER''/flankophile/.snakemake/conda/50e62e607e6a24bb70ce9a5a50888445</code>
	# '''Run the pipeline.'''		# '''Run the pipeline.'''
	## <code>snakemake --use-conda --cores 16</code>		## <code>snakemake --use-conda --cores 16</code>

Isaiah: Corrected the grammar in the description of the metadata file (in Requirements section) so that it refers to the input files as plural instead of singular

2024-03-06T20:13:34Z

Corrected the grammar in the description of the metadata file (in Requirements section) so that it refers to the input files as plural instead of singular

← Older revision		Revision as of 16:13, 6 March 2024
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	## One or more FASTA files that ''Flankophile'' should use as input.		## One or more FASTA files that ''Flankophile'' should use as input.
	# '''[[Flankophile-Sapelo2#Example .tsv Metadata File\|A tab-separated value (''.tsv'') metadata file]]'''		# '''[[Flankophile-Sapelo2#Example .tsv Metadata File\|A tab-separated value (''.tsv'') metadata file]]'''
	## Describes the assembly ~~name~~, ~~the filepath~~, and the genus for each input FASTA file.		## Describes the assembly names, their filepaths, and the genus for each input FASTA file.
	# '''[[Flankophile-Sapelo2#Example .yaml Configuration File\|An analysis configuration file in YAML (''.yaml'')]]'''		# '''[[Flankophile-Sapelo2#Example .yaml Configuration File\|An analysis configuration file in YAML (''.yaml'')]]'''
	## Describes the analysis for ''Flankophile'' to perform and the parameters to use during analysis.		## Describes the analysis for ''Flankophile'' to perform and the parameters to use during analysis.

Isaiah: Updated the steps for using the pre-built pipeline so that it explicitly instructs users to enter into an interactive session before loading the Flankophile module

2024-03-06T19:23:37Z

Updated the steps for using the pre-built pipeline so that it explicitly instructs users to enter into an interactive session before loading the Flankophile module

← Older revision		Revision as of 15:23, 6 March 2024
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	GACRC provides a complete ''Flankophile'' directory in a module.		GACRC provides a complete ''Flankophile'' directory in a module.

	To use it, load the module and copy the directory into your user's <code>/scratch</code> directory. It may take a while to copy the directory due to its size.		To use it, enter into an interactive session, load the module, and copy the directory into your user's <code>/scratch</code> directory. It may take a while to copy the directory due to its size.

			#<code>interact --cpus-per-task 16 --mem 32GB</code>
	# <code>module load Flankophile/0.2.10</code>		# <code>module load Flankophile/0.2.10</code>
	# <code>cp -r $EBROOTFLANKOPHILE/flankophile /scratch/$USER/</code>		# <code>cp -r $EBROOTFLANKOPHILE/flankophile /scratch/$USER/</code>

Isaiah: Changed "Setup" to "Setting up the Pipeline" for added clarity

2024-03-06T19:15:55Z

Changed "Setup" to "Setting up the Pipeline" for added clarity

← Older revision		Revision as of 15:15, 6 March 2024
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	## Should be located at the root of the ''Flankophile'' repository directory.		## Should be located at the root of the ''Flankophile'' repository directory.

	==== ~~Setup~~ ====		==== Setting up the Pipeline ====
	Before running ''Flankophile'', the pipeline must be cloned and the dependencies must be installed. For convenience, a ''Flankophile'' directory has already been setup in a module that can be copied and used directly.		Before running ''Flankophile'', the pipeline must be cloned and the dependencies must be installed. For convenience, a ''Flankophile'' directory has already been setup in a module that can be copied and used directly.