PatternQuery:Command Line - Revision history

Lukas: /* Running the Offline Service */

2015-04-30T23:26:23Z

Running the Offline Service

← Older revision		Revision as of 23:26, 30 April 2015
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	<pre>mono WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>		<pre>mono WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>

	Both of the commands immediately executes a calculation, which produces all the output into the <code>workingFolder</code>. A description ~~of the results hierarchy~~ can be found when running the program with the <code>--help</code> option. e.g.		Both of the commands immediately executes a calculation, which produces all the output into the <code>workingFolder</code>. A further description can be found when running the program with the <code>--help</code> option. e.g.

	<pre>WebChemistry.Queries.Service.exe --help</pre> or <pre>mono WebChemistry.Queries.Service.exe --help</pre>		<pre>WebChemistry.Queries.Service.exe --help</pre> or <pre>mono WebChemistry.Queries.Service.exe --help</pre>

Lukas: /* Running the Offline Service */

2015-04-30T23:24:28Z

Running the Offline Service

← Older revision		Revision as of 23:24, 30 April 2015
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	<pre>mono WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>		<pre>mono WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>

			Both of the commands immediately executes a calculation, which produces all the output into the <code>workingFolder</code>. A description of the results hierarchy can be found when running the program with the <code>--help</code> option. e.g.

			<pre>WebChemistry.Queries.Service.exe --help</pre> or <pre>mono WebChemistry.Queries.Service.exe --help</pre>

	== Configuration ==		== Configuration ==

Lukas: /* Running the Offline Service */

2015-04-29T13:18:02Z

Running the Offline Service

← Older revision		Revision as of 13:18, 29 April 2015
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	= Running the Offline Service =		= Running the Offline Service =
	-----------------------		-----------------------
	Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. A simple [http://webchem.ncbr.muni.cz/~~Wiki~~/~~File:PQ_examples.zip~~ demo] is available as well. The service can be executed using the command (latest .NET Framework required):		Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. A simple [http://webchem.ncbr.muni.cz/Platform/PatternQuery/CmdExample demo] is available as well. The service can be executed using the command (latest .NET Framework required):
	<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>		<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>
	In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:		In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:

Lukas: /* Running the Offline Service */

2015-04-29T09:08:45Z

Running the Offline Service

← Older revision		Revision as of 09:08, 29 April 2015
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	= Running the Offline Service =		= Running the Offline Service =
	-----------------------		-----------------------
	Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. ~~You can download a~~ simple [[http://webchem.ncbr.muni.cz/Wiki/File:PQ_examples.zip demo]] as well. The service can be executed using the command (latest .NET Framework required):		Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. A simple [http://webchem.ncbr.muni.cz/Wiki/File:PQ_examples.zip demo] is available as well. The service can be executed using the command (latest .NET Framework required):
	<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>		<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>
	In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:		In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:

Lukas: /* Running the Offline Service */

2015-04-29T09:08:14Z

Running the Offline Service

← Older revision		Revision as of 09:08, 29 April 2015
Line 18:		Line 18:
	= Running the Offline Service =		= Running the Offline Service =
	-----------------------		-----------------------
	Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. The service can be executed using the command (latest .NET Framework required):		Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. You can download a simple [[http://webchem.ncbr.muni.cz/Wiki/File:PQ_examples.zip demo]] as well. The service can be executed using the command (latest .NET Framework required):
	<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>		<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>
	In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:		In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:

Lukas: Lukas moved page MotiveQuery:Command Line to PatternQuery:Command Line

2015-04-25T13:26:39Z

Lukas moved page MotiveQuery:Command Line to PatternQuery:Command Line

← Older revision	Revision as of 13:26, 25 April 2015
(No difference)

Dave: /* MotiveQuery Specific Structure */

2015-04-23T20:34:37Z

MotiveQuery Specific Structure

← Older revision		Revision as of 20:34, 23 April 2015
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	:::: '''patterns.csv''' - ''Information about the patterns in CSV format.''		:::: '''patterns.csv''' - ''Information about the patterns in CSV format.''
	:::: '''metadata_summary.csv''' - ''Information about the metadata (origin organism, EC number, etc.) in CSV format.''		:::: '''metadata_summary.csv''' - ''Information about the metadata (origin organism, EC number, etc.) in CSV format.''
	:::: '''structures.csv''' - ''Information about structures that contain the given ~~fragments~~ in CSV format.''		:::: '''structures.csv''' - ''Information about structures that contain the given patterns in CSV format.''
	:: '''structures.csv''' - ''Information about all structures that were queried in CSV format.''		:: '''structures.csv''' - ''Information about all structures that were queried in CSV format.''
	:: '''structures.json''' - ''Information about all structures that were queried in JSON format.''		:: '''structures.json''' - ''Information about all structures that were queried in JSON format.''
	:: '''summary.json''' - ''Summary information (number of found patterns, etc.) about the computation in JSON format.''		:: '''summary.json''' - ''Summary information (number of found patterns, etc.) about the computation in JSON format.''

Dave: /* What you need in order to run MotiveQuery */

2015-04-23T20:34:10Z

What you need in order to run MotiveQuery

← Older revision		Revision as of 20:34, 23 April 2015
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	'''PatternQuery''' is freely available online since May 2014 at http://ncbr.muni.cz/PatternQuery. There is no login requirement for accessing '''PatternQuery'''.		'''PatternQuery''' is freely available online since May 2014 at http://ncbr.muni.cz/PatternQuery. There is no login requirement for accessing '''PatternQuery'''.

	===What you need in order to run ~~MotiveQuery~~===		===What you need in order to run PatternQuery===
	* Up to date internet browser with WebGL support.		* Up to date internet browser with WebGL support.
	* JavaScript enabled.		* JavaScript enabled.

Dave: /* Where to find MotiveQuery */

2015-04-23T20:33:58Z

Where to find MotiveQuery

← Older revision		Revision as of 20:33, 23 April 2015
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	=Technical details=		=Technical details=
	===Where to find ~~MotiveQuery~~===		===Where to find PatternQuery===
	'''PatternQuery''' is freely available online since May 2014 at http://ncbr.muni.cz/PatternQuery. There is no login requirement for accessing '''PatternQuery'''.		'''PatternQuery''' is freely available online since May 2014 at http://ncbr.muni.cz/PatternQuery. There is no login requirement for accessing '''PatternQuery'''.

Dave at 20:33, 23 April 2015

2015-04-23T20:33:41Z

← Older revision		Revision as of 20:33, 23 April 2015
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	This is help for version 1.0.14.11.28 or newer. The help text for other versions can be viewed using the ''--help'' command when running the application.		This is help for version 1.0.15.4.22 or newer. The help text for other versions can be viewed using the ''--help'' command when running the application.

	=Technical details=		=Technical details=
	===Where to find MotiveQuery===		===Where to find MotiveQuery===
	'''~~MotiveQuery~~''' is freely available online since May 2014 at http://ncbr.muni.cz/~~MotiveQuery~~. There is no login requirement for accessing '''~~MotiveQuery~~'''.		'''PatternQuery''' is freely available online since May 2014 at http://ncbr.muni.cz/PatternQuery. There is no login requirement for accessing '''PatternQuery'''.

	===What you need in order to run MotiveQuery===		===What you need in order to run MotiveQuery===
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	Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.		Check if your browser is [http://get.webgl.org WebGL] and [http://www.enable-javascript.com/ Javascript] compliant.

	Note that you can run '''~~MotiveQuery~~''' and download the results even if your browser doesn't support WebGL.		Note that you can run '''PatternQuery''' and download the results even if your browser doesn't support WebGL.
	WebGL is only necessary for the 3D visualization functionality.		WebGL is only necessary for the 3D visualization functionality.

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	= Running the Offline Service =		= Running the Offline Service =
	-----------------------		-----------------------
	Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/~~MotiveQuery~~/DownloadService ~~MotiveQuery~~ application]. The service can be executed using the command (latest .NET Framework required):		Just download the latest release of [http://webchem.ncbr.muni.cz/Platform/PatternQuery/DownloadService PatternQuery application]. The service can be executed using the command (latest .NET Framework required):
	<pre>WebChemistry.~~MotiveQuery~~.Service.exe workingFolder configuration.json</pre>		<pre>WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>
	In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:		In Linux (where available) and MacOS, the latest version the Mono Framework (http://mono-project.com/) must be used to run the application:
	<pre>mono WebChemistry.~~MotiveQuery~~.Service.exe workingFolder configuration.json</pre>		<pre>mono WebChemistry.Queries.Service.exe workingFolder configuration.json</pre>


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	* '''result''' - ''Folder with computation result''		* '''result''' - ''Folder with computation result''
	:* '''query_id''' - ''Folder for each query named by its unique id.''		:* '''query_id''' - ''Folder for each query named by its unique id.''
	::* '''~~fragments~~''' - ''Folder with ~~fragments~~ stored in PDB format.''		::* '''patterns''' - ''Folder with patterns stored in PDB format.''
	:::: '''data.json''' - ''Information about the result in JSON format.''		:::: '''data.json''' - ''Information about the result in JSON format.''
	:::: '''~~fragments~~.csv''' - ''Information about the ~~fragments~~ in CSV format.''		:::: '''patterns.csv''' - ''Information about the patterns in CSV format.''
	:::: '''metadata_summary.csv''' - ''Information about the metadata (origin organism, EC number, etc.) in CSV format.''		:::: '''metadata_summary.csv''' - ''Information about the metadata (origin organism, EC number, etc.) in CSV format.''
	:::: '''structures.csv''' - ''Information about structures that contain the given fragments in CSV format.''		:::: '''structures.csv''' - ''Information about structures that contain the given fragments in CSV format.''
	:: '''structures.csv''' - ''Information about all structures that were queried in CSV format.''		:: '''structures.csv''' - ''Information about all structures that were queried in CSV format.''
	:: '''structures.json''' - ''Information about all structures that were queried in JSON format.''		:: '''structures.json''' - ''Information about all structures that were queried in JSON format.''
	:: '''summary.json''' - ''Summary information (number of found ~~fragments~~, etc.) about the computation in JSON format.''		:: '''summary.json''' - ''Summary information (number of found patterns, etc.) about the computation in JSON format.''