Customize shell - Revision history

Frodo at 00:24, 23 October 2012

2012-10-23T00:24:34Z

← Older revision		Revision as of 00:24, 23 October 2012
Line 30:		Line 30:
	Warnings:		Warnings:
	* 1) We do not recommend that you make personal copies of env.csh and vars.csh. Using the system standards means that you are more likely to stay in sync with standard lab practice.		* 1) We do not recommend that you make personal copies of env.csh and vars.csh. Using the system standards means that you are more likely to stay in sync with standard lab practice.
	* 2) If you want to use software that is not available in the lab (or a more recent version of something we do have), please advise your [[~~Sysadmins~~]]. If more than one person uses the software, it probably makes sense to install it somewhere central. Doing so proactively retards the progress towards chaos, and probably saves you and your colleagues time, even in the short term.		* 2) If you want to use software that is not available in the lab (or a more recent version of something we do have), please advise your [[Sysadmin]]. If more than one person uses the software, it probably makes sense to install it somewhere central. Doing so proactively retards the progress towards chaos, and probably saves you and your colleagues time, even in the short term.


	[[Category:Internal]]		[[Category:Internal]]

Frodo at 00:23, 23 October 2012

2012-10-23T00:23:35Z

← Older revision		Revision as of 00:23, 23 October 2012
Line 20:		Line 20:

	Notes:		Notes:
	1) If you have your own dockenv, or you want to use one other than the lab default, you must set up DOCK_BASE before sourcing vars.csh		* 1) If you have your own dockenv, or you want to use one other than the lab default, you must set up DOCK_BASE before sourcing vars.csh
	2) If you have all you software (Schrodinger, Openeye, etc) installed elsewhere, you need to set SOFT before sourcing vars.csh. Generally, you don't want this.		* 2) If you have all you software (Schrodinger, Openeye, etc) installed elsewhere, you need to set SOFT before sourcing vars.csh. Generally, you don't want this.
	3) You can override individual choices of software packages between vars.csh and env.csh by setting ENV_* variables. To see what these are, do		* 3) You can override individual choices of software packages between vars.csh and env.csh by setting ENV_* variables. To see what these are, do
	printenv \| grep ENV_		printenv \| grep ENV_
	4) Thus say you want to use the 2012-10 version of Schrodinger instead of the default current version. You would add the following line after source vars.csh:		* 4) Thus say you want to use the 2012-10 version of Schrodinger instead of the default current version. You would add the following line after source vars.csh:
	setenv ENV_SCHRODINGER $SOFT/schrodinger/2012-10/env.csh		setenv ENV_SCHRODINGER $SOFT/schrodinger/2012-10/env.csh
	Then, in env.csh, the file pointed to by ENV_SCHRODINGER will be sourced to set up the correct enviroment. Note that ENV_SCHRODINGER can point anywhere, including to places in your own home directory.		Then, in env.csh, the file pointed to by ENV_SCHRODINGER will be sourced to set up the correct enviroment. Note that ENV_SCHRODINGER can point anywhere, including to places in your own home directory.

	Warnings:		Warnings:
	1) We do not recommend that you make personal copies of env.csh and vars.csh. Using the system standards means that you are more likely to stay in sync with standard lab practice.		* 1) We do not recommend that you make personal copies of env.csh and vars.csh. Using the system standards means that you are more likely to stay in sync with standard lab practice.
	2) If you want to use software that is not available in the lab (or a more recent version of something we do have), please advise your [[Sysadmins]]. If more than one person uses the software, it probably makes sense to install it somewhere central. Doing so proactively retards the progress towards chaos, and probably saves you and your colleagues time, even in the short term.		* 2) If you want to use software that is not available in the lab (or a more recent version of something we do have), please advise your [[Sysadmins]]. If more than one person uses the software, it probably makes sense to install it somewhere central. Doing so proactively retards the progress towards chaos, and probably saves you and your colleagues time, even in the short term.


	[[:Category:Internal]]		[[Category:Internal]]

Frodo at 00:23, 23 October 2012

2012-10-23T00:23:01Z

← Older revision		Revision as of 00:23, 23 October 2012
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	How to customize .cshrc		How to customize .cshrc. There are four parts:

	There are four parts:
	* 1) Define a custom DOCK_BASE if you are not using the lab default		* 1) Define a custom DOCK_BASE if you are not using the lab default
	* 2) Set up standard shell variables (vars.csh), the "nouns" of what you will use.		* 2) Set up standard shell variables (vars.csh), the "nouns" of what you will use.

Frodo at 00:22, 23 October 2012

2012-10-23T00:22:46Z

← Older revision		Revision as of 00:22, 23 October 2012
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	* 4) Define the environment (env.csh), the "verbs" that enable the software.		* 4) Define the environment (env.csh), the "verbs" that enable the software.

	First let's look at the standard file:		First let's look at the standard file, which you can get from /raid3/software/labenv/defaults.cshrc:
	# .cshrc		# .cshrc
	#setenv DOCK_BASE /raid1/people/jji/dockenv		#setenv DOCK_BASE /raid1/people/jji/dockenv

Frodo at 00:21, 23 October 2012

2012-10-23T00:21:42Z

← Older revision		Revision as of 00:21, 23 October 2012
Line 2:		Line 2:

	There are four parts:		There are four parts:
	1) Define a custom DOCK_BASE if you are not using the lab default		* 1) Define a custom DOCK_BASE if you are not using the lab default
	2) Set up standard shell variables (vars.csh), the "nouns" of what you will use.		* 2) Set up standard shell variables (vars.csh), the "nouns" of what you will use.
	3) Define personal customization of and exceptions to the standard environment.		* 3) Define personal customization of and exceptions to the standard environment.
	4) Define the environment (env.csh), the "verbs" that enable the software.		* 4) Define the environment (env.csh), the "verbs" that enable the software.

	First let's look at the standard file:		First let's look at the standard file:

Frodo at 21:40, 18 October 2012

2012-10-18T21:40:58Z

← Older revision		Revision as of 21:40, 18 October 2012
Line 2:		Line 2:

	There are four parts:		There are four parts:
	1) ~~set up~~ a custom DOCK_BASE~~, SOFT~~ if ~~required~~		1) Define a custom DOCK_BASE if you are not using the lab default
	2) ~~set~~ up standard shell variables (vars.csh)		2) Set up standard shell variables (vars.csh), the "nouns" of what you will use.
	3) ~~custom paths,~~ environment		3) Define personal customization of and exceptions to the standard environment.
	4) ~~define~~ environment (env.csh)		4) Define the environment (env.csh), the "verbs" that enable the software.

	First let's look at the standard file:		First let's look at the standard file:
Line 29:		Line 29:
	setenv ENV_SCHRODINGER $SOFT/schrodinger/2012-10/env.csh		setenv ENV_SCHRODINGER $SOFT/schrodinger/2012-10/env.csh
	Then, in env.csh, the file pointed to by ENV_SCHRODINGER will be sourced to set up the correct enviroment. Note that ENV_SCHRODINGER can point anywhere, including to places in your own home directory.		Then, in env.csh, the file pointed to by ENV_SCHRODINGER will be sourced to set up the correct enviroment. Note that ENV_SCHRODINGER can point anywhere, including to places in your own home directory.

			Warnings:
			1) We do not recommend that you make personal copies of env.csh and vars.csh. Using the system standards means that you are more likely to stay in sync with standard lab practice.
			2) If you want to use software that is not available in the lab (or a more recent version of something we do have), please advise your [[Sysadmins]]. If more than one person uses the software, it probably makes sense to install it somewhere central. Doing so proactively retards the progress towards chaos, and probably saves you and your colleagues time, even in the short term.


	[[:Category:Internal]]		[[:Category:Internal]]

Frodo: Created page with "How to customize .cshrc There are four parts: 1) set up a custom DOCK_BASE, SOFT if required 2) set up standard shell variables (vars.csh) 3) custom paths, environment 4) def..."

2012-10-18T21:30:27Z

Created page with "How to customize .cshrc There are four parts: 1) set up a custom DOCK_BASE, SOFT if required 2) set up standard shell variables (vars.csh) 3) custom paths, environment 4) def..."

New page

How to customize .cshrc

There are four parts:
1) set up a custom DOCK_BASE, SOFT if required
2) set up standard shell variables (vars.csh)
3) custom paths, environment
4) define environment (env.csh)

First let's look at the standard file:
# .cshrc
#setenv DOCK_BASE /raid1/people/jji/dockenv
#
# initial step
source /raid3/software/labenv/vars.csh
#
# custom changes here
setenv EDITOR vi
unset autologout
#
# final step
source $SOFT/labenv/env.csh

Notes:
1) If you have your own dockenv, or you want to use one other than the lab default, you must set up DOCK_BASE before sourcing vars.csh
2) If you have all you software (Schrodinger, Openeye, etc) installed elsewhere, you need to set SOFT before sourcing vars.csh. Generally, you don't want this.
3) You can override individual choices of software packages between vars.csh and env.csh by setting ENV_* variables. To see what these are, do
printenv | grep ENV_
4) Thus say you want to use the 2012-10 version of Schrodinger instead of the default current version. You would add the following line after source vars.csh:
setenv ENV_SCHRODINGER $SOFT/schrodinger/2012-10/env.csh
Then, in env.csh, the file pointed to by ENV_SCHRODINGER will be sourced to set up the correct enviroment. Note that ENV_SCHRODINGER can point anywhere, including to places in your own home directory.

[[:Category:Internal]]