GotCloud: Source Releases - Revision history

Mktrost at 21:34, 15 May 2014

2014-05-15T21:34:53Z

← Older revision		Revision as of 17:34, 15 May 2014
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	Back to parent: [[GotCloud]]		Back to parent: [[GotCloud]]

	The [[GotCloud]] software has been developed and tested on Linux Ubuntu 12.10 and 12.04.2 LTS. While it should work on other Linux systems, they have not yet been tested. It is not supported on Windows.		The [[GotCloud]] software has been developed and tested on Linux Ubuntu 13.10, 13.04, 12.10, and 12.04.2 LTS. While it should work on other Linux systems, they have not yet been tested. It is not supported on Windows.

Terry Gliedt: /* Test snp calling */

2013-10-14T12:40:22Z

Test snp calling

← Older revision		Revision as of 08:40, 14 October 2013
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	* replace the beginining ~/ with the actual path to where you downloaded gotcloud		* replace the beginining ~/ with the actual path to where you downloaded gotcloud
	* replace ~/testsnp with the directory where you want the test results to go		* replace ~/testsnp with the directory where you want the test results to go
			* To test the software in a cluster environment add the option -batchtype. For instance, using Sun Grid Engine in a Starcluster cluster, use
			~/gotcloud/gotcloud snpcall --test ~/testsnp -batchtype sgei

	Output you should see something like:		Output you should see something like:

Terry Gliedt: /* Test the aligner */

2013-10-14T12:39:59Z

Test the aligner

← Older revision		Revision as of 08:39, 14 October 2013
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	* replace the beginining ~/ with the actual path to where you downloaded gotcloud		* replace the beginining ~/ with the actual path to where you downloaded gotcloud
	* replace ~/testalign with the directory where you want the test results to go		* replace ~/testalign with the directory where you want the test results to go
	* To test the software in a cluster environment add the option -batchtype.		* To test the software in a cluster environment add the option -batchtype. For instance, using Sun Grid Engine in a Starcluster cluster, use
	For instance, using Sun Grid Engine in a Starcluster cluster, use
	~/gotcloud/gotcloud align --test ~/testalign -batchtype sgei		~/gotcloud/gotcloud align --test ~/testalign -batchtype sgei

Terry Gliedt: /* Test the aligner */

2013-10-14T12:39:30Z

Test the aligner

← Older revision		Revision as of 08:39, 14 October 2013
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	* replace the beginining ~/ with the actual path to where you downloaded gotcloud		* replace the beginining ~/ with the actual path to where you downloaded gotcloud
	* replace ~/testalign with the directory where you want the test results to go		* replace ~/testalign with the directory where you want the test results to go
			* To test the software in a cluster environment add the option -batchtype.
			For instance, using Sun Grid Engine in a Starcluster cluster, use
			~/gotcloud/gotcloud align --test ~/testalign -batchtype sgei

	Output you should see something like:		Output you should see something like:

Terry Gliedt: /* Building */

2013-10-14T12:35:19Z

Building

← Older revision		Revision as of 08:35, 14 October 2013
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	# cd into the gotcloud directory you just created (via clone/unzip/untar)		# cd into the gotcloud directory you just created (via clone/unzip/untar)
			# Check that your system has all of the requirements. Install whatever is needed.
			#: <pre>scripts/check_requirements.sh</pre>
	# Build (compile) the source		# Build (compile) the source
	#: <pre>cd src; make; cd ..</pre>		#: <pre>cd src; make; cd ..</pre>

Mktrost: /* Test snp calling */

2013-08-08T20:37:51Z

Test snp calling

← Older revision		Revision as of 16:37, 8 August 2013
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	=== Test snp calling ===		=== Test snp calling ===

	The snp calling test takes about 7 minutes +/- 2 minutes.		The snp calling test takes about 5 minutes +/- 2 minutes.

	To run, replace ~/testsnp with the directory where you want the test results to go:		To run, replace ~/testsnp with the directory where you want the test results to go:

Mktrost: /* Test the aligner */

2013-08-08T20:22:36Z

Test the aligner

← Older revision		Revision as of 16:22, 8 August 2013
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	=== Test the aligner ===		=== Test the aligner ===

	The aligner test takes about 3 minutes +/- 1 minute.		The aligner test takes about 3 minutes +/- 2 minute.

	To run:		To run:

Mktrost at 19:34, 8 August 2013

2013-08-08T19:34:00Z

← Older revision		Revision as of 15:34, 8 August 2013
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	If you run into any problems with GotCloud, please check: [[GotCloud: FAQs]] or for problems/solutions for a specific version, [[GotCloud:_FAQs#Version_Problems\|Version Problems]].		If you run into any problems with GotCloud, please check: [[GotCloud: FAQs]] or for problems/solutions for a specific version, [[GotCloud:_FAQs#Version_Problems\|Version Problems]].

	= Where to Find It =		= Where to Find the GotCloud Source =

	{{ToolGitRepo\|repoName=gotcloud\|nolibStatGen=true\|noDownload=true\|latestReleaseBranch=latest\|skipBuild=true}}		{{ToolGitRepo\|repoName=gotcloud\|nolibStatGen=true\|noDownload=true\|latestReleaseBranch=latest\|skipBuild=true}}

Mktrost at 19:33, 8 August 2013

2013-08-08T19:33:18Z

← Older revision		Revision as of 15:33, 8 August 2013
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	If you run into any problems with GotCloud, please check: [[GotCloud: FAQs]] or for problems/solutions for a specific version, [[GotCloud:_FAQs#Version_Problems\|Version Problems]].		If you run into any problems with GotCloud, please check: [[GotCloud: FAQs]] or for problems/solutions for a specific version, [[GotCloud:_FAQs#Version_Problems\|Version Problems]].

	~~Tar versions of gotcloud can be downloaded from github.~~		= Where to Find It =

	~~You can download either a specific release, the~~ latest ~~release, or the current development version.~~		{{ToolGitRepo\|repoName=gotcloud\|nolibStatGen=true\|noDownload=true\|latestReleaseBranch=latest\|skipBuild=true}}

	==~~=Downloading a specific release=~~==		== Releases ==
			Released Versions are documented at [[GotCloud: Versions]] with details on the changes for each version.

	~~See https://github.com/statgen/gotcloud/releases for the list of specific releases that can be downloaded.~~

	~~You can download by:~~		= Building =
	* Selecting the <code>zip</code> or <code>tar.gz</code> button near the ~~version~~.		Prior to running gotcloud, you need to compile the source.
	* Using wget to pull it directly:

	~~===Downloading the latest release===~~		# cd into the gotcloud directory you just created (via clone/unzip/untar)

	~~We track the latest release using a branch called <code>latest</code>.~~

	~~The commandline for downloading this branch is:~~


	~~=== Downloading the current development version===~~

	~~If you are using~~ the ~~current development, I'd recommend using git.~~


	~~== Previous GotCloud Versions ==~~
	~~You can access previous~~ gotcloud ~~versions using the git tags by either directly downloading the previous version or by using git to set the view to a specific tag.~~

	~~See [[GotCloud: Versions]] for details on the changes for each version.~~


	~~== Downloading & Building GotCloud ==~~

	~~Here are the steps for installing from the source tar:~~
	~~# Create & change to the~~ directory ~~where~~ you ~~want gotcloud installed~~
	~~#: <pre>cd ~ # Replace ~ with the location where you want gotcloud installed.<~~/~~pre>~~
	~~# Download the gotcloud tar from the ftp site.~~
	~~#: <pre>wget ftp:~~/~~/share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz</pre>~~
	~~# Extract the tar (In this example, it is the tar with the test files~~)
	~~#: <pre>tar xzf gotcloud_latest.tgz</pre>~~
	~~#* This will create a gotcloud directory containing the contents of the tar.~~
	# Build (compile) the source		# Build (compile) the source
	#: <pre>cd ~~gotcloud/~~src; make; cd ..</pre>		#: <pre>cd src; make; cd ..</pre>
	#* Note: as the source builds, many messages will scroll through your terminal. You may even see some warnings. These messages are normal and expected. As long as the build does not end with an error, you have successfully built the source.		#* Note: as the source builds, many messages will scroll through your terminal. You may even see some warnings. These messages are normal and expected. As long as the build does not end with an error, you have successfully built the source.

			= GotCloud Script =
	GotCloud ~~requires~~ the ~~following tools to be installed.~~		The gotcloud script that is the gateway to running GotCloud is found in the directory you created via clone/unzip/untar and is called gotcloud.
	* java (java-common default-jre on ubuntu)
	* make (make on ubuntu)
	* libssl (libssl0.9.8 on ubuntu)
	* gcc 4.~~4 or newer~~

	~~To check these requirements~~, ~~run~~:		If you cloned into your home directory, it would be:
	~~scripts~~/~~check_requirements.sh .~~		~/gotcloud/gotcloud
			If you downloaded "latest" into your home directory, it would be:
			~/gotcloud-latest/gotcloud


	~~The gotcloud script that is the gateway to running GotCloud is found in the path where you untarred the program under the gotcloud directory and is called gotcloud:~~
	~~gotcloud/gotcloud~~
	~~If you downloaded and untarred into your home directory, it would be:~~
	~~~/gotcloud/gotcloud~~

	== Testing GotCloud ==		== Testing GotCloud ==
	~~If you installed the test files, you~~ can run an automated test that will tell you if it passes or fails.		You can run an automated test that will tell you if it passes or fails.

	This test will ensure that everything is setup/installed properly and ~~produces~~ the expected results.		This test will ensure that everything is setup/installed properly and the expected results are produced.

	=== Test the aligner ===		=== Test the aligner ===
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	Successfully ran the test case, congratulations!		Successfully ran the test case, congratulations!

	You can ~~then~~ remove the output directory if there were no errors.		You can remove the output directory if there were no errors.
	rm -rf ~/testalign		rm -rf ~/testalign

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	Successfully ran the test case, congratulations!		Successfully ran the test case, congratulations!

	You can ~~then~~ remove the output directory if there were no errors.		You can remove the output directory if there were no errors.
	rm -rf ~/testsnp		rm -rf ~/testsnp

Mktrost at 17:27, 8 August 2013

2013-08-08T17:27:40Z

← Older revision		Revision as of 13:27, 8 August 2013
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	If you run into any problems with GotCloud, please check: [[GotCloud: FAQs]] or for problems/solutions for a specific version, [[GotCloud:_FAQs#Version_Problems\|Version Problems]].		If you run into any problems with GotCloud, please check: [[GotCloud: FAQs]] or for problems/solutions for a specific version, [[GotCloud:_FAQs#Version_Problems\|Version Problems]].

			Tar versions of gotcloud can be downloaded from github.

	~~There are 3 tar files that~~ can ~~be downloaded:~~		You can download either a specific release, the latest release, or the current development version.
	~~# both~~ the ~~gotcloud programs/source and~~ the ~~test files~~
	~~#:ftp://share~~.~~sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz~~
	~~# just the gotcloud programs/source~~
	~~#:ftp://share.sph.umich.edu/gotcloud/gotcloud_latest.tgz~~
	~~# just the gotcloud test files~~
	~~#:ftp://share.sph.umich.edu/gotcloud/gotcloudTest_latest.tgz~~

	~~Previous versions are also available (where M.n is the desired version number):~~		===Downloading a specific release===
	~~# both the gotcloud programs/source and the test files~~
	~~#:ftp~~://~~share~~.~~sph.umich.edu~~/gotcloud/~~M.n/gotcloudWithTest_M~~.~~n.tgz~~		See https://github.com/statgen/gotcloud/releases for the list of specific releases that can be downloaded.
	~~# just the gotcloud programs/source~~
	#:~~ftp:/~~/~~share.sph.umich~~.~~edu~~/~~gotcloud/M~~.n/~~gotcloud_M~~.~~n.tgz~~		You can download by:
	~~# just~~ the ~~gotcloud test files~~		* Selecting the <code>zip</code> or <code>tar.gz</code> button near the version.
	~~#:ftp://share~~.~~sph.umich.edu/~~gotcloud~~/M.n/gotcloudTest_M.n~~.~~tgz~~		* Using wget to pull it directly:

			===Downloading the latest release===

			We track the latest release using a branch called <code>latest</code>.

			The commandline for downloading this branch is:


			=== Downloading the current development version===

			If you are using the current development, I'd recommend using git.


			== Previous GotCloud Versions ==
			You can access previous gotcloud versions using the git tags by either directly downloading the previous version or by using git to set the view to a specific tag.

	See [[GotCloud: Versions]] for details on the changes for each version.		See [[GotCloud: Versions]] for details on the changes for each version.