Changes in 83e6af5: declutter

				_Sidebar.md
			
          @@ -2,7 +2,6 @@

           Installing Software

           * [Overview](installation_overview)

          -* [Supported Operating Systems](operatingsystems)

           * [Full Site installation](managing_install)

           * [Graphical installation client](client_install)

           * [Command line installation client](client_CLI_install)

				client_usage.md
			
          @@ -1,83 +0,0 @@

          -## SBGrid installation client - Usage

          -

          -**Instructions for installing the SBGrid software installation client can be found here** -->  [Installation Instructions](client_install)

          -

          -### General

          -The SBGrid software installation client is a GUI-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.

          -

          -  ![installed](images/client_install.png)

          -

          -The client GUI is displays software 'Collections' on the right panel with folder icons under the 'Packages' heading. These Collections control the list of titles displayed in the center 'main' panel.

          -

          -The first of two of these 'Collections' are shortcut meta-collections of the local machine. The first is the currently installed titles. The second icon, Updates, shows updates available from SBGrid. 'Pending' is a collection of pending installs and removals. Below these shortcuts are packages are grouped by primary scientific uses. Installation status is also indicated in theses collections.

          -

          -Information about each title, including a description and links to documentation are shown in the upper right panel when that title is selected in the main pane.

          -

          -Once packages have been configured for installation and/or removal by selecting their checkbox, clicking the 'Apply Changes' button will perform update the titles, adding pending installations and removing pending deletions.

          -

          -### Example : Installing Albula

          -Check the box to select Albula, then click the 'Apply Changes' button.

          -Notice the text turns green for pending installations. Pending updates are Orange.

          -![apply](images/client_apply2.png)

          -

          -### Example : Removing Albula

          -Uncheck the box for Albula. Removals are shown in red text.

          -![apply](images/client_remove1.png)

          -

          -Click apply changes. Albula will be removed.

          -![apply](images/client_remove2.png)

          -

          -### Version selection

          -

          -Default versions are installed by default for each application, though individual versions can be selected for each title. To do so, show the version pane by selecting **"Show all package versions"** from the **"View"** menu. Then, in the bottom right, select a desired version with the check boxes. Multiple versions of a given title can be installed and are indicated in the main panel.

          -

          -Enable version panel

          -![all](images/client_versions1.png)

          -

          -Check old/non-default versions

          -![all](images/client_versions2.png)

          -

          -

          -### Versions and the SBGrid environment

          -If you have a single version of an application installed, explicitly version selection in your environment will not be needed. In the case of multiple installed versions, the *SBGrid Default* version will be the version available at the terminal when installed, unless configured otherwise in *~/.sbgrid.conf*.

          -

          -If you have multiple non-default versions installed, the *latest release* will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use either an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file as in the standard SBGrid environment.

          -

          -**Version priority in the shell**

          -  1. *~/.sbgrid.conf*

          -  2. Installed Default version

          -  3. Latest installed release

          -

          -You can do open the configuration file by selecting the *"Edit Configuration File"* from the *"SBGrid Installer"* menu.

          -

          -![all](images/client_config1.png)

          -

          -This will open a text editor with a sample configuration file, or your *~/.sbgrid.conf* file if you have one already.

          -

          -![all](images/client_config2.png)

          -

          -There is more info on how to do that here -->  [SBGrid version overrides](versions)

          -

          -

          -### Running the software

          -

          -To run the software, you can click the "SBGrid Shell" button for an initialized bash shell.

          -

          -You may also run the software from another terminal on your machine.

          -To use the software at the terminal in bash, open a new terminal and run

          -

          -    source /programs/sbgrid.shrc

          -

          -or in tcsh

          -

          -    source /programs/sbgrid.cshrc

          -

          -### Questions, Problems and Known Issues

          -For questions or problems, the Help menu will direct to the SBGrid help page. Or just email *bugs@sbgrid.org*.

          -If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/SBGrid/sbgrid.log file with your report.

          -

          -**Known issues**

          -

          -* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

          -

          -* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior SBGrid install on your machine at /programs or /opt/sbgrid.

				client_usage.md
			
          @@ -0,0 +1 @@

          +client_install.md

          \ No newline at end of file

				installation_overview.md
			
          @@ -1,4 +1,4 @@

          -### Installing the SBGrid software collection

          +## Installing the SBGrid software collection

           The SBGrid Software Suite contains 400+ Scientific software applications for [Linux and OS X](operatingsystems).

          @@ -19,3 +19,39 @@ The MacOS GUI installation client allows users to select the applications they n

           The SBGrid CLI tool allows users to choose the titles they wish to install using a command-line driven package manager. Applications can be installed and updated as convenient. Updates are released on a rolling basis and can be installed by the user as necessary. This client can be made automatic or used in manual mode.

           Member labs may use any/all of the installation types above for as many Computers as they require. 

          +

          +## Supported Operating Systems

          +

          +The SBGrid Software Suite can run on Linux, OS X and IRIX machines.

          +

          +### Linux

          +We build and test software under 64-bit Red Hat 6.  The majority of our Linux users are using the Red Hat/CentOS/Scientific Linux or Fedora distributions, but we also have labs using the software with Ubuntu, Debian and OpenSuSE.  We don't explicitly test the software on these distributions, but it is known to work, and we will work to resolve problems reported by users of these Linux distributions.

          +

          +We officially support the two most recent releases of Red Hat/CentOS/Scientific Linux (currently 6 and 7) and the two most recent releases of Fedora Linux. At this time, only 64-bit versions of linux are fully supported. As of January 2015, we are no longer updating the 32-bit software branch, though we will work to resolve reported problems.

          +

          +Currently Supported:

          +

          +* Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.

          +* We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible.

          +

          +## OS X Intel

          +We build and test the programs under the most five most recent OS X releases.

          +

          +Currently Supported:

          +

          +* OS X Intel 10.9 - 10.12

          +* As above with earlier versions of linux, there are many software applications that are fully functional on earlier versions of MacOSX in the SBGrid tree. We work to maintain an environment compatible with these OS versions, though they may not receive the latest applications available.

          +

          +## OS X PowerPC

          +The OS X PowerPC branch is currently frozen.  The applications are stable and work well on our PowerPC hardware, but they are not being updated.

          +

          +Currently Supported:

          +

          +* OS X PowerPC 10.4 - 10.5

          +

          +## IRIX

          +The IRIX programs branch is currently frozen.  The applications are stable and work well on our SGI hardware, but they are not being updated.

          +

          +Currently Supported:

          +

          +* IRIX 6.5.26 + bugfix releases

...	...	@@ -0,0 +1 @@
	1	+client_install.md
...	...	\ No newline at end of file

...	...	@@ -1,4 +1,4 @@
1		-### Installing the SBGrid software collection
	1	+## Installing the SBGrid software collection
2	2
3	3	The SBGrid Software Suite contains 400+ Scientific software applications for [Linux and OS X](operatingsystems).
4	4
...	...	@@ -19,3 +19,39 @@ The MacOS GUI installation client allows users to select the applications they n
19	19	The SBGrid CLI tool allows users to choose the titles they wish to install using a command-line driven package manager. Applications can be installed and updated as convenient. Updates are released on a rolling basis and can be installed by the user as necessary. This client can be made automatic or used in manual mode.
20	20
21	21	Member labs may use any/all of the installation types above for as many Computers as they require.
	22	+
	23	+## Supported Operating Systems
	24	+
	25	+The SBGrid Software Suite can run on Linux, OS X and IRIX machines.
	26	+
	27	+### Linux
	28	+We build and test software under 64-bit Red Hat 6. The majority of our Linux users are using the Red Hat/CentOS/Scientific Linux or Fedora distributions, but we also have labs using the software with Ubuntu, Debian and OpenSuSE. We don't explicitly test the software on these distributions, but it is known to work, and we will work to resolve problems reported by users of these Linux distributions.
	29	+
	30	+We officially support the two most recent releases of Red Hat/CentOS/Scientific Linux (currently 6 and 7) and the two most recent releases of Fedora Linux. At this time, only 64-bit versions of linux are fully supported. As of January 2015, we are no longer updating the 32-bit software branch, though we will work to resolve reported problems.
	31	+
	32	+Currently Supported:
	33	+
	34	+* Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.
	35	+* We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible.
	36	+
	37	+## OS X Intel
	38	+We build and test the programs under the most five most recent OS X releases.
	39	+
	40	+Currently Supported:
	41	+
	42	+* OS X Intel 10.9 - 10.12
	43	+* As above with earlier versions of linux, there are many software applications that are fully functional on earlier versions of MacOSX in the SBGrid tree. We work to maintain an environment compatible with these OS versions, though they may not receive the latest applications available.
	44	+
	45	+## OS X PowerPC
	46	+The OS X PowerPC branch is currently frozen. The applications are stable and work well on our PowerPC hardware, but they are not being updated.
	47	+
	48	+Currently Supported:
	49	+
	50	+* OS X PowerPC 10.4 - 10.5
	51	+
	52	+## IRIX
	53	+The IRIX programs branch is currently frozen. The applications are stable and work well on our SGI hardware, but they are not being updated.
	54	+
	55	+Currently Supported:
	56	+
	57	+* IRIX 6.5.26 + bugfix releases

...	...	@@ -2,7 +2,6 @@
2	2
3	3	Installing Software
4	4	* [Overview](installation_overview)
5		-* [Supported Operating Systems](operatingsystems)
6	5	* [Full Site installation](managing_install)
7	6	* [Graphical installation client](client_install)
8	7	* [Command line installation client](client_CLI_install)

...	...	@@ -1,83 +0,0 @@
1		-## SBGrid installation client - Usage
2		-
3		-Instructions for installing the SBGrid software installation client can be found here --> [Installation Instructions](client_install)
4		-
5		-### General
6		-The SBGrid software installation client is a GUI-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.
7		-
8		- ![installed](images/client_install.png)
9		-
10		-The client GUI is displays software 'Collections' on the right panel with folder icons under the 'Packages' heading. These Collections control the list of titles displayed in the center 'main' panel.
11		-
12		-The first of two of these 'Collections' are shortcut meta-collections of the local machine. The first is the currently installed titles. The second icon, Updates, shows updates available from SBGrid. 'Pending' is a collection of pending installs and removals. Below these shortcuts are packages are grouped by primary scientific uses. Installation status is also indicated in theses collections.
13		-
14		-Information about each title, including a description and links to documentation are shown in the upper right panel when that title is selected in the main pane.
15		-
16		-Once packages have been configured for installation and/or removal by selecting their checkbox, clicking the 'Apply Changes' button will perform update the titles, adding pending installations and removing pending deletions.
17		-
18		-### Example : Installing Albula
19		-Check the box to select Albula, then click the 'Apply Changes' button.
20		-Notice the text turns green for pending installations. Pending updates are Orange.
21		-![apply](images/client_apply2.png)
22		-
23		-### Example : Removing Albula
24		-Uncheck the box for Albula. Removals are shown in red text.
25		-![apply](images/client_remove1.png)
26		-
27		-Click apply changes. Albula will be removed.
28		-![apply](images/client_remove2.png)
29		-
30		-### Version selection
31		-
32		-Default versions are installed by default for each application, though individual versions can be selected for each title. To do so, show the version pane by selecting "Show all package versions" from the "View" menu. Then, in the bottom right, select a desired version with the check boxes. Multiple versions of a given title can be installed and are indicated in the main panel.
33		-
34		-Enable version panel
35		-![all](images/client_versions1.png)
36		-
37		-Check old/non-default versions
38		-![all](images/client_versions2.png)
39		-
40		-
41		-### Versions and the SBGrid environment
42		-If you have a single version of an application installed, explicitly version selection in your environment will not be needed. In the case of multiple installed versions, the SBGrid Default version will be the version available at the terminal when installed, unless configured otherwise in ~/.sbgrid.conf.
43		-
44		-If you have multiple non-default versions installed, the latest release will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use either an older release or the non-default version when a default version is installed, you must set this explicitly in your ~/.sbgrid.conf file as in the standard SBGrid environment.
45		-
46		-Version priority in the shell
47		- 1. ~/.sbgrid.conf
48		- 2. Installed Default version
49		- 3. Latest installed release
50		-
51		-You can do open the configuration file by selecting the "Edit Configuration File" from the "SBGrid Installer" menu.
52		-
53		-![all](images/client_config1.png)
54		-
55		-This will open a text editor with a sample configuration file, or your ~/.sbgrid.conf file if you have one already.
56		-
57		-![all](images/client_config2.png)
58		-
59		-There is more info on how to do that here --> [SBGrid version overrides](versions)
60		-
61		-
62		-### Running the software
63		-
64		-To run the software, you can click the "SBGrid Shell" button for an initialized bash shell.
65		-
66		-You may also run the software from another terminal on your machine.
67		-To use the software at the terminal in bash, open a new terminal and run
68		-
69		- source /programs/sbgrid.shrc
70		-
71		-or in tcsh
72		-
73		- source /programs/sbgrid.cshrc
74		-
75		-### Questions, Problems and Known Issues
76		-For questions or problems, the Help menu will direct to the SBGrid help page. Or just email bugs@sbgrid.org.
77		-If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/SBGrid/sbgrid.log file with your report.
78		-
79		-Known issues
80		-
81		-* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
82		-
83		-* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior SBGrid install on your machine at /programs or /opt/sbgrid.