66a3376d1f53a19a6a952f186922c76519399a3f
AWS.md
| ... | ... | @@ -37,8 +37,8 @@ First login to your running instance and install **tcsh**. It is not provided on |
| 37 | 37 | Download the SBGrid CLI installation manager. |
| 38 | 38 | |
| 39 | 39 | ``` |
| 40 | -curl -LO https://sbgrid.org/wiki/downloads/sbgrid-cli_2.2.9_linux.tar.gz |
|
| 41 | -tar -zxvf sbgrid-cli_2.2.9_linux.tar.gz |
|
| 40 | +curl -LO https://sbgrid.org/downloads/latest/sbgrid-cli_linux.tar.gz |
|
| 41 | +tar -zxvf sbgrid-cli_linux.tar.gz |
|
| 42 | 42 | ``` |
| 43 | 43 | |
| 44 | 44 | ### Activate your installation |
account_migration.md
| ... | ... | @@ -71,11 +71,11 @@ You only need to run three commands. In a terminal, run: |
| 71 | 71 | |
| 72 | 72 | On macOS : |
| 73 | 73 | ``` |
| 74 | - $ curl -k -LO https://sbgrid-installation-manager.s3.amazonaws.com/2.2.40/sbgrid-cli_2.2.40-macos.tar.gz |
|
| 74 | + $ curl -k -LO https://sbgrid.org/downloads/latest/sbgrid-cli_macos.tar.gz |
|
| 75 | 75 | ``` |
| 76 | 76 | On Linux: |
| 77 | 77 | ``` |
| 78 | - $ curl -k -LO https://sbgrid-installation-manager.s3.amazonaws.com/2.2.40/sbgrid-cli_2.2.40-linux.tar.gz |
|
| 78 | + $ curl -k -LO https://sbgrid.org/downloads/latest/sbgrid-cli_linux.tar.gz |
|
| 79 | 79 | ``` |
| 80 | 80 | |
| 81 | 81 | 2) **Decompress** and untar the archive |
big-sur.md.junk
| ... | ... | @@ -0,0 +1,31 @@ |
| 1 | +## MacOS 11.0 Big Sur |
|
| 2 | + |
|
| 3 | +Apple has released MacOS 11.0 "Big Sur". This OS includes compatibilty for Apple's new 'Apple Silicon' ARM-based computers as well as numerous changes and security enhancements. Because this is a major update, we reccommend waiting to upgrade any system required for scientific data processing. MacOS 10.14 "Mojave" or 10.15 "Catalina" are currently supported by SBGrid. |
|
| 4 | + |
|
| 5 | +<!-- TOC --> |
|
| 6 | + |
|
| 7 | +- [MacOS 11.0 Big Sur](#macos-110-big-sur) |
|
| 8 | + - [Apple M1 Silicon](#apple-m1-silicon) |
|
| 9 | + - [Installing SBGrid on Big Sur](#installing-sbgrid-on-big-sur) |
|
| 10 | + - [Known issues](#known-issues) |
|
| 11 | + |
|
| 12 | +<!-- /TOC --> |
|
| 13 | + |
|
| 14 | +### Apple M1 Silicon |
|
| 15 | + |
|
| 16 | +ARM64 compatibility |
|
| 17 | + |
|
| 18 | +Apple released the first of its new ARM64 "apple silicon" macs with the "M1" CPU. We are testing the SBGrid software stack on the M1 chip and, so far, compatibility and performance look very good. Most of the SBGrid applications work on the new M1 CPU with macOS 11 and Apple's Rosetta compatibility environment. Standards like COOT, PyMOL, Chimera, CCP4, and PHENIX work seamlessly, but there are exceptions (CCPEM, RELION). We expect to support most titles on BigSur with the new M1 hardware early in 2021. |
|
| 19 | + |
|
| 20 | +### Installing SBGrid on Big Sur |
|
| 21 | + |
|
| 22 | +Installation of SBGrid on Big Sur is basically the same as on Catalina. Due to Apple's filesystem protections and our current requirement of a symlink at `/programs`, a `/etc/synthetic.conf` file is necessary. See the [installation page for macOS Catalina for more info](catalina) |
|
| 23 | + |
|
| 24 | +### Known issues |
|
| 25 | + |
|
| 26 | +- Ilastik 1.3.3 and earlier are no supported. Support coming in 1.4. |
|
| 27 | +- No 32-bit support (dropped in Catalina) means no support for nmrDraw, other 32-bit applications. |
|
| 28 | +- Rosetta fails ( from Baker lab, not Apple Rosetta2 ). Needs to be recompiled with clang. |
|
| 29 | +- CCP-EM ( possibly fixed in latest nightly) |
|
| 30 | +- No GUI in FLTK applications (like RELION) |
|
| 31 | +- Xquartz window border takes a few seconds to appear. It does appear eventually. Possibly fixed in XQuartz 2.8 series. |
client_install.md
| ... | ... | @@ -1,11 +1,10 @@ |
| 1 | 1 | ## SBGrid Installation Manager GUI Installation and Usage |
| 2 | 2 | |
| 3 | -This page covers the usage of the installation manager graphical user interface (GUI). This application is available for Linux and macOS computers. For more information on our latest command-line interface (CLI) installation manager, [see here](sbgrid-cli). Latest versions are [available for **download** here](client_downloads.md) |
|
| 3 | +This page covers the usage of the installation manager graphical user interface (GUI) which is available for Linux and macOS computers. For more information on our latest command-line interface (CLI) installation manager, [see here](sbgrid-cli). Latest versions of all isntallation managers are [available for **download** here](client_downloads.md) |
|
| 4 | 4 | |
| 5 | -A [video tutorial of the new SBGrid Installation manager is available here](https://www.youtube.com/watch?v=8t0ZVPOjZZo) |
|
| 5 | +A [video tutorial of the SBGrid Installation manager is available here](https://www.youtube.com/watch?v=8t0ZVPOjZZo) |
|
| 6 | 6 | |
| 7 | 7 | <!-- TOC --> |
| 8 | - |
|
| 9 | 8 | - [SBGrid Installation Manager GUI Installation and Usage](#sbgrid-installation-manager-gui-installation-and-usage) |
| 10 | 9 | - [Requirements and recommendations](#requirements-and-recommendations) |
| 11 | 10 | - [Activation](#activation) |
| ... | ... | @@ -16,7 +15,6 @@ A [video tutorial of the new SBGrid Installation manager is available here](http |
| 16 | 15 | - [Installing, Upgrading and Removing software](#installing-upgrading-and-removing-software) |
| 17 | 16 | - [Docs and Contact Panes](#docs-and-contact-panes) |
| 18 | 17 | - [Using an HTTP proxy](#using-an-http-proxy) |
| 19 | - |
|
| 20 | 18 | <!-- /TOC --> |
| 21 | 19 | |
| 22 | 20 | ### Requirements and recommendations |
client_install_legacy.md
| ... | ... | @@ -1,3 +1,6 @@ |
| 1 | +# THIS PAGE IS DEPRECATED |
|
| 2 | + |
|
| 3 | +The information here is likey to be out of date. |
|
| 1 | 4 | ## SBGrid installation manager |
| 2 | 5 | |
| 3 | 6 | The SBGrid installation manager is available as command-line tool for macOS and Linux, and as a graphical application for macOS. The command-line and graphical versions are not mutually exclusive - they can be used interchangeably on mac. |
| ... | ... | @@ -11,19 +14,20 @@ For the graphical version, see below. |
| 11 | 14 | |
| 12 | 15 | Looking to get started with the SBGrid installation manager? First, set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/) |
| 13 | 16 | |
| 14 | -- [SBGrid installation manager](#sbgrid-installation-manager) |
|
| 15 | -- [Installation](#installation) |
|
| 16 | - - [Pre-installation](#pre-installation) |
|
| 17 | - - [Download, Installation and activation](#download-installation-and-activation) |
|
| 18 | - - [Installation on an external drive or USB key](#installation-on-an-external-drive-or-usb-key) |
|
| 19 | -- [Usage](#usage) |
|
| 20 | - - [General](#general) |
|
| 21 | - - [Example : Installing Albula](#example--installing-albula) |
|
| 22 | - - [Example : Removing Albula](#example--removing-albula) |
|
| 23 | - - [Version selection](#version-selection) |
|
| 24 | - - [Versions and the SBGrid environment](#versions-and-the-sbgrid-environment) |
|
| 25 | - - [Running the software](#running-the-software) |
|
| 26 | - - [Questions, Problems and Known Issues](#questions-problems-and-known-issues) |
|
| 17 | +- [THIS PAGE IS DEPRECATED](#this-page-is-deprecated) |
|
| 18 | + - [SBGrid installation manager](#sbgrid-installation-manager) |
|
| 19 | + - [Installation](#installation) |
|
| 20 | + - [Pre-installation](#pre-installation) |
|
| 21 | + - [Download, Installation and activation](#download-installation-and-activation) |
|
| 22 | + - [Installation on an external drive or USB key](#installation-on-an-external-drive-or-usb-key) |
|
| 23 | + - [Usage](#usage) |
|
| 24 | + - [General](#general) |
|
| 25 | + - [Example : Installing Albula](#example--installing-albula) |
|
| 26 | + - [Example : Removing Albula](#example--removing-albula) |
|
| 27 | + - [Version selection](#version-selection) |
|
| 28 | + - [Versions and the SBGrid environment](#versions-and-the-sbgrid-environment) |
|
| 29 | + - [Running the software](#running-the-software) |
|
| 30 | + - [Questions, Problems and Known Issues](#questions-problems-and-known-issues) |
|
| 27 | 31 | |
| 28 | 32 | ## Installation |
| 29 | 33 |
sbgrid-cli.md
| ... | ... | @@ -1,17 +1,26 @@ |
| 1 | 1 | ## SBGrid Installation Manager CLI Installation and Usage |
| 2 | 2 | |
| 3 | 3 | `sbgrid-cli` is a command line installation manager application for the SBGrid software collection. |
| 4 | -The SBGrid installation manager is available in graphical and command-line flavors for macOS and Linux. These can be interchanged for the same installation. You can [find the latest version on our **download** page](client_downloads). |
|
| 4 | +The SBGrid installation manager is available in graphical and command-line flavors for macOS and Linux. These can be interchanged for the same installation. |
|
| 5 | 5 | |
| 6 | +### Download |
|
| 7 | +You can [find all versions including GUI and CLI on our **download** page](client_downloads). |
|
| 8 | + |
|
| 9 | +**latest sbgrid-cli download** |
|
| 10 | +[sbgrid-cli for linux](https://sbgrid.org/download/latest/sbgrid-cli_latest-linux.tar.gz) |
|
| 11 | +[sbgrid-cli for macOS](https://sbgrid.org/download/latest/sbgrid-cli_latest-macos.tar.gz) |
|
| 12 | + |
|
| 13 | +### Usage |
|
| 6 | 14 | This page covers the usage of the installation manager graphical user interface (CLI). For usage information on the latest graphical interface (GUI), [see here](sbgrid-gui). |
| 7 | 15 | |
| 8 | 16 | The SBGrid installation manager requires an SBGrid Consortium user account. |
| 9 | 17 | Set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/) |
| 10 | 18 | |
| 11 | - |
|
| 12 | 19 | <!-- TOC --> |
| 13 | 20 | |
| 14 | 21 | - [SBGrid Installation Manager CLI Installation and Usage](#sbgrid-installation-manager-cli-installation-and-usage) |
| 22 | + - [Download](#download) |
|
| 23 | + - [Usage](#usage) |
|
| 15 | 24 | - [Requirements and recommendations](#requirements-and-recommendations) |
| 16 | 25 | - [Installation](#installation) |
| 17 | 26 | - [General Usage](#general-usage) |
sbgrid-cloudinstall.sh
| ... | ... | @@ -1,7 +1,7 @@ |
| 1 | 1 | #!/bin/bash |
| 2 | 2 | |
| 3 | 3 | #echo "Downloading sbgrid installation client" |
| 4 | -curl -LO https://sbgrid.org/wiki/downloads/sbgrid-1.0.695-Linux.tgz |
|
| 4 | +curl -LO https://sbgrid.org/downloads/latest/sbgrid-cli_linux.tar.gz |
|
| 5 | 5 | |
| 6 | 6 | # Echo "" |
| 7 | 7 | tar -zxvf sbgrid-1.0.695-Linux.tgz |
sharp.md
| ... | ... | @@ -1,5 +1,8 @@ |
| 1 | 1 | ## SBGrid Sharp server |
| 2 | 2 | |
| 3 | -Due to decreased user demand and security considerations, SBGrid no longer maintains a user-accessible server for Global Phasing's application Sharp/AutoSharp. We now include Sharp in the SBGrid programs collection and it can be accessed through the CCP4 interface. A license from Global Phasing is required and must be locally installed. |
|
| 3 | +Due to decreased user demand and increased security considerations, SBGrid no longer maintains a user-accessible server for Global Phasing's application Sharp/AutoSharp. We now include Sharp in the SBGrid programs collection and it can be accessed through the CCP4 interface. A license from Global Phasing is required and must be locally installed. |
|
| 4 | + |
|
| 5 | +Note that Global Phasing offers several Web-based applications for data processing. |
|
| 6 | +Those can be accesses here : [https://www.globalphasing.com/](https://www.globalphasing.com/) |
|
| 4 | 7 | |
| 5 | 8 | For more information see [here](https://sbgrid.org/software/titles/sharpautosharp). Documentation for using Sharp can be found [here](http://www.globalphasing.com/sharp/manual/) |