GotCloud: Amazon Demo - Revision history

Mktrost at 16:55, 31 October 2014

2014-10-31T16:55:52Z

← Older revision		Revision as of 12:55, 31 October 2014
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	* [[SeqShop: Variant Calling and Filtering for INDELs Practical]]		* [[SeqShop: Variant Calling and Filtering for INDELs Practical]]
	* [[SeqShop: Analysis of Structural Variation Practical]]		* [[SeqShop: Analysis of Structural Variation Practical]]


			To run this Demo on an Amazon Cluster rather than on a single node, see: [[StarCluster#Run_GotCloud_Demo_Using_StarCluster\|StarCluster -> Run GotCloud Demo Using StarCluster]]


	== Starting up a Node ==		== Starting up a Node ==

Mktrost: /* Run GotCloud ldrefine */

2014-10-31T16:52:39Z

Run GotCloud ldrefine

← Older revision		Revision as of 12:52, 31 October 2014
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	#:[[File:SnpSummary.png\|700px]]		#:[[File:SnpSummary.png\|700px]]
	#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''		#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''


	~~=== Run GotCloud ldrefine ===~~
	~~Now run GotCloud ldrefine~~
	~~# <pre>gotcloud ldrefine --conf example/test.conf --outdir output --numjobs 8</pre>~~
	~~#* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found~~
	~~#: [[File:RunIndel.png\|700px]]~~
	~~#:* This will take a few minutes to run.~~
	~~#:* GotCloud first generates a makefile, and then runs the makefile~~
	~~# When complete, GotCloud ldrefine will indicate success/failure~~
	~~#:[[File:LdrefineSuccess.png\|700px]]~~

	~~==== Examining ldrefine Output ====~~

Mktrost: /* Run GotCloud Indel */

2014-10-31T16:52:25Z

Run GotCloud Indel

@@ Line 80: / Line 80: @@
 === Run GotCloud Indel ===
-Now run GotCloud indel
+Now that we have examined the instance files, run GotCloud indel
 # <pre>gotcloud indel --conf example/test.conf --outdir output --numjobs 8</pre>
 #* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
@@ Line 90: / Line 90: @@
 ==== Examining Indel Output ====

Mktrost at 16:48, 31 October 2014

2014-10-31T16:48:39Z

← Older revision		Revision as of 12:48, 31 October 2014
Line 64:		Line 64:
	#:[[File:SnpSummary.png\|700px]]		#:[[File:SnpSummary.png\|700px]]
	#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''		#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''


			=== Run GotCloud ldrefine ===
			Now run GotCloud ldrefine
			# <pre>gotcloud ldrefine --conf example/test.conf --outdir output --numjobs 8</pre>
			#* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
			#: [[File:RunIndel.png\|700px]]
			#:* This will take a few minutes to run.
			#:* GotCloud first generates a makefile, and then runs the makefile
			# When complete, GotCloud ldrefine will indicate success/failure
			#:[[File:LdrefineSuccess.png\|700px]]

			==== Examining ldrefine Output ====


			=== Run GotCloud Indel ===
			Now run GotCloud indel
			# <pre>gotcloud indel --conf example/test.conf --outdir output --numjobs 8</pre>
			#* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
			#: [[File:RunIndel.png\|700px]]
			#:* This will take a few minutes to run.
			#:* GotCloud first generates a makefile, and then runs the makefile
			# When complete, GotCloud indel will indicate success/failure
			#:[[File:IndelSuccess.png\|700px]]

			==== Examining Indel Output ====

Mktrost: /* Running the Demo on Already Running Node */

2014-10-31T12:37:33Z

Running the Demo on Already Running Node

@@ Line 21: / Line 21: @@
 == Running the Demo on Already Running Node ==
-=== Examine the Setup ===
+{{GotCloud: Amazon Demo Setup}}
 === Run GotCloud SnpCall ===

Mktrost: /* Examining SnpCall Output */

2014-10-29T19:31:09Z

Examining SnpCall Output

← Older revision		Revision as of 15:31, 29 October 2014
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	# Look at the filtered file.		# Look at the filtered file.
	#: <pre>zless -S output/vcfs/chr22/chr22.filtered.vcf.gz</pre>		#: <pre>zless -S output/vcfs/chr22/chr22.filtered.vcf.gz</pre>
	#: Scroll down some: [[File::SnpVcfOutput.png\|700px]]		#: Scroll down some: [[File:SnpVcfOutput.png\|700px]]
	## Check that GotCloud found the expected SNP at 22:36661906		## Check that GotCloud found the expected SNP at 22:36661906
	##:<pre>tabix output/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 \|head -1</pre>		##:<pre>tabix output/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 \|head -1</pre>
	#:[[File::SnpTabix.png\|700px]]		#:[[File:SnpTabix.png\|700px]]
	# Look at the summary information		# Look at the summary information
	#:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre>		#:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre>
	#:[[File:SnpSummary.png\|700px]]		#:[[File:SnpSummary.png\|700px]]
	#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''		#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''

Mktrost at 21:50, 19 October 2014

2014-10-19T21:50:45Z

@@ Line 1: / Line 1: @@
 == Introduction ==
 This Amazon demo runs through the GotCloud SNP and INDEL calling pipelines.
@@ Line 82: / Line 88: @@
 #:[[File:SnpSummary.png|700px]]
 #:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''

Mktrost: /* Exit & Terminate */

2014-10-19T21:47:34Z

Exit & Terminate

← Older revision		Revision as of 17:47, 19 October 2014
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	== Exit & Terminate ==		== Exit & Terminate ==
			Prior to terminating, make sure you copy any data off of the root EBS volume attached to the instance as it will be deleted when you terminate.
	# Exit from your terminal		# Exit from your terminal
	# Terminate your Amazon Instance		# Terminate your Amazon Instance
			#* Right click on the instance you want to terminate in the EC2 dashboard
			#* Select Terminate
			#* Select "Yes, Terminate" to indicate you would like to terminate and the storage will be deleted.

Mktrost: /* Run GotCloud Indel */

2014-10-17T18:24:50Z

Run GotCloud Indel

← Older revision		Revision as of 14:24, 17 October 2014
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	# Look inside the output directory to see the new indel directories:		# Look inside the output directory to see the new indel directories:
	#:<pre>ls output</pre>		#:<pre>ls output</pre>
	#:[[File:IndelSnpOutput~~.png~~.png\|~~700px~~]]		#:[[File:IndelSnpOutput.png\|900px]]
	#:#<code>aux</code> - intermediate indel files		#:#<code>aux</code> - intermediate indel files
	#:#<code>final</code> - final output of Indel pipeline		#:#<code>final</code> - final output of Indel pipeline
Line 105:		Line 105:
	# Important Indel output is in <code>output/final</code>		# Important Indel output is in <code>output/final</code>
	#:<pre> ls output/final/</pre>		#:<pre> ls output/final/</pre>
	#: [[File:IndelFinal.png\|~~700px~~]]		#: [[File:IndelFinal.png\|900px]]
	# Look at the final Indel VCF file.		# Look at the final Indel VCF file.
	#: <pre>zless output/final/all.genotypes.vcf.gz</pre>		#: <pre>zless output/final/all.genotypes.vcf.gz</pre>
	#: Scroll down some: [[File::IndelLess.png\|~~700px~~]]		#: Scroll down some: [[File::IndelLess.png\|900px]]
	## Check that GotCloud found the expected Indel at 22:36662041		## Check that GotCloud found the expected Indel at 22:36662041
	##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041\|less -S</pre>		##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041\|less -S</pre>
	#:[[File::IndelTabix.png\|~~700px~~]]		##:[[File:IndelTabix.png\|900px]]

	== Exit & Terminate ==		== Exit & Terminate ==
	# Exit from your terminal		# Exit from your terminal
	# Terminate your Amazon Instance		# Terminate your Amazon Instance

Mktrost: /* Examining Indel Output */

2014-10-17T18:23:30Z

Examining Indel Output

← Older revision		Revision as of 14:23, 17 October 2014
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	==== Examining Indel Output ====		==== Examining Indel Output ====
			# Look inside the output directory to see the new indel directories:
			#:<pre>ls output</pre>
			#:[[File:IndelSnpOutput.png.png\|700px]]
			#:#<code>aux</code> - intermediate indel files
			#:#<code>final</code> - final output of Indel pipeline
			#:#<code>indelvcf</code> - intermediate indel files
			#:#<code>gotcloud.indel.conf</code> - file containing all of the configuration settings used for this run of GotCloud
			#:#<code>gotcloud.indel.Makefile</code> - Makefile containing commands for this run of GotCloud
			#:#<code>gotcloud.indel.Makefile.log</code> - log of the GotCloud run
			# Important Indel output is in <code>output/final</code>
			#:<pre> ls output/final/</pre>
			#: [[File:IndelFinal.png\|700px]]
			# Look at the final Indel VCF file.
			#: <pre>zless output/final/all.genotypes.vcf.gz</pre>
			#: Scroll down some: [[File::IndelLess.png\|700px]]
			## Check that GotCloud found the expected Indel at 22:36662041
			##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041\|less -S</pre>
			#:[[File::IndelTabix.png\|700px]]

			== Exit & Terminate ==
			# Exit from your terminal
			# Terminate your Amazon Instance