VAT/download - Revision history

Lukas.habegger: /* Setup of the web server */

2011-06-15T15:33:30Z

Setup of the web server

← Older revision		Revision as of 15:33, 15 June 2011
Line 179:		Line 179:
	SetEnv VAT_CONFIG_FILE /path/to/vatConfirgurationTemplate.txt		SetEnv VAT_CONFIG_FILE /path/to/vatConfirgurationTemplate.txt
	* The web data directory (defined by WEB_DATA_DIR in the configuration file) requires the following information:		* The web data directory (defined by WEB_DATA_DIR in the configuration file) requires the following information:
	** '''~~Preprocessed~~ annotation sets'''		** '''Pre-processed annotation sets'''
	** The '''tabix''' and '''bgzip''' executables		** The '''tabix''' and '''bgzip''' executables
	** Two images provided by the VAT source code: '''check.png''' and '''processing.gif''' (referred to by vat_cgi)		** Two images provided by the VAT source code: '''check.png''' and '''processing.gif''' (referred to by vat_cgi)

Lukas.habegger: /* Setup of the web server */

2011-06-15T15:33:09Z

Setup of the web server

← Older revision		Revision as of 15:33, 15 June 2011
Line 188:		Line 188:
	*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])		*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
	*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])		*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
	** The construction of the vat_cgi URL requires following item/value pairs (for example: http://dynamic.gersteinlab.org/people/lh372/vat_cgi?~~'''~~mode=process~~'''~~&~~'''~~dataSet=ALL.2of4intersection.20100804.chr22~~'''~~&~~'''~~annotationSet=gencode3c~~'''~~&~~'''~~type=coding~~'''~~):		** The construction of the vat_cgi URL requires following item/value pairs (for example: http://dynamic.gersteinlab.org/people/lh372/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c&type=coding):
	*** mode=process		*** mode=process
	*** dataSet=SampleData		*** dataSet=SampleData

Lukas.habegger: /* Setup of the web server */

2011-06-15T15:32:27Z

Setup of the web server

← Older revision		Revision as of 15:32, 15 June 2011
Line 188:		Line 188:
	*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])		*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
	*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])		*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
	** The construction of the vat_cgi URL requires following item/value pairs:		** The construction of the vat_cgi URL requires following item/value pairs (for example: http://dynamic.gersteinlab.org/people/lh372/vat_cgi?'''mode=process'''&'''dataSet=ALL.2of4intersection.20100804.chr22'''&'''annotationSet=gencode3c'''&'''type=coding'''):
	*** mode=process		*** mode=process
	*** dataSet=SampleData		*** dataSet=SampleData
	*** annotationSet=nameOfAnnotationSet		*** annotationSet=nameOfAnnotationSet
	*** type=coding or nonCoding		*** type=coding or nonCoding
	~~http://dynamic.gersteinlab.org/people/lh372/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c&type=coding~~

	For additional information please refer to the [http://info.gersteinlab.org/VAT#Setting_up_the_web_server example workflow].		For additional information please refer to the [http://info.gersteinlab.org/VAT#Setting_up_the_web_server example workflow].

Lukas.habegger: /* Setup of the web server */

2011-06-15T15:30:54Z

Setup of the web server

← Older revision		Revision as of 15:30, 15 June 2011
Line 188:		Line 188:
	*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])		*** SampleData.sampleSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
	*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])		*** SampleData.geneSummary.txt (generated by [http://info.gersteinlab.org/VAT#vcfSummary vcfSummary])
			** The construction of the vat_cgi URL requires following item/value pairs:
			*** mode=process
			*** dataSet=SampleData
			*** annotationSet=nameOfAnnotationSet
			*** type=coding or nonCoding
			http://dynamic.gersteinlab.org/people/lh372/vat_cgi?mode=process&dataSet=ALL.2of4intersection.20100804.chr22&annotationSet=gencode3c&type=coding

	For additional information please refer to the [http://info.gersteinlab.org/VAT#Setting_up_the_web_server example workflow].		For additional information please refer to the [http://info.gersteinlab.org/VAT#Setting_up_the_web_server example workflow].

Lukas.habegger: /* Setup of the web server */

2011-06-15T15:24:20Z

Setup of the web server

← Older revision		Revision as of 15:24, 15 June 2011
Line 179:		Line 179:
	SetEnv VAT_CONFIG_FILE /path/to/vatConfirgurationTemplate.txt		SetEnv VAT_CONFIG_FILE /path/to/vatConfirgurationTemplate.txt
	* The web data directory (defined by WEB_DATA_DIR in the configuration file) requires the following information:		* The web data directory (defined by WEB_DATA_DIR in the configuration file) requires the following information:
	** '''Preprocessed annotation sets''' ~~(gencode3b.interval, gencode3b.fa, gencode3c.interval, gencode3c.fa)~~		** '''Preprocessed annotation sets'''
	** The '''tabix''' and '''bgzip''' executables		** The '''tabix''' and '''bgzip''' executables
	** Two images provided by the VAT source code: '''check.png''' and '''processing.gif''' (referred to by vat_cgi)		** Two images provided by the VAT source code: '''check.png''' and '''processing.gif''' (referred to by vat_cgi)

Lukas.habegger: /* Executables */

2011-06-14T18:23:19Z

Executables

← Older revision		Revision as of 18:23, 14 June 2011
Line 55:		Line 55:

	Statically built binaries for UNIX can be found here:		Statically built binaries for UNIX can be found here:
	* [http://homes.gersteinlab.org/people/lh372/VAT/vat-1.0.0_32bit.zip vat-1.0.0_32bit.zip] - Initial upload (6/14/2011)
	* [http://homes.gersteinlab.org/people/lh372/VAT/vat-1.0.0_64bit.zip vat-1.0.0_64bit.zip] - Initial upload (6/14/2011)		* [http://homes.gersteinlab.org/people/lh372/VAT/vat-1.0.0_64bit.zip vat-1.0.0_64bit.zip] - Initial upload (6/14/2011)

Lukas.habegger at 18:20, 14 June 2011

2011-06-14T18:20:15Z

← Older revision		Revision as of 18:20, 14 June 2011
Line 55:		Line 55:

	Statically built binaries for UNIX can be found here:		Statically built binaries for UNIX can be found here:
	* [http://~~archive~~.gersteinlab.org/~~proj~~/VAT/~~src~~ VAT-0.5-~~UNIX~~.~~tar~~.gz] - ~~64bit version~~		* [http://homes.gersteinlab.org/people/lh372/VAT/vat-1.0.0_32bit.zip vat-1.0.0_32bit.zip] - Initial upload (6/14/2011)
			* [http://homes.gersteinlab.org/people/lh372/VAT/vat-1.0.0_64bit.zip vat-1.0.0_64bit.zip] - Initial upload (6/14/2011)

	<br>		<br>

Lukas.habegger: /* Source code */

2011-06-14T18:18:20Z

Source code

← Older revision		Revision as of 18:18, 14 June 2011
Line 45:		Line 45:

	VAT is a based on a general C library, called libBIOS. A TAR ball of libBIOS and VAT can be downloaded here:		VAT is a based on a general C library, called libBIOS. A TAR ball of libBIOS and VAT can be downloaded here:
	* [http://~~archive~~.gersteinlab.org/~~proj~~/VAT/~~src libBIOS~~-1.1.0.tar.gz]		* [http://homes.gersteinlab.org/people/lh372/VAT/libbios-1.0.0.tar.gz libbios-1.0.0.tar.gz] - Initial upload (6/14/2011)
	* [http://~~archive~~.gersteinlab.org/~~proj~~/VAT/~~src VAT~~-0.5.tar.gz] - Initial upload		* [http://homes.gersteinlab.org/people/lh372/VAT/vat-1.0.0.tar.gz vat-1.0.0.tar.gz] - Initial upload (6/14/2011)

	<br>		<br>

Lukas.habegger at 17:45, 14 June 2011

2011-06-14T17:45:17Z

← Older revision		Revision as of 17:45, 14 June 2011
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	Download VARNA jar file and add the jar file path to CLASSPATH environment variable.		Download VARNA jar file and add the jar file path to CLASSPATH environment variable.

			<br>

	<center>[[#top\|Top]]</center>		<center>[[#top\|Top]]</center>

Lukas.habegger at 17:24, 14 June 2011

2011-06-14T17:24:53Z

← Older revision		Revision as of 17:24, 14 June 2011
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	<br>		<br>

			<center>[[#top\|Top]]</center>

	=== Installation of RNAstructure and VARNA ===		=== Installation of RNAstructure and VARNA ===
	Download RNAstructure and follow the building instructions. Make sure that the build directory is included in PATH enrivonment variable. In addition, RNAstructure needs an environment variable named DATAPATH to be set to the directory of thermodynamic parameter files that are distributed with RNAstructure package.

	Download VARNA jar file and add the jar file path to CLASSPATH ~~enrivonment~~ variable.		Download RNAstructure and follow the building instructions. Make sure that the build directory is included in PATH environment variable. In addition, RNAstructure needs an environment variable named DATAPATH to be set to the directory of thermodynamic parameter files that are distributed with RNAstructure package.

			Download VARNA jar file and add the jar file path to CLASSPATH environment variable.

	<center>[[#top\|Top]]</center>		<center>[[#top\|Top]]</center>