Changes in cce136d: update client

				client_CLI_install.md
			
          @@ -6,7 +6,6 @@ This page is for the BioGrids CLI (command line interface) software installation

           - BioGrids Installation Manager - Downloads

             - [Requirements](https://biogrids.org/wiki/client_downloads#requirements)

          -  - [BioGrids nstallation Manager for MacOS and Linux, v2.4.0](https://biogrids.org/wiki/client_downloads#biogrids-installation-manager-for-macos-and-linux-v240)

             - [BioGrids Command-line Installation Manager for MacOS and Linux, v2.4.0](https://biogrids.org/wiki/client_downloads#biogrids-command-line-installation-manager-for-macos-and-linux-v240)

          @@ -28,61 +27,115 @@ Step 1 : [BioGrids registration](https://biogrids.org/registration/register/)

           **Hard Drive Space**

             Depending on what you install, ensure you have enough free hard drive space on your machine.

          -**For large packages (R, Bioconductor), a wired  connection is recommended.**

          +**For large packages a wired  connection is recommended.**

             Some packages are quite large and can be slow to download, especially over WiFi.

           ### Binary releases : MacOS and Linux Installation

          -  There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.

          +There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.

          +

          +The latest version of the command line interface BioGrids Installation Manager, v2.4.0, is now available for Linux and MacOS computers:

          +

          +

          +Linux : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-linux.tar.gz)

          +

          +macOS : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-macos.tar.gz)

          -  [Mac : 1.0.695, 2020-05-31](downloads/biogrids-1.0.695-Darwin.tgz)

          -  [Linux : 1.0.695, 2020-05-31](downloads/biogrids-1.0.695-Linux.tgz)

             ```

          -  $ tar -zxf biogrids-1.0.695-Darwin.tgz

          -

          -  $ cd biogrids-1.0.695-Darwin

          -

          -  $ ./biogrids

          -  usage:

          -  biogrids <command> [<command_args>]

          -

          -  Available commands are:

          -      activate      activate new installation

          -      grids         list available grids

          -      info          print package metadata

          -      install       install single package

          -      install-all   install all packages from collection

          -      installed     list installed packages

          -      list          list available packages

          -      rebuild       rebuild installation

          -      remove        remove installed package

          -      resume        resume interrupted installations

          -      update        update package to latest release/version

          -      update-all    update all packages to latest release/version

          -      updates       list available updates for installed packages

          -      version       print package version string

          -  biogrids: error: too few arguments

          +$ tar zxf ./wbiogrids-cli_2.4.0-macos.tar.gz 

          +$ ./biogrids-cli -h

          +

          +  BioGrids Installer 2.4.0 01da16b7bf — 

          +                   _______  _____    _    __

          +                  / __/ _ )/ ___/___(_)__/ /

          +                 _\ \/ _  / (_ / __/ / _  /

          +                /___/____/\___/_/ /_/\_,_/

          +                    C o n s o r t i u m

          +  

          +

          +  USAGE 

          +  

          +    ▸ biogrids-cli <command> [ARGUMENTS...] [OPTIONS...]

          +

          +

          +  COMMANDS — Type 'biogrids-cli help <command>' to get some help about a command

          +

          +  * Installation management:

          +    activate                             Activate a new installation with the provided          

          +                                         credentials. The activation credentials are sent via   

          +                                         email and can either be a single credential-key, or a  

          +                                         <site> <username> <key> triplet.                       

          +    admin                                Periodic update & installation command                 

          +    crontab                              Generate the admin crontab script                      

          +    clean                                Removes obsolete versions & titles                     

          +    rebuild                              Rebuilds your installation environment                 

          +    save                                 Exports your current installation's configuration      

          +    reactivate                           Reactivates a new instance of an installation using an 

          +                                         exported configuration file.                           

          +    migrate-account                      Migrates an existing installation to a new account     

          +

          +  * Diagnostics and troubleshooting:

          +    check-connection                     Performs a connectivity test                           

          +    verify                               Lists missing software versions and .rc files          

          +    diag                                 Run diagnostics for your installation                  

          +

          +  * List commands (subsets of available titles)

          +    collections                          List the available software collections                

          +    grids                                List the available grids                               

          +    installed                            List the installed software titles                     

          +    list                                 List the available software titles                     

          +    obsolete                             List the obsolete software versions installed          

          +    pending                              List the software versions that are pending            

          +                                         installation                                           

          +    updates                              List the installed software versions with available    

          +                                         updates                                                

          +

          +  * Installation, Update and removal  (title required as argument, @version optional)

          +    install                              Install a software title or collection                 

          +    update                               Update a software title or collection                  

          +    resume                               Resume any pending installations                       

          +    remove                               Remove a software title or collection                  

          +

          +  * Informational

          +    info                                 Get detailed information on a particular package       

          +    search                               Search the available software titles                   

          +

          +  * Miscellaneous

          +    shell                                Starts the BioGrids shell                              

          +

          +  GLOBAL OPTIONS

          +

          +    -h, --help                           Display global help or command-related help.           

          +    -V, --version                        Display version.                                       

          +    --no-color                           Disable use of colors in output.                       

          +    -v, --verbose                        Verbose mode: will also output debug messages.         

          +    --quiet                              Quiet mode - only displays warn and error messages.    

          +    --silent                             Silent mode: does not output anything, giving no       

          +                                         indication of success or failure other than the exit   

          +                                         code.                                                  

          +    -y, --yes                            Skips confirmation prompts                             

          +    --no-progress-bar                    Disables the progress bar

             ```

           ** Activate the installation**

           Enter your site and key which you should have received these by email.

          -    $ biogrids activate <site name> <user name> <activation key>

          +    $ ./biogrids-cli activate <site name> <user name> <activation key>

           You may be prompted for your sudo password to create /programs and /opt/biogrids.

           **5. On successful activation, list software titles.**

          -    $ biogrids list

          +    $ ./biogrids-cli list

            If activation continues to fail, you may have an old BioGrids installation at /programs or /opt/biogrids. These should be removed.

           You may also be blocked from accessing BioGrids servers on port 873 and port 8080 by your institution's firewall. You can check if you can access [port 873 here](http://portquiz.net:873) and [port 8080 here](http://portquiz.net:8080)

          -For help, email *bugs@biogrids.org.*

          +For help, email help@biogrids.org.

           ### Installation on an external drive or USB key

           Currently the installer application installs the software tree in /opt/biogrids and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/biogrids. This functionality is not yet included in the BioGrids application, but can be set up manually with a symlink.

				version_management.md
			
          @@ -25,8 +25,9 @@ When set to BOTH|BOTH:path logging is sent to a file as above and also to BioGri

           Sample Entries in the log file have this form:

           ```

          -hostname BIOGRIDS osx-10.13.6 biogrid-production_1.0.695 newrc_sh CA5BBF5F-F41E-4CFA-8AA4-37182C9DD366 /programs/i386-mac/samtools/1.10/bin/samtools 0 0

          -hostname BIOGRIDS osx-10.13.6 biogrid-production_1.0.695 newrc_sh 3355483F-A04B-4575-868F-88D22173C957 /programs/i386-mac/python/3.6.5/bin/python 0 0

          +

          +2021-09-20T07:32:00EDT jjv5 M1-Air BIOGRIDS osx-11.2.1 biogrid-production_2.4.0 newrc_sh 4AADF0D0-3ADF-43EE-BD7E-6DCA9C85A627 NONE:samtools 0:22208 /programs/i386-mac/samtools/1.13/bin/samtools 1 3 

          +

           ```

           The path to the executable provides the architecture, name of the BioGrids title, version used and name of the executable called. 

          @@ -38,18 +39,14 @@ The biogrids-info tool can be used to list all available versions of a title whe

           ```

           $ biogrids-info -l samtools

          +  Version information for: /programs/i386-mac/samtools

          -Version information for: /programs/x86_64-linux/samtools

          -

          -Default version: 1.10

          -

          -In-use version:  1.10

          -

          -Installed versions:  1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19

          -

          -Other available versions:  1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 

          +Default version:                    1.13

          +In-use version:                     1.13

          -Overrides use this shell variable: SAMTOOLS_X

          +Installed versions:                 1.13

          +Other available versions:           1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 

          +Overrides use this shell variable:  SAMTOOLS_M

           ```

          @@ -60,7 +57,7 @@ If you need to use a non-default version of a title you can specify this version

           If the version of a title is not available on your platform you can install that version by specifying it either in the BioGrids GUI Installer or on the command line:

          -./biogrids install samtools@1.7 

          +./biogrids-cli install samtools@1.7 

           BioGrids versions are retained for every title.	We do not delete or remove versions of any title. If you are unable to find the version you need or have difficulty installing, please send a note to help@biogrids.org.

...	...	@@ -6,7 +6,6 @@ This page is for the BioGrids CLI (command line interface) software installation
6	6
7	7	- BioGrids Installation Manager - Downloads
8	8	- [Requirements](https://biogrids.org/wiki/client_downloads#requirements)
9		- - [BioGrids nstallation Manager for MacOS and Linux, v2.4.0](https://biogrids.org/wiki/client_downloads#biogrids-installation-manager-for-macos-and-linux-v240)
10	9	- [BioGrids Command-line Installation Manager for MacOS and Linux, v2.4.0](https://biogrids.org/wiki/client_downloads#biogrids-command-line-installation-manager-for-macos-and-linux-v240)
11	10
12	11
...	...	@@ -28,61 +27,115 @@ Step 1 : [BioGrids registration](https://biogrids.org/registration/register/)
28	27	Hard Drive Space
29	28	Depending on what you install, ensure you have enough free hard drive space on your machine.
30	29
31		-For large packages (R, Bioconductor), a wired connection is recommended.
	30	+For large packages a wired connection is recommended.
32	31	Some packages are quite large and can be slow to download, especially over WiFi.
33	32
34	33	### Binary releases : MacOS and Linux Installation
35	34
36		- There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.
	35	+There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.
	36	+
	37	+The latest version of the command line interface BioGrids Installation Manager, v2.4.0, is now available for Linux and MacOS computers:
	38	+
	39	+
	40	+Linux : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-linux.tar.gz)
	41	+
	42	+macOS : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-macos.tar.gz)
37	43
38		- [Mac : 1.0.695, 2020-05-31](downloads/biogrids-1.0.695-Darwin.tgz)
39	44
40		- [Linux : 1.0.695, 2020-05-31](downloads/biogrids-1.0.695-Linux.tgz)
41	45
42	46	```
43		- $ tar -zxf biogrids-1.0.695-Darwin.tgz
44		-
45		- $ cd biogrids-1.0.695-Darwin
46		-
47		- $ ./biogrids
48		- usage:
49		- biogrids <command> [<command_args>]
50		-
51		- Available commands are:
52		- activate activate new installation
53		- grids list available grids
54		- info print package metadata
55		- install install single package
56		- install-all install all packages from collection
57		- installed list installed packages
58		- list list available packages
59		- rebuild rebuild installation
60		- remove remove installed package
61		- resume resume interrupted installations
62		- update update package to latest release/version
63		- update-all update all packages to latest release/version
64		- updates list available updates for installed packages
65		- version print package version string
66		- biogrids: error: too few arguments
	47	+$ tar zxf ./wbiogrids-cli_2.4.0-macos.tar.gz
	48	+$ ./biogrids-cli -h
	49	+
	50	+ BioGrids Installer 2.4.0 01da16b7bf —
	51	+ _______ _____ _ __
	52	+ / __/ _ )/ ___/___(_)__/ /
	53	+ _\ \/ _ / (_ / __/ / _ /
	54	+ /___/____/\___/_/ /_/\_,_/
	55	+ C o n s o r t i u m
	56	+
	57	+
	58	+ USAGE
	59	+
	60	+ ▸ biogrids-cli <command> [ARGUMENTS...] [OPTIONS...]
	61	+
	62	+
	63	+ COMMANDS — Type 'biogrids-cli help <command>' to get some help about a command
	64	+
	65	+ * Installation management:
	66	+ activate Activate a new installation with the provided
	67	+ credentials. The activation credentials are sent via
	68	+ email and can either be a single credential-key, or a
	69	+ <site> <username> <key> triplet.
	70	+ admin Periodic update & installation command
	71	+ crontab Generate the admin crontab script
	72	+ clean Removes obsolete versions & titles
	73	+ rebuild Rebuilds your installation environment
	74	+ save Exports your current installation's configuration
	75	+ reactivate Reactivates a new instance of an installation using an
	76	+ exported configuration file.
	77	+ migrate-account Migrates an existing installation to a new account
	78	+
	79	+ * Diagnostics and troubleshooting:
	80	+ check-connection Performs a connectivity test
	81	+ verify Lists missing software versions and .rc files
	82	+ diag Run diagnostics for your installation
	83	+
	84	+ * List commands (subsets of available titles)
	85	+ collections List the available software collections
	86	+ grids List the available grids
	87	+ installed List the installed software titles
	88	+ list List the available software titles
	89	+ obsolete List the obsolete software versions installed
	90	+ pending List the software versions that are pending
	91	+ installation
	92	+ updates List the installed software versions with available
	93	+ updates
	94	+
	95	+ * Installation, Update and removal (title required as argument, @version optional)
	96	+ install Install a software title or collection
	97	+ update Update a software title or collection
	98	+ resume Resume any pending installations
	99	+ remove Remove a software title or collection
	100	+
	101	+ * Informational
	102	+ info Get detailed information on a particular package
	103	+ search Search the available software titles
	104	+
	105	+ * Miscellaneous
	106	+ shell Starts the BioGrids shell
	107	+
	108	+ GLOBAL OPTIONS
	109	+
	110	+ -h, --help Display global help or command-related help.
	111	+ -V, --version Display version.
	112	+ --no-color Disable use of colors in output.
	113	+ -v, --verbose Verbose mode: will also output debug messages.
	114	+ --quiet Quiet mode - only displays warn and error messages.
	115	+ --silent Silent mode: does not output anything, giving no
	116	+ indication of success or failure other than the exit
	117	+ code.
	118	+ -y, --yes Skips confirmation prompts
	119	+ --no-progress-bar Disables the progress bar
67	120	```
68	121
69	122
70	123	Activate the installation
71	124	Enter your site and key which you should have received these by email.
72	125
73		- $ biogrids activate <site name> <user name> <activation key>
	126	+ $ ./biogrids-cli activate <site name> <user name> <activation key>
74	127
75	128	You may be prompted for your sudo password to create /programs and /opt/biogrids.
76	129
77	130	5. On successful activation, list software titles.
78	131
79		- $ biogrids list
	132	+ $ ./biogrids-cli list
80	133
81	134	If activation continues to fail, you may have an old BioGrids installation at /programs or /opt/biogrids. These should be removed.
82	135
83	136	You may also be blocked from accessing BioGrids servers on port 873 and port 8080 by your institution's firewall. You can check if you can access [port 873 here](http://portquiz.net:873) and [port 8080 here](http://portquiz.net:8080)
84	137
85		-For help, email bugs@biogrids.org.
	138	+For help, email help@biogrids.org.
86	139
87	140	### Installation on an external drive or USB key
88	141	Currently the installer application installs the software tree in /opt/biogrids and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/biogrids. This functionality is not yet included in the BioGrids application, but can be set up manually with a symlink.

...	...	@@ -25,8 +25,9 @@ When set to BOTH\|BOTH:path logging is sent to a file as above and also to BioGri
25	25	Sample Entries in the log file have this form:
26	26
27	27	```
28		-hostname BIOGRIDS osx-10.13.6 biogrid-production_1.0.695 newrc_sh CA5BBF5F-F41E-4CFA-8AA4-37182C9DD366 /programs/i386-mac/samtools/1.10/bin/samtools 0 0
29		-hostname BIOGRIDS osx-10.13.6 biogrid-production_1.0.695 newrc_sh 3355483F-A04B-4575-868F-88D22173C957 /programs/i386-mac/python/3.6.5/bin/python 0 0
	28	+
	29	+2021-09-20T07:32:00EDT jjv5 M1-Air BIOGRIDS osx-11.2.1 biogrid-production_2.4.0 newrc_sh 4AADF0D0-3ADF-43EE-BD7E-6DCA9C85A627 NONE:samtools 0:22208 /programs/i386-mac/samtools/1.13/bin/samtools 1 3
	30	+
30	31	```
31	32
32	33	The path to the executable provides the architecture, name of the BioGrids title, version used and name of the executable called.
...	...	@@ -38,18 +39,14 @@ The biogrids-info tool can be used to list all available versions of a title whe
38	39
39	40	```
40	41	$ biogrids-info -l samtools
	42	+ Version information for: /programs/i386-mac/samtools
41	43
42		-Version information for: /programs/x86_64-linux/samtools
43		-
44		-Default version: 1.10
45		-
46		-In-use version: 1.10
47		-
48		-Installed versions: 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
49		-
50		-Other available versions: 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
	44	+Default version: 1.13
	45	+In-use version: 1.13
51	46
52		-Overrides use this shell variable: SAMTOOLS_X
	47	+Installed versions: 1.13
	48	+Other available versions: 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
	49	+Overrides use this shell variable: SAMTOOLS_M
53	50	```
54	51
55	52
...	...	@@ -60,7 +57,7 @@ If you need to use a non-default version of a title you can specify this version
60	57
61	58	If the version of a title is not available on your platform you can install that version by specifying it either in the BioGrids GUI Installer or on the command line:
62	59
63		-./biogrids install samtools@1.7
	60	+./biogrids-cli install samtools@1.7
64	61
65	62	BioGrids versions are retained for every title. We do not delete or remove versions of any title. If you are unable to find the version you need or have difficulty installing, please send a note to help@biogrids.org.
66	63