Getting Started - Revision history

David: /* Windows */

2016-05-19T00:23:34Z

Windows

← Older revision		Revision as of 00:23, 19 May 2016
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	* TODO		* TODO
	==Windows==		==Windows==
			Do all of the following in cmd (that is what is meant by terminal)
	===Install Reach-Examples===		===Install Reach-Examples===
	* download the JDK for Java 8 (or choose the latest Java version) from [http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html the java website]		* download the JDK for Java 8 (or choose the latest Java version) from [http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html the java website]

David: /* Install BIDS dependencies */

2016-05-19T00:01:04Z

Install BIDS dependencies

← Older revision		Revision as of 00:01, 19 May 2016
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	* in a new terminal, install virtual env from pip:		* in a new terminal, install virtual env from pip:
	> pip install virtualenvwrapper-win		> pip install virtualenvwrapper-win
	* make a bids environment		* make a bids environment. If you do not use Python 2.7.x as your python interpreter (calling <source lang=winbatch>python --version</source> on the command line will tell you), you'll need to do
			> mkvirtualenv --python=C:\Python27\python.exe bids
			possibly substituting a different path to the python.exe for Python2.7.x if it's not in the default location. If you do use python 2.7.x, you can just do
	> mkvirtualenv bids		> mkvirtualenv bids
	** you should now see (bids) in your command prompt		** you should now see (bids) in your command prompt

David: /* Install BIDS dependencies */

2016-05-18T23:46:10Z

Install BIDS dependencies

← Older revision		Revision as of 23:46, 18 May 2016
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	* in a new terminal, install virtual env from pip:		* in a new terminal, install virtual env from pip:
	> pip install virtualenvwrapper-win		> pip install virtualenvwrapper-win
	* make a bids environment ~~(replace PATH_TO_CONDA_PYTHON_EXE with the path for your system)~~		* make a bids environment
	~~> mkvirtualenv bids~~
	** for example, I put
	> mkvirtualenv bids		> mkvirtualenv bids
	** you should now see (bids) in your command prompt		** you should now see (bids) in your command prompt

David: /* Install BIDS dependencies */ removed miniconda vestiges

2016-05-18T23:44:31Z

Install BIDS dependencies: removed miniconda vestiges

← Older revision		Revision as of 23:44, 18 May 2016
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	> pip install virtualenvwrapper-win		> pip install virtualenvwrapper-win
	* make a bids environment (replace PATH_TO_CONDA_PYTHON_EXE with the path for your system)		* make a bids environment (replace PATH_TO_CONDA_PYTHON_EXE with the path for your system)
	> mkvirtualenv ~~--python=PATH_TO_CONDA_PYTHON_EXE~~ bids		> mkvirtualenv bids
	** for example, I put		** for example, I put
	> mkvirtualenv ~~--python=c:\Miniconda2\python.exe~~ bids		> mkvirtualenv bids
	** you should now see (bids) in your command prompt		** you should now see (bids) in your command prompt
	* install the Visual C++ compiler for Python 2.7 (try not to cry)		* install the Visual C++ compiler for Python 2.7 (try not to cry)

David: /* Install Reach-Examples */ fixed quotation marks in setting JAVA_OPTS

2016-05-18T23:36:39Z

Install Reach-Examples: fixed quotation marks in setting JAVA_OPTS

← Older revision		Revision as of 23:36, 18 May 2016
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	* install the JDK with default options		* install the JDK with default options
	* set JAVA_OPTS		* set JAVA_OPTS
	> set JAVA_OPTS "-server -Xms3g -Xmx6g"		> set JAVA_OPTS=-server -Xms3g -Xmx6g
	* download SBT from [https://www.scala-sbt.org/download.html the scala website]		* download SBT from [https://www.scala-sbt.org/download.html the scala website]
	* run the installer with default options		* run the installer with default options

David: /* Install Reach-Examples */

2016-05-18T23:13:48Z

Install Reach-Examples

← Older revision		Revision as of 23:13, 18 May 2016
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	> cd Src		> cd Src
	> mkdir BIDS		> mkdir BIDS
			> cd BIDS

	* clone the reach-examples repository		* clone the reach-examples repository

David: /* Install Reach-Examples */

2016-05-18T22:59:11Z

Install Reach-Examples

← Older revision		Revision as of 22:59, 18 May 2016
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	* install the JDK with default options		* install the JDK with default options
	* set JAVA_OPTS		* set JAVA_OPTS
	> ~~setx~~ JAVA_OPTS "-server -Xms3g -Xmx6g"		> set JAVA_OPTS "-server -Xms3g -Xmx6g"
	* download SBT from [https://www.scala-sbt.org/download.html the scala website]		* download SBT from [https://www.scala-sbt.org/download.html the scala website]
	* run the installer with default options		* run the installer with default options

David: /* Install Reach-Examples */ fixed so that setx is used

2016-05-18T22:23:46Z

Install Reach-Examples: fixed so that setx is used

← Older revision		Revision as of 22:23, 18 May 2016
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	</source>		</source>
	** now highlight the path to the left of the ">" (not including the ">") and do <ctrl><c> to copy it		** now highlight the path to the left of the ">" (not including the ">") and do <ctrl><c> to copy it
	** ~~Click Start, then Settings. Type "environment" into the search box in the corner of the settings window~~		** right click the cmd icon on the task bar, and click "run as administrator"
	*** Click "edit the ~~system environment variables"~~		*** set the path <source lang=winbatch>
	*** Click the ~~"Environment Variables..." button~~		> setx path "%path%;<ctrl><v> /M"
	*** Select "Path" from the "System variables" box, and click "~~Edit...~~"		</source> where <ctrl><v> is you pressing those keys to paste in the path you just copied.
	*** ~~Click at~~ the ~~end of the Variable value field to edit the text.~~
	*** Add a semicolon ";"~~, then right click and select~~ paste.
	*** Click OK in ~~all windows, close~~ the ~~settings window, and close all open terminals~~
	* In a new terminal, change to the reach-examples directory. For my case, this is		* In a new terminal, change to the reach-examples directory. For my case, this is

David: /* Install Reach-Examples */

2016-05-18T20:02:23Z

Install Reach-Examples

← Older revision		Revision as of 20:02, 18 May 2016
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	> cd reach-examples		> cd reach-examples
	* edit your PATH variable. (NOTE: this may be replaced with setx at the command line in the future. I need to look into it. -David)		* edit your PATH variable. (NOTE: this may be replaced with setx at the command line in the future. I need to look into it. -David)
	** In a terminal, do (you may need to replace jdk1.8.0_91 with something similar but different)		** In a terminal, do (you may need to replace jdk1.8.0_91 with something similar but different) <source lang=winbatch>
	> cd c:\Program Files\Java\jdk1.8.0_91\bin		> cd c:\Program Files\Java\jdk1.8.0_91\bin
			</source>
	** now highlight the path to the left of the ">" (not including the ">") and do <ctrl><c> to copy it		** now highlight the path to the left of the ">" (not including the ">") and do <ctrl><c> to copy it
	** Click Start, then Settings. Type "environment" into the search box in the corner of the settings window		** Click Start, then Settings. Type "environment" into the search box in the corner of the settings window

David: /* Add BIDS paths to PYTHONPATH */

2016-05-18T20:00:31Z

Add BIDS paths to PYTHONPATH

← Older revision		Revision as of 20:00, 18 May 2016
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	* we need to add the path to bioCausalRelationLearner to your path (similar to what we did before to add javac to the path)		* we need to add the path to bioCausalRelationLearner to your path (similar to what we did before to add javac to the path)
	** first get the path to the bioCausalRelationLearner		** first get the path to the bioCausalRelationLearner
	*** in a new terminal, go to the directory containing the file bioCausalRelationLearner.py. This file is in the directory for BIDS that you cloned earlier. For me it is in		*** in a new terminal, go to the directory containing the file bioCausalRelationLearner.py. This file is in the directory for BIDS that you cloned earlier. For me it is in <source lang=winbatch> > cd Src\BIDS\bigmech\bioIncrementalDistantSupervision </source>
	> cd Src\BIDS\bigmech\bioIncrementalDistantSupervision
	*** highlight the path to the left of the ">" (not including the ">"), and copy with <ctrl><c>		*** highlight the path to the left of the ">" (not including the ">"), and copy with <ctrl><c>
	*** close the terminal		*** close the terminal