Changes in 39278b2: add sbgrid-cli version 2.2.2

				AWS.md
			
          @@ -24,8 +24,8 @@ It is not provided on linux by default but is required by several SBGrid titles.

           Download the SBGrid CLI installation manager.

           ```

          -curl -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_linux.tar.gz

          -tar -zxvf sbgrid-cli_2.2.1_linux.tar.gz

          +curl -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_linux.tar.gz

          +tar -zxvf sbgrid-cli_2.2.2_linux.tar.gz

           ```

           ### Activate your installation

				SBGrid-Wiki.md
			
          @@ -7,10 +7,14 @@

           ```

           ## Welcome to the SBGrid Consortium Wiki

          +SBGrid is a global consortium of research labs in academia and industry using structural biology (cryoEM, X-ray crystallography and scattering, NMR, molecular dynamics, etc) to address scientific questions. Based at Harvard Medical School in Boston, MA, our team supports research computing for structural biologists with scientific software and computing support.  

          +

           This site provides information on how to install, use, and get help with your SBGrid software installation. Here you can also find information about SBGrid services. Please let us know if you have questions.

           ### Recent Posts

          +[2021.03.05 - new sbgrid-cli version, 2.2.2](sbgrid-cli)

          +

           [2021.02.23 - new sbgrid-cli version, 2.2.1](sbgrid-cli)

           [2021.02.02 - new sbgrid-cli version, 2.1.5](sbgrid-cli)

				catalina.md
			
          @@ -17,13 +17,13 @@ Activation with our latest command-line installation manager is possible in 3 st

           ### 1.  Download the installation manager, sbgrid-cli :

           First, download the latest installation manager from here

          -[sbgrid-cli version 2.2.1](downloads/sbgrid-cli_2.2.1_macos.tar.gz)

          +[sbgrid-cli version 2.2.2](downloads/sbgrid-cli_2.2.2_macos.tar.gz)

           You can use *curl* to download the tarball directly in your terminal. 

           This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the *xattr* step below.

           ```

          -curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_macos.tar.gz

          +curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_macos.tar.gz

           ```

          @@ -31,7 +31,7 @@ Untar and run the application to test.

           Untar :

           ```

          -tar -zxf sbgrid-cli_2.2.1_macos.tar.gz

          +tar -zxf sbgrid-cli_2.2.2_macos.tar.gz

           ```

           then run :

				downloads/sbgrid-cli_2.0.44_linux.tar.gz
			
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				downloads/sbgrid-cli_2.0.44_macOS.tar.gz
			
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				downloads/sbgrid-cli_2.1.3_linux.tar.gz
			
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				downloads/sbgrid-cli_2.1.3_macos.tar.gz
			
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				downloads/sbgrid-cli_2.1.4_linux.tar.gz
			
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				downloads/sbgrid-cli_2.1.4_macos.tar.gz
			
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				downloads/sbgrid-cli_2.2.2_linux.tar.gz
			
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				downloads/sbgrid-cli_2.2.2_macos.tar.gz
			
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				sbgrid-cli.md
			
          @@ -18,11 +18,11 @@ Set up an account by registering here : [SBGrid registration](https://sbgrid.org

             While not strictly required, we recommend a dedicated 'sbgrid' user account for software management, particularly on multiuser systems. This ensures the software can't be modified by user accounts and that data won't be mistakenly saved into the software stack and lost inadvertantly during software updates. The `sbgrid-cli` program will add and remove software. **If data files are accidentally saved into the software collection, they are likely to be lost.** 

          -### Latest version : v2.2.1

          +### Latest version : v2.2.2

          -[LINUX : sbgrid-cli_2.2.1_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_linux.tar.gz)

          +[LINUX : sbgrid-cli_2.2.2_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_linux.tar.gz)

          -[macOS : sbgrid-cli_2.2.1_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_macos.tar.gz)

          +[macOS : sbgrid-cli_2.2.2_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_macos.tar.gz)

           ### Installation

          @@ -68,7 +68,7 @@ Activate with the `activate` subcommand

           ```

             $ sbgrid-cli activate --help 

          -  SBGrid Installer 2.2.1 f593932a17 — 

          +  SBGrid Installer 2.2.2 f593932a17 — 

                              _______  _____    _    __

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

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

          @@ -241,7 +241,7 @@ Description:

           class averages in cryo-electron microscopy.

           Technical notes:

          -## SBGrid Usage Info RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpuCUDA builds of RELION re designated by a '_cu' suffix in the version of the application. For example, 3.1.0_cu9.2 is linked against CUDA v9.2 libraries. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.RELION builds without CUDA support are compiled with Intel 2019.5 with accelation options and Intel math libraries. ### RELION and MPI versionsRELION uses the 'mpirun' executable to manage MPI "ranks" for parallel processing. SBGrid includes several OpenMPI versions which are matched to specific RELION versions. When called from the SBGrid capsule environment, the relion GUI is configured to use the correct version of OpenMPI to manage parallel processing. When calling RELION binaries from the command line, the `mpirun.relion` executable can be used. `mpirun.relion` is configured to used the correct version of OpenMPI for each version of RELION. The 3.1.* versions for RELION use the default configuration of OpenMPI (3.1.6 on Linux, 2.1.3 on macOS) and do not require the version to be defined. Older releases use OpenMPI 2.1.2 which should be specified in $HOME/.sbgrid.conf. To set the OpenMPI version, add : OPENMPI_X=2.1.2"to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun. As noted above, you can also use the `mpirun.relion` executable in place of `mpirun` to use the MPI that matches the currently configured version of RELION. In this case, no other configuration is needed.Version 3.1.0_cu8.0 is compiled to support legacy CPUs (pre-Haswell). OpenMPI 3.1.6_compat is also needed for this version.Versions 3.1.0_cu8.0_slurm20 3.1-beta_cu8.0_slurm20 and 3.0.8_cu8.0_slurm20 support Slurm v20 PMI library. ## Recent Changes20201111 : Add 3.1.1 RELION versions20200703 : Add 3.1.0 release version20200629 : reconfigure RELION gui to automatically use correct 'mpirun' in capsules.20200610 : rebuild of 3.1-beta releases with OpenMPI 3.1.6 from commit 5997001.

          +## SBGrid Usage Info RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpuCUDA builds of RELION re designated by a '_cu' suffix in the version of the application. For example, 3.1.0_cu9.2 is linked against CUDA v9.2 libraries. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.RELION builds without CUDA support are compiled with Intel 2019.5 with accelation options and Intel math libraries. ### RELION and MPI versionsRELION uses the 'mpirun' executable to manage MPI "ranks" for parallel processing. SBGrid includes several OpenMPI versions which are matched to specific RELION versions. When called from the SBGrid capsule environment, the relion GUI is configured to use the correct version of OpenMPI to manage parallel processing. When calling RELION binaries from the command line, the `mpirun.relion` executable can be used. `mpirun.relion` is configured to used the correct version of OpenMPI for each version of RELION. The 3.1.* versions for RELION use the default configuration of OpenMPI (3.1.6 on Linux, 2.1.3 on macOS) and do not require the version to be defined. Older releases use OpenMPI 2.1.2 which should be specified in $HOME/.sbgrid.conf. To set the OpenMPI version, add : OPENMPI_X=2.1.2"to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun. As noted above, you can also use the `mpirun.relion` executable in place of `mpirun` to use the MPI that matches the currently configured version of RELION. In this case, no other configuration is needed.Version 3.1.0_cu8.0 is compiled to support legacy CPUs (pre-Haswell). OpenMPI 3.1.6_compat is also needed for this version.Versions 3.1.0_cu8.0_slurm20 3.1-beta_cu8.0_slurm20 and 3.0.8_cu8.0_slurm20 support Slurm v20 PMI library. ## Recent Changes2.2.2111 : Add 3.1.1 RELION versions20200703 : Add 3.1.0 release version20200629 : reconfigure RELION gui to automatically use correct 'mpirun' in capsules.20200610 : rebuild of 3.1-beta releases with OpenMPI 3.1.6 from commit 5997001.

           ## Known Issues20200610 : Empty values in GUI during autopicking can be interpreted as Text instead of Float values. ## Deprecated versionsThe following verions are deprecated and will be removed in a future SBGrid update.20200706: 3.0.8_cu10.1 3.0.8_cu9.2 3.0.8_avx2 3.1-beta_cu9.2 3.1-beta_cu10.1

...	...	@@ -24,8 +24,8 @@ It is not provided on linux by default but is required by several SBGrid titles.
24	24	Download the SBGrid CLI installation manager.
25	25
26	26	```
27		-curl -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_linux.tar.gz
28		-tar -zxvf sbgrid-cli_2.2.1_linux.tar.gz
	27	+curl -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_linux.tar.gz
	28	+tar -zxvf sbgrid-cli_2.2.2_linux.tar.gz
29	29	```
30	30
31	31	### Activate your installation

...	...	@@ -7,10 +7,14 @@
7	7	```
8	8	## Welcome to the SBGrid Consortium Wiki
9	9
	10	+SBGrid is a global consortium of research labs in academia and industry using structural biology (cryoEM, X-ray crystallography and scattering, NMR, molecular dynamics, etc) to address scientific questions. Based at Harvard Medical School in Boston, MA, our team supports research computing for structural biologists with scientific software and computing support.
	11	+
10	12	This site provides information on how to install, use, and get help with your SBGrid software installation. Here you can also find information about SBGrid services. Please let us know if you have questions.
11	13
12	14	### Recent Posts
13	15
	16	+[2021.03.05 - new sbgrid-cli version, 2.2.2](sbgrid-cli)
	17	+
14	18	[2021.02.23 - new sbgrid-cli version, 2.2.1](sbgrid-cli)
15	19
16	20	[2021.02.02 - new sbgrid-cli version, 2.1.5](sbgrid-cli)

...	...	@@ -17,13 +17,13 @@ Activation with our latest command-line installation manager is possible in 3 st
17	17	### 1. Download the installation manager, sbgrid-cli :
18	18	First, download the latest installation manager from here
19	19
20		-[sbgrid-cli version 2.2.1](downloads/sbgrid-cli_2.2.1_macos.tar.gz)
	20	+[sbgrid-cli version 2.2.2](downloads/sbgrid-cli_2.2.2_macos.tar.gz)
21	21
22	22	You can use curl to download the tarball directly in your terminal.
23	23	This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the xattr step below.
24	24
25	25	```
26		-curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_macos.tar.gz
	26	+curl -k -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_macos.tar.gz
27	27	```
28	28
29	29
...	...	@@ -31,7 +31,7 @@ Untar and run the application to test.
31	31	Untar :
32	32
33	33	```
34		-tar -zxf sbgrid-cli_2.2.1_macos.tar.gz
	34	+tar -zxf sbgrid-cli_2.2.2_macos.tar.gz
35	35	```
36	36
37	37	then run :

...	...	@@ -18,11 +18,11 @@ Set up an account by registering here : [SBGrid registration](https://sbgrid.org
18	18
19	19	While not strictly required, we recommend a dedicated 'sbgrid' user account for software management, particularly on multiuser systems. This ensures the software can't be modified by user accounts and that data won't be mistakenly saved into the software stack and lost inadvertantly during software updates. The `sbgrid-cli` program will add and remove software. If data files are accidentally saved into the software collection, they are likely to be lost.
20	20
21		-### Latest version : v2.2.1
	21	+### Latest version : v2.2.2
22	22
23		-[LINUX : sbgrid-cli_2.2.1_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_linux.tar.gz)
	23	+[LINUX : sbgrid-cli_2.2.2_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_linux.tar.gz)
24	24
25		-[macOS : sbgrid-cli_2.2.1_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.1_macos.tar.gz)
	25	+[macOS : sbgrid-cli_2.2.2_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.2_macos.tar.gz)
26	26
27	27
28	28	### Installation
...	...	@@ -68,7 +68,7 @@ Activate with the `activate` subcommand
68	68	```
69	69	$ sbgrid-cli activate --help
70	70
71		- SBGrid Installer 2.2.1 f593932a17 —
	71	+ SBGrid Installer 2.2.2 f593932a17 —
72	72	_______ _____ _ __
73	73	/ __/ _ )/ ___/___(_)__/ /
74	74	_\ \/ _ / (_ / __/ / _ /
...	...	@@ -241,7 +241,7 @@ Description:
241	241	class averages in cryo-electron microscopy.
242	242
243	243	Technical notes:
244		-## SBGrid Usage Info RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpuCUDA builds of RELION re designated by a '_cu' suffix in the version of the application. For example, 3.1.0_cu9.2 is linked against CUDA v9.2 libraries. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.RELION builds without CUDA support are compiled with Intel 2019.5 with accelation options and Intel math libraries. ### RELION and MPI versionsRELION uses the 'mpirun' executable to manage MPI "ranks" for parallel processing. SBGrid includes several OpenMPI versions which are matched to specific RELION versions. When called from the SBGrid capsule environment, the relion GUI is configured to use the correct version of OpenMPI to manage parallel processing. When calling RELION binaries from the command line, the `mpirun.relion` executable can be used. `mpirun.relion` is configured to used the correct version of OpenMPI for each version of RELION. The 3.1.* versions for RELION use the default configuration of OpenMPI (3.1.6 on Linux, 2.1.3 on macOS) and do not require the version to be defined. Older releases use OpenMPI 2.1.2 which should be specified in $HOME/.sbgrid.conf. To set the OpenMPI version, add : OPENMPI_X=2.1.2"to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun. As noted above, you can also use the `mpirun.relion` executable in place of `mpirun` to use the MPI that matches the currently configured version of RELION. In this case, no other configuration is needed.Version 3.1.0_cu8.0 is compiled to support legacy CPUs (pre-Haswell). OpenMPI 3.1.6_compat is also needed for this version.Versions 3.1.0_cu8.0_slurm20 3.1-beta_cu8.0_slurm20 and 3.0.8_cu8.0_slurm20 support Slurm v20 PMI library. ## Recent Changes20201111 : Add 3.1.1 RELION versions20200703 : Add 3.1.0 release version20200629 : reconfigure RELION gui to automatically use correct 'mpirun' in capsules.20200610 : rebuild of 3.1-beta releases with OpenMPI 3.1.6 from commit 5997001.
	244	+## SBGrid Usage Info RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpuCUDA builds of RELION re designated by a '_cu' suffix in the version of the application. For example, 3.1.0_cu9.2 is linked against CUDA v9.2 libraries. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.RELION builds without CUDA support are compiled with Intel 2019.5 with accelation options and Intel math libraries. ### RELION and MPI versionsRELION uses the 'mpirun' executable to manage MPI "ranks" for parallel processing. SBGrid includes several OpenMPI versions which are matched to specific RELION versions. When called from the SBGrid capsule environment, the relion GUI is configured to use the correct version of OpenMPI to manage parallel processing. When calling RELION binaries from the command line, the `mpirun.relion` executable can be used. `mpirun.relion` is configured to used the correct version of OpenMPI for each version of RELION. The 3.1.* versions for RELION use the default configuration of OpenMPI (3.1.6 on Linux, 2.1.3 on macOS) and do not require the version to be defined. Older releases use OpenMPI 2.1.2 which should be specified in $HOME/.sbgrid.conf. To set the OpenMPI version, add : OPENMPI_X=2.1.2"to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun. As noted above, you can also use the `mpirun.relion` executable in place of `mpirun` to use the MPI that matches the currently configured version of RELION. In this case, no other configuration is needed.Version 3.1.0_cu8.0 is compiled to support legacy CPUs (pre-Haswell). OpenMPI 3.1.6_compat is also needed for this version.Versions 3.1.0_cu8.0_slurm20 3.1-beta_cu8.0_slurm20 and 3.0.8_cu8.0_slurm20 support Slurm v20 PMI library. ## Recent Changes2.2.2111 : Add 3.1.1 RELION versions20200703 : Add 3.1.0 release version20200629 : reconfigure RELION gui to automatically use correct 'mpirun' in capsules.20200610 : rebuild of 3.1-beta releases with OpenMPI 3.1.6 from commit 5997001.
245	245
246	246	## Known Issues20200610 : Empty values in GUI during autopicking can be interpreted as Text instead of Float values. ## Deprecated versionsThe following verions are deprecated and will be removed in a future SBGrid update.20200706: 3.0.8_cu10.1 3.0.8_cu9.2 3.0.8_avx2 3.1-beta_cu9.2 3.1-beta_cu10.1
247	247