_Sidebar.md
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1 1
![SBGrid](images/sbgrid_small_logo.gif) **[SBGrid Wiki](Home)**
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-Support for Users
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-* [Getting Started with SBGrid](getting_started)
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-* [Software Help and Requests](help)
3
+Installing Software
4
+* [Installation: Overview](installation_overview)
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* [Supported Operating Systems](operatingsystems)
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+* [Installation: 'Site' installation](installation_admin)
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+* [Installation: MacOS GUI](client_install)
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+* [Installation: CLI](client_CLI_install)
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+
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+Using the SBGrid Environment
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+* [Getting Started with SBGrid](getting_started)
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* [Overriding Software Versions](versions)
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-* [Install SBGrid: MacOS GUI](client_install)
9
-* [Install SBGrid: CLI](client_CLI_install)
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-* [SBGrid SHARP server](sharp)
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+* [SBGrid environment: Capsules](capsules)
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+* [SBGrid environment: Legacy](monolithic)
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+
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+Getting Help
17
+* [Software Help and Requests](help)
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12 19
Support for Site Administrators
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-* [Software Installation](installation_admin)
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* [Preparing Workstations to run the Software](workstation_setup)
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* [Managing your Installation](managing_install)
16 22
* [Administrator Software Version Overrides](admin_overrides)
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@@ -21,9 +27,10 @@ Support for Developers
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* [Build and Test Network](resources)
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23 29
Hardware Support Notes
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-* [GPU computing](gpu)
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* [SBGrid Recommended Hardware](recommended)
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+* [GPU computing](gpu)
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* [Setup Stereo 3D](stereo)
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-WSMR
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+Portals
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* [Data Processing After WSMR](wsmr-worked)
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+* [SBGrid SHARP server](sharp)
admin_overrides.md
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## Site Administrator Overrides
2 2
3
+SBGrid installations allow site-level software control for Administrators
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+
3 5
### Software Blacklist
4 6
Site administrators can prevent the shell initialization files from configuring software on a host by creating an empty file at
5 7
client_CLI_install.md
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-## SBGrid installation client CLI
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+## SBGrid package mangager installation client
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-This page is for the SBGrid CLI (command line interface) software installation client for computers running Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.
3
+The SBGrid software stack can be installed using our CLI (command line interface) installation client for [Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.](operatingsystems)
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-Looking to get started with the SBGrid installation client? First, set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/)
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-
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-A GUI version is also available for MacOS / OSX - [installation instructions can be found here](client_install).
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-[GUI usage info is here](client_usage).
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+The SBGrid installation client requires an individual account. To get started, first, set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/)
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10 7
### Pre-installation requirements
11 8
... ...
@@ -30,7 +27,7 @@ A GUI version is also available for MacOS / OSX - [installation instructions can
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$ sudo easy_install pip
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-###pip - Linux Installation
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+### pip - Linux Installation
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35 32
On CentOS6, you can install pip from the EPEL repository (yum -y install python-pip) or as [per these directions](https://pip.pypa.io/en/stable/installing/)
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... ...
@@ -120,9 +117,7 @@ Now we have */Volumes/sbgrid_client_install/sbgrid*. Create a symlink from */opt
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The symlink at */programs* still points to */opt/sbgrid*, and that is a link that points to the external location. Open the installer and add the desired applications. These will now install to the external drive.
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-[SBGrid install client -- Usage info](client_usage)
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-
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-### Known issues
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+### Some known issues
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* **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
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client_CLI_usage.md
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## SBGrid installation client - Usage
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-This page is for the SBGrid CLI software installation client for computers running Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.
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-
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-A GUI version is also available for mac - [installation instructions can be found here](client_install).
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-[GUI usage info is here](client_usage).
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-
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-**Make sure you have installed the SBGrid software installation client according to the instructions here** --> [Installation Instructions](client_CLI_install).
3
+**Instructions for installation of the SBGrid software installation client can be found here** --> [Installation Instructions](client_CLI_install).
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10 5
All SBGrid software is run from the the terminal.
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For information on how to run software from the SBGrid collection and configure your shell, check the [getting started page.](getting_started).
client_beta_CLI_install.md
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-## SBGrid installation client - beta
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-
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-Thanks for registering for our SBGrid installation client beta trial.
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-
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-This page is for the SBGrid CLI (command line interface) software installation client for computers running Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.
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-
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-A GUI version is also available for MacOS / OSX - [installation instructions can be found here](client_beta_install).
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-[GUI usage info is here](client_beta_usage).
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-
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-### Pre-installation requirements
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-
12
-**Admin access required.**
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- The SBGrid installation client will install the software tree to /opt/sbgrid and create a symlink from this directory to /programs. While admin privileges are not required to run the application, you will need admin privileges to create /opt/sbgrid and /programs .
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-
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-**Existing SBGrid installations must be renamed or removed.**
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- If you have previously installed SBGrid software on your computer at /programs or at /opt/sbgrid, these directories should be removed or renamed. The client will create these on first run.
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-
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-**Hard Drive Space**
19
- Depending on what you install, ensure you have enough free hard drive space on your machine.
20
-
21
-**For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended.**
22
- Some packages are quite large and can be slow to download, especially over WiFi.
23
-
24
-**pip**
25
- pip is a package management system used to install and manage software packages written in Python. The software installation client is installable by pip. This may not be on you machine by default, instructions for adding it are included here.
26
-
27
-### pip - Mac Installation
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-
29
- On mac, pip is available from [macports](https://www.macports.org/), [homebrew](http://brew.sh/), and [fink](http://finkproject.org/). It also can be added using **easy_install**. easy_install will install pip into your system python.
30
-
31
- $ sudo easy_install pip
32
-
33
-###pip - Linux Installation
34
-
35
- On CentOS6, you can install pip from the EPEL repository (yum -y install python-pip) or as [per these directions](https://pip.pypa.io/en/stable/installing/)
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-
37
-## CLI client - Installation and activation
38
-**1. Download the latest SBGrid installation client from here.**
39
-
40
- [--> SBGrid CLI client download <-- ](downloads/SBGrid_Installer-1.0b2.dev412-py2.py3-none-any.whl)
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-
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-**2. Install / Upgrade with pip**
43
-
44
- $ sudo pip install SBGrid_Installer-1.0b2.dev412-py2.py3-none-any.whl
45
-
46
- Which should produce output similar to :
47
-
48
-```
49
-Unpacking ./SBGrid_Installer-1.0b2.dev412-py2.py3-none-any.whl
50
-Requirement already satisfied (use --upgrade to upgrade): pyasn1 in /nfs/programs-dev/i386-mac/python/2.7.5/lib/python2.7/site-packages (from SBGrid-Installer==1.0b2.dev412)
51
-Downloading/unpacking requests (from SBGrid-Installer==1.0b2.dev412)
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- Downloading requests-2.11.1.tar.gz (485kB): 485kB downloaded
53
- Running setup.py egg_info for package requests
54
-
55
- warning: no files found matching 'test_requests.py'
56
-Installing collected packages: SBGrid-Installer, requests
57
- Running setup.py install for requests
58
-
59
- warning: no files found matching 'test_requests.py'
60
-Successfully installed SBGrid-Installer requests
61
-Cleaning up...
62
-```
63
-
64
-The *sbgrid* command will produce this usage info :
65
-
66
- $ sbgrid
67
-
68
-```
69
-usage:
70
-sbgrid <command> [<command_args>]
71
-
72
-Available commands are:
73
- activate Activate new installation
74
- list List available packages
75
- info Print package metadata
76
- install Install single package
77
- install-all Install all packages from collection
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- installed List installed packages
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- remove Remove installed package
80
- resume Resume interrupted installations
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- upgrades List available upgrades for installed packages
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- upgrade Upgrade package to latest version
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- upgrade-all Upgrade all packages to latest version
84
- version Print package version string
85
-sbgrid: error: too few arguments
86
-
87
-```
88
-
89
-**4. Activate the installation**
90
-Enter your site and key which you should have received these by email. This key will expire at the end of the trial.
91
-
92
- $ sbgrid activate <site name> <user name> <activation key>
93
-
94
-You may be prompted for your sudo password to create /programs and /opt/sbgrid.
95
-
96
-**5. On successful activation, list software titles.**
97
-
98
- $ sbgrid list
99
-
100
- If activation continues to fail, you may have an old SBGrid installation at /programs or /opt/sbgrid. These should be removed.
101
-
102
-You may also be blocked from accessing SBGrid 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)
103
-
104
-For help, email *bugs@sbgrid.org.*
105
-
106
-### Installation on an external drive or USB key
107
-Currently the installer application installs the software tree in /opt/sbgrid and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be anywhere. This functionality is not yet included in the SBGrid application, but can be set up manually with a symlink.
108
-
109
-An installation can be made on an external drive if you first do an install (into /opt/sbgrid), then move it and symlink to the new location.
110
-
111
-**Example:** 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the SSDs that come in Mac laptops. To install on an external drive like this, mount it on your computer. For this example, the mount is */Volumes/sbgrid_client_install*. Then, using the SBGrid installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.
112
-
113
-Next move */opt/sbgrid* to the USB key at */Volumes/sbgrid_client_install*. You will likely need sudo for this.
114
-
115
- $ sudo mv /opt/sbgrid /Volumes/sbgrid_client_install/.
116
-
117
-Now we have */Volumes/sbgrid_client_install/sbgrid*. Create a symlink from */opt/sbgrid* to */Volumes/sbgrid_client_install/sbgrid*.
118
-
119
- $ sudo ln -s /Volumes/sbgrid_client_install/sbgrid /opt/sbgrid
120
-
121
-The symlink at */programs* still points to */opt/sbgrid*, and that is a link that points to the external location. Open the installer and add the desired applications. These will now install to the external drive.
122
-
123
-[SBGrid install client -- Usage info](client_beta_usage)
124
-
125
-### Known issues
126
-
127
-* **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
128
-
129
-* **Activation Failed**. In some cases the Authorization dialog for admin privileges does not appear during activation. This causes the client activation to fail. This is usually due to a previously existing /programs directory or symlink from a prior installation. This must be removed for activation to be successful. Other users have reported successful activation after a restart.
client_beta_CLI_usage.md
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1
-## SBGrid installation client beta - Usage
2
-
3
-Thanks for registering for our SBGrid installation client beta trial.
4
-This page is for the SBGrid CLI software installation client for computers running Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.
5
-
6
-A GUI version is also available for mac - [installation instructions can be found here](client_beta_install).
7
-[GUI usage info is here](client_beta_usage).
8
-
9
-**Make sure you have installed the SBGrid software installation client according to the instructions here** --> [Installation Instructions](client_beta_CLI_install). Only BSD, GPL, and "Free for Academic Use" Software is currently available in this release.
10
-
11
-### General
12
-The SBGrid software installation client is a command line-based installer for the SBGrid software collection. The application allows for selected applications to be installed in the familiar SBGrid environment.
13
-
14
-The client displays software 'Collections' as a list.
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-
16
- $ sbgrid list
17
-
18
-```
19
-Crystallography
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- 3dna
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- adxv
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- albula
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- autoproc
24
- ...
25
-
26
-NMR
27
- aqua
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- aria
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- cara
30
- ccpnmr
31
- ccpnmr-chembuild
32
- ...
33
-
34
-Electron Microscopy
35
- 2dx
36
- ace2
37
- auto3dem
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- bfactor
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- bsoft
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- burnham-brandeis-helical-package
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- chimera
42
- ...
43
-
44
-Structure Visualization & Analysis
45
- 3dna
46
- anaconda
47
- apbs
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- aqua
49
- bobscript
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- caver
51
- caver-analyst
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- ccp4mg
53
- chimera
54
- ...
55
-
56
-Computational Chemistry
57
- ambertools
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- apbs
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- appion
60
- autodock
61
- autodock-vina
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- avogadro
63
- concoord
64
- dock
65
- gromacs
66
- ...
67
-
68
-Other
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- a2ps
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- abyss
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- aline
72
- amigos-ii
73
- amps
74
- assemble2
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- bamtools
76
- ...
77
-```
78
-
79
-Information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command.
80
-
81
-### Example : Installing Albula
82
-
83
- $ sbgrid info albula
84
-
85
-```
86
-Package: ALBULA
87
-Name slug: albula
88
-
89
-Available versions:
90
-* 3.2.0-2 (default)
91
-* 3.1.0-13
92
-* 3.0.0-14
93
-* 2.2.12
94
-
95
-Collection(s): Crystallography
96
-
97
-Description:
98
- consists of the standalone program ALBULA VIEWER, a fast and easy-to-
99
-use program that allows optimal visualization of PILATUS and EIGER data,
100
-and ALBULA API, a Python programming interface for displaying images and
101
-performing operations and calculations. The API enables you to easily
102
-integrate the viewer functionality into your beamline infrastructure or
103
-experimental setup.
104
-
105
-Links:
106
-* Website: https://www.dectris.com/Albula_Overview.html
107
-```
108
-
109
-To install:
110
-
111
- $ sbgrid install albula
112
-
113
-```
114
-Installing: albula
115
-Updating installation configuration...
116
-Installation was successfull!
117
-```
118
-
119
-To get started, load the SBGrid environment :
120
-
121
- $ source /programs/sbgrid.shrc
122
-
123
-```
124
- Software Support by SBGrid (www.sbgrid.org)
125
-********************************************************************************
126
-
127
-...
128
-
129
-SBGrid installation last updated: 2016-10-21
130
-Please submit bug reports and help requests to: <bugs@sbgrid.org> or
131
- <http://sbgrid.org/bugs>
132
-********************************************************************************
133
-```
134
-
135
-### Example : Removing Albula
136
-
137
- $ sbgrid remove albula
138
-
139
-results in :
140
-
141
-```
142
-Removing: albula
143
-Updating installation configuration...
144
-Package removed!
145
-```
146
-
147
-### Version selection
148
-
149
-Default versions are installed by default for each application, though individual versions can be selected for each title.
150
-
151
-To do so, include the version after the title followed the version. To see what versions are available, use the *sbgrid info <title>* command. Let;s us the title epmr as an example here:
152
-
153
- $ sbgrid info epmr
154
-
155
-```
156
-Package: EPMR
157
-Name slug: epmr
158
-
159
-Available versions:
160
-* 16.04 (default)
161
-* 16.01
162
-* 15.12
163
-* 15.04
164
-* 13.07
165
-* 11.02
166
-
167
-Collection(s): Crystallography
168
-
169
-Description:
170
- a program that finds crystallographic molecular replacement solutions
171
-using an evolutionary search algorithm. The program directly optimizes
172
-three rotational and three positional parameters for the search model with
173
-respect to the correlation coefficient between Fo and Fc.
174
-
175
-Links:
176
-* Website: http://www.epmr.info/
177
-* Manual: http://www.epmr.info/UsersGuide.html
178
-```
179
-
180
-To install version 11.02, add the version string like so:
181
-
182
- $ sbgrid install epmr 11.02
183
-
184
-which will produce :
185
-
186
-```
187
-Installing: epmr (11.02)
188
-Updating installation configuration...
189
-Installation was successfull!
190
-key@key-mbp [20161021-21:05:56] ~/Downloads
191
-```
192
-
193
-Check which versions are installed with the sbgrid info command again
194
-
195
- $ sbgrid info epmr
196
-
197
-```
198
-epPackage: EPMR
199
-Name slug: epmr
200
-
201
-Available versions:
202
-* 16.04 (default)
203
-* 16.01
204
-* 15.12
205
-* 15.04
206
-* 13.07
207
-* 11.02 (installed)
208
-
209
-...
210
-
211
-```
212
-
213
-Confirm with the *sbwhich* command
214
-
215
-
216
- $ sbwhich epmr
217
-```
218
-/programs/i386-mac/epmr/11.02/epmr
219
-```
220
-
221
-Reload the sbgrid shell to use the new version ( or set the environment variable EPMR_M=11.02 ).
222
-
223
-### Software Versions Management in the SBGrid environment
224
-If you have a single version of an application installed, explicit version selection in your environment is not needed.
225
-
226
-In the case of multiple installed versions, the *SBGrid Default* version will be the version available at the terminal when it is installed, unless configured otherwise in *~/.sbgrid.conf*.
227
-
228
-In the case of 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 an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file. This is the same as in the standard SBGrid environment.
229
-
230
-**Version priority in the shell**
231
- 1. *~/.sbgrid.conf*
232
- 2. Installed single version
233
- 3. Installed Default version
234
- 4. Latest installed release
235
-
236
-There is more info on how to do that here --> [SBGrid version overrides](versions)
237
-
238
-### Running SBGrid software
239
-
240
-To use the software at the terminal in bash, open a new terminal and run
241
-
242
- $ source /programs/sbgrid.shrc
243
-
244
-or in tcsh
245
-
246
- $ source /programs/sbgrid.cshrc
247
-
248
-### Questions, Problems and Known Issues
249
-For questions or problems, the Help menu will direct to the SBGrid help page. Or just email *bugs@sbgrid.org*.
250
-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.
251
-
252
-**Known issues**
253
-
254
-* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
255
-
256
-* 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_beta_install.md
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1
-## SBGrid installation client - beta
2
-
3
-Thanks for registering for our SBGrid installation client beta trial.
4
-
5
-This page is for the SBGrid GUI installation client for Apple OSX computers running MacOSX v10.9 - 10.12 .
6
-A command line version is also available for mac and linux - [installation instuctions can be found here](client_beta_CLI_install).
7
-[Command line usage info is here](client_beta_CLI_usage).
8
-
9
-### Pre-installation
10
-
11
-**1. Admin access required.**
12
- The SBGrid installation client will install the software tree to /opt/sbgrid and create a symlink from this directory to /programs. While admin privileges are not required to run the application, you will need admin privileges to create /opt/sbgrid and /programs .
13
-
14
-**2. Existing installations must be renamed or removed.**
15
- If you have previously installed SBGrid software on your computer at /programs or at /opt/sbgrid, these directories should be removed or renamed. The client will create these on first run.
16
-
17
-**3. Ctrl-click or Allow Applications from 'Anywhere'.**
18
- While the SBGrid installer will eventually be signed with the appropriate Apple developer's certificate, the beta builds are not. To run these, you need to give MacOSX's GateKeeper permission to run the application. You can either 'Ctrl-click' the icon and select 'Open' and then approve the application (see below), or permit your Mac to run applications from Anywhere in Preferences. You can do this under 'Preferences' -> 'Security and Privacy'. You may need admin privileges to change this setting.
19
-
20
- ![GateKeeper](images/gatekeeper.png)
21
-
22
-**4. Hard Drive Space**
23
- Depending on what you install, ensure you have enough free hard drive space on your machine.
24
-
25
-**5. For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended.**
26
- Some packages are quite large and can be slow to download, especially over WiFi.
27
-
28
-### Installation and activation
29
-
30
-**1. Download the latest SBGrid installation client from here.**
31
-
32
- [--> SBGrid MacOSX client download <-- ](downloads/SBGrid_Installer-21c46a9.dmg)
33
-
34
- This client may be updated throughout the beta trial.
35
-
36
-**2. Mount the .dmg disk image on your Mac.** Copy the 'SBGrid installer.app' to a convenient location - it does not need to be in /Applications. The .app bundle can be run directly from the mounted dmg image with no installation if desired.
37
-
38
-**3. Run the SBGrid installer application. You may need to ctrl-click (or right-click) and select 'Open' to satisfy GateKeeper settings.**
39
-
40
-![ctrl-click](images/ctrl-click.png)
41
-![ctrl-click](images/client_permit.png)
42
-
43
-**4. Enter your site, user name, and key.** You should have received these by email.
44
-This key will expire at the end of the trial.
45
-
46
-![activation](images/client_activation.png)
47
-
48
-On activation you will be prompted to provide admin credentials for your mac. This is to create the /opt/sbgrid directory and /programs symlink.
49
-
50
-![activation](images/client_permissions.png)
51
-
52
-**5. On successful activation, you should see the client populate with software titles.** If not, please close the application and try again. If activation continues to fail, you may have an old SBGrid installation at /programs or /opt/sbgrid. These should be removed. You may also be blocked from accessing SBGrid 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)
53
-For help, email *bugs@sbgrid.org.*
54
-
55
-### Installation on an external drive or USB key
56
-Currently the installer application installs the software tree in /opt/sbgrid and uses a symlink at /programs. The /programs link is required for the software to work, but in principle the software can be anywhere by linking /opt/sbgrid to the desired installation point. This functionality is not yet included in the SBGrid application, but can be set up manually post-install with a symlink. First do an install (into /opt/sbgrid), then move it to the desired localtion. Then symlink to the new location from /opt/sbgrid.
57
-
58
-**Example:** 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the small SSDs that come in Mac laptops. To install on an external drive in this way, first mount it on your computer. For this example, the mount is */Volumes/sbgrid_client_install*. Then, using the SBGrid installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.
59
-
60
-Next move */opt/sbgrid* to the USB key at */Volumes/sbgrid_client_install*. You will likely need sudo for this.
61
-
62
- sudo mv /opt/sbgrid /Volumes/sbgrid_client_install/.
63
-
64
-Now we have */Volumes/sbgrid_client_install/sbgrid*. Create a symlink from */opt/sbgrid* to */Volumes/sbgrid_client_install/sbgrid*.
65
-
66
- sudo ln -s /Volumes/sbgrid_client_install/sbgrid /opt/sbgrid
67
-
68
-The symlink at */programs* still points to */opt/sbgrid*, and that is a link that points to the external location. Open the installer and add the desired applications. These will now install to the external drive.
69
-
70
-[SBGrid install client -- Usage info](client_beta_usage)
71
-
72
-### Known issues
73
-
74
-* **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
75
-
76
-* **Activation Failed**. In some cases the Authorization dialog for admin privileges does not appear during activation. This causes the client activation to fail. This is usually due to a previously existing /programs directory or symlink from a prior installation. This must be removed for activation to be successful. Other users have reported successful activation after a restart.
client_beta_usage.md
... ...
@@ -1,88 +0,0 @@
1
-## SBGrid installation client beta - Usage
2
-
3
-Thanks for registering for our SBGrid installation client beta trial.
4
-
5
-This trial is currently only for Apple OSX computers running MacOSX v10.9 - 10.12.
6
-Only BSD, GPL, and "Free for Academic Use" Software is currently available in this release.
7
-
8
-**Make sure you have installed the SBGrid software installation client according to the instructions here** --> [Installation Instructions](client_beta_install)
9
-
10
-### General
11
-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.
12
-
13
- ![installed](images/client_install.png)
14
-
15
-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.
16
-
17
-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.
18
-
19
-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.
20
-
21
-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.
22
-
23
-### Example : Installing Albula
24
-Check the box to select Albula, then click the 'Apply Changes' button.
25
-Notice the text turns green for pending installations. Pending updates are Orange.
26
-![apply](images/client_apply2.png)
27
-
28
-### Example : Removing Albula
29
-Uncheck the box for Albula. Removals are shown in red text.
30
-![apply](images/client_remove1.png)
31
-
32
-Click apply changes. Albula will be removed.
33
-![apply](images/client_remove2.png)
34
-
35
-### Version selection
36
-
37
-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.
38
-
39
-Enable version panel
40
-![all](images/client_versions1.png)
41
-
42
-Check old/non-default versions
43
-![all](images/client_versions2.png)
44
-
45
-
46
-### Versions and the SBGrid environment
47
-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*.
48
-
49
-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.
50
-
51
-**Version priority in the shell**
52
- 1. *~/.sbgrid.conf*
53
- 2. Installed Default version
54
- 3. Latest installed release
55
-
56
-You can do open the configuration file by selecting the *"Edit Configuration File"* from the *"SBGrid Installer"* menu.
57
-
58
-![all](images/client_config1.png)
59
-
60
-This will open a text editor with a sample configuration file, or your *~/.sbgrid.conf* file if you have one already.
61
-
62
-![all](images/client_config2.png)
63
-
64
-There is more info on how to do that here --> [SBGrid version overrides](versions)
65
-
66
-
67
-### Running the software
68
-
69
-To run the software, you can click the "SBGrid Shell" button for an initialized bash shell.
70
-
71
-You may also run the software from another terminal on your machine.
72
-To use the software at the terminal in bash, open a new terminal and run
73
-
74
- source /programs/sbgrid.shrc
75
-
76
-or in tcsh
77
-
78
- source /programs/sbgrid.cshrc
79
-
80
-### Questions, Problems and Known Issues
81
-For questions or problems, the Help menu will direct to the SBGrid help page. Or just email *bugs@sbgrid.org*.
82
-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.
83
-
84
-**Known issues**
85
-
86
-* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
87
-
88
-* 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_install.md
... ...
@@ -1,12 +1,12 @@
1 1
## SBGrid installation client
2 2
3
-This page is for the SBGrid GUI installation client for Apple OSX computers running MacOSX v10.9 - 10.12 .
3
+The SBGrid softare collection can be installed using our graphical installation client for Apple OSX computers running MacOSX v10.9 - 10.12 .
4 4
5 5
![](images/client_all.png)
6 6
7 7
Looking to get started with the SBGrid installation client? First, set up an account by registering here : [SBGrid registration](https://sbgrid.org/registration/register/)
8 8
9
-A command line version is also available for mac and linux - installation instuctions can be found here : [CLI installation](client_CLI_install).
9
+A command line version is also available for mac and linux - installation instructions can be found here : [CLI installation](client_CLI_install).
10 10
11 11
Usage info for the GUI and command line clients can be found here : [GUI Usage](client_usage) and here : [CLI usage](client_CLI_usage) respectively.
12 12
client_usage.md
... ...
@@ -1,8 +1,6 @@
1 1
## SBGrid installation client - Usage
2 2
3
-This software is currently only for Apple OSX computers running MacOSX v10.9 - 10.12.
4
-
5
-**Make sure you have installed the SBGrid software installation client according to the instructions here** --> [Installation Instructions](client_install)
3
+**Instructions for installing the SBGrid software installation client can be found here** --> [Installation Instructions](client_install)
6 4
7 5
### General
8 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.
d117_mr01_hl.mtz
... ...
Binary files a/d117_mr01_hl.mtz and /dev/null differ
installation_overview.md
... ...
@@ -0,0 +1,18 @@
1
+## The SBGrid software stack : Overview
2
+
3
+The SBGrid Software Suite contains 400+ Scientific software applications for [Linux and OS X](operatingsystems).
4
+
5
+The software can be installed using one of 3 methods:
6
+
7
+[Site installation : A script-based installation that includes the complete software collection for Linux and/or MacOS.](installation_admin)
8
+* This is ideal for large labs, shared and departmental installations that use a shared network file storage for their programs. The installation is updated automatically on a monthly basis. [This installation is large and can take some time to install.](size_graph)
9
+
10
+[Graphical installation for MacOS](client_install)
11
+
12
+ * The MacOS GUI installation client allows users to select the applications they need when they need them through a MacOS-native graphical client. Applications are updated on a rolling basis and are available to the user at their convenience. Updates are reported to be available, but are managed by the user.
13
+
14
+
15
+[Command line installation using the SBGrid package mangager for Linux and MacOS ](client_CLI_install)
16
+* 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.
17
+
18
+Member labs may use any/all of the installation types above for as many Computers as they require. 
monolithic.md
... ...
@@ -0,0 +1,14 @@
1
+# SBGrid software environment
2
+## Overview
3
+
4
+The SBGrid 'Monolithic' software environment provides access to all installed packages using standard shell PATH with minimal required dependencies. [Standard system libraries should be sufficient to run all applications.](workstation_setup) The environment includes added features for users to manage their software version selection.
5
+
6
+
7
+You can switch between the legacy SBGrid environment and the new [capsule](capsules) environment with the *sbcap* command. *sbcap on* will enable the capsule environment.
8
+You can always return to the legacy configuration with the *sbcap off* command.
9
+
10
+The sbcap setting is persistent across shells - You don't need to do this for every shell.
11
+
12
+[Version Overrides](overrides) can be configured using the sbgrid-overide or by editing .sbgrid.conf. Duplicate executables in path must be handled explicitly by the user. See [here](capsules).
13
+
14
+Please report any bugs to bugs@sbgrid.org
sbgrid-phenix2016-data.md
... ...
@@ -1,86 +0,0 @@
1
-## SBGrid PHENIX 2016
2
-
3
-Looking forward to seeing you at PHENIX 2016.
4
-
5
-## Software
6
-We will be using PHENIX during the workshop but
7
-you may also want to install PyMOL, CCP4 (includes COOT), and any other tools you prefer to use.
8
-https://sbgrid.org/wiki/client_install
9
-
10
-## Reference Datasets
11
-We have assembled a set of reference data for discussion during workshop.
12
-
13
-You can download the data as a tarball here :
14
-**[Workshop2016Datasets.tar.bz2](downloads/Workshop2016Datasets.tar.bz2)** - 37.5Mb
15
-
16
-or
17
-
18
-**[Workshop2016Datasets.zip](downloads/Workshop2016Datasets.zip)** - 37.5Mb
19
-
20
-### Directory names
21
- - **kd** : processing results from Kay Diederichs
22
- - **sbdb** : automated data reduction results
23
- - **_PDB CODE_.fasta** : sequence file from RCSB
24
-
25
-See Archive directory structure below.
26
-
27
-Images are not necessary but can be downloaded from the SBDB with:
28
-
29
- rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/<dataset number> .
30
-
31
-### Dataset info
32
-Each dataset includes a readme.txt file with a description.
33
-
34
-**Dataset #3** : [X-Ray Diffraction data from Lin28/let-7d microRNA complex, source of 3TRZ structure](https://data.sbgrid.org/dataset/3/), Zn-SAD dataset
35
-
36
-**Dataset #97** : [X-Ray Diffraction data from Thermoanaerobacter tengcongensis SONO (H-NOX) in complex with dioxygen, source of 1XBN structure](https://data.sbgrid.org/dataset/97/), MAD dataset collected at the iron edge
37
-
38
-**Dataset #111** : [X-Ray Diffraction data from 'Spinach' RNA-chromophore complex, source of 4TS0 structure](https://data.sbgrid.org/dataset/111/)
39
-
40
-**Dataset #123** : [X-Ray Diffraction data from HSV-2 gH/gL complex, source of 3M1C structure](https://data.sbgrid.org/dataset/123/), A selenomethionine single-wavelength anomalous diffraction dataset
41
-
42
-### Archive directory structure
43
-
44
-```
45
-├── 111
46
-│   ├── 4TSO.fasta
47
-│   ├── kd
48
-│   │   ├── CORRECT.LP
49
-│   │   ├── XDS_ASCII.HKL
50
-│   │   └── XDS.INP
51
-│   ├── readme.txt
52
-│   └── sbdb
53
-│   ├── proc-0.mtz
54
-│   ├── proc-1.mtz
55
-│   ├── proc-2.mtz
56
-│   └── proc-3.mtz
57
-├── 123
58
-│   ├── 3M1C.fasta
59
-│   ├── kd
60
-│   │   ├── CORRECT.LP
61
-│   │   ├── XDS_ASCII.HKL
62
-│   │   └── XDS.INP
63
-│   ├── readme.txt
64
-│   └── sbdb
65
-│   ├── proc-0.mtz
66
-│   ├── proc-1.mtz
67
-│   ├── proc-2.mtz
68
-│   └── proc-3.mtz
69
-├── 3
70
-│   ├── 3TRZ.fasta
71
-│   ├── kd
72
-│   │   ├── CORRECT.LP
73
-│   │   ├── XDS_ASCII.HKL
74
-│   │   └── XDS.INP
75
-│   ├── readme.txt
76
-│   └── sbdb
77
-│   ├── proc-1.mtz
78
-│   ├── proc-2.mtz
79
-│   └── proc-3.mtz
80
-└── 97
81
- ├── 1XBN.fasta
82
- ├── readme.txt
83
- └── sbdb
84
- ├── proc-1.mtz
85
- └── proc-2.mtz
86
-```
sbgrid-qv2016
... ...
@@ -1,147 +0,0 @@
1
-#!/bin/bash
2
-
3
-USAGE="$(basename $0): a tool for installing software for SBGRID QuoVadis 2016
4
-
5
-Usage: $(basename $0) [-hi]
6
-
7
-General Options:
8
- -h This message.
9
- -i Install the software suite on this machine.
10
-"
11
-
12
-# Getopts loop
13
-while getopts "hi" Option
14
-do
15
- case $Option in
16
- h) echo "$USAGE"
17
- exit 0;;
18
- i) export INSTALL=true;;
19
- *) echo "$USAGE"
20
- exit 1;;
21
- esac
22
-done
23
-shift $(($OPTIND - 1))
24
-
25
-printf " -- SBGrid Quo Vadis 2016 -- \n"
26
-printf "\n"
27
-printf "This script will install: \n"
28
-printf " - CCP4\n"
29
-printf " - DIALS\n"
30
-printf " - XDS and XDSGUI \n"
31
-printf "with the SBGrid environment\n"
32
-printf "\n"
33
-printf "This script uses rsync to download the software from SBGrid Servers.\n"
34
-printf "This download may take a while depending on your connection speed,\n"
35
-printf "but interupted transfers will be resumed when the script is re-run. \n"
36
-printf "Exit at any time with a CTRL-c.\n\n"
37
-printf "\n"
38
-
39
-printf "This script will install software in $HOME/programs and requires ~8.5 Gb of disk space.\n"
40
-printf "Ready for installation? (y/N) \n"
41
- read ready
42
- case "$ready" in
43
- n|N) printf " No installation - Exiting\n\n"
44
- exit 0
45
- ;;
46
- y|Y) printf " Installing software\n\n"
47
- ;;
48
- *) printf "Please enter Y or N \n"
49
- printf " No installation - Exiting\n\n"
50
- exit 0
51
- ;;
52
- esac
53
-
54
-printf "Be sure to create a symlink to $HOME/programs after the script completes.\n"
55
-printf "\n"
56
-
57
-SB_SITENAME=sbgrid-qv2016
58
-SB_SITEKEY=yEMxe5hjZ7rT3Qz0WOw1vstx4CkqrDFh9FjmOg==
59
-
60
-export USER=$SB_SITENAME
61
-export RSYNC_PASSWORD=$SB_SITEKEY
62
-
63
-sync_server=sync2.sbgrid.org
64
-target=$HOME
65
-unset ARCH
66
-
67
- # Figure out the system type
68
- if [ "$(uname)" = "Linux" ]; then
69
- if [ $(uname -m) = x86_64 ]; then
70
- osname=linux64
71
- ARCH='x86_64-linux'
72
- else
73
- osname=linux32
74
- printf "32-bit linux is not supported byt this script \n"
75
- printf "exiting ...\n"
76
- exit 0
77
- fi
78
- elif [ "$(uname)" = "Darwin" ]; then # OS X found
79
- if [ "$(uname -m)" = "i386" ] || [ "$(uname -m)" = "x86_64" ]; then # OS X Intel
80
- osname=osx86
81
- ARCH='i386-mac'
82
- else # OS X PowerPC
83
- osname=osxppc
84
- printf "PPC is not supported byt this script \n"
85
- printf "exiting ...\n"
86
- exit 0
87
- fi
88
- osxminorver=$(sw_vers | grep ProductVersion | awk '{print $2}')
89
- osxver=$(echo $osxminorver | awk -F. '{print $1"."$2}')
90
- else
91
- osname=unknown
92
- printf "This OS is not supported byt this script \n"
93
- printf "exiting ...\n"
94
- exit 0
95
- fi
96
-
97
-## test connectivity
98
-rsync rsync://$sync_server/sbgrid-test/test/OK >& /dev/null
99
-if [ $? -ne 0 ]; then
100
- printf "Connectivity test failed!\n"
101
- printf "Error reaching $sync_server on port 873.\n"
102
- printf "This is a fatal error. exiting ...\n"
103
- exit 0
104
-fi
105
-
106
-## bootstrap rsync
107
-mkdir -p $target/programs/$ARCH/system
108
-mkdir -p $target/programs/share/sbgrid
109
-mkdir -p $target/programs/share/bin
110
-rsync -aq rsync://${sync_server}/${SB_SITENAME}/main/programs/$ARCH/system/rsync ${target}/programs/$ARCH/system/
111
-
112
-if [ $? -ne 0 ] ; then
113
- printf "Error bootstrapping a modern rsync binary.\n"
114
- printf "This is a fatal error. exiting ..."
115
- exit 0
116
-fi
117
-
118
-rsync -aq rsync://${sync_server}/${SB_SITENAME}/main/programs/$ARCH/system/curl ${target}/programs/$ARCH/system/
119
-
120
-#get software
121
-$target/programs/$ARCH/system/rsync/current/bin/rsync -zrlptODP --progress rsync://$sync_server/sbgrid-qv2016/sites/sbgrid-qv2016/*rc $target/programs
122
-$target/programs/$ARCH/system/rsync/current/bin/rsync -zrlptODP --progress rsync://$sync_server/sbgrid-qv2016/sites/sbgrid-qv2016/share/bin/*** $target/programs/share/bin
123
-$target/programs/$ARCH/system/rsync/current/bin/rsync -zrlptODP --progress rsync://$sync_server/sbgrid-qv2016/sites/sbgrid-qv2016/share/sbgrid/*** $target/programs/share/sbgrid
124
-$target/programs/$ARCH/system/rsync/current/bin/rsync -zrlptODP --progress rsync://$sync_server/sbgrid-qv2016/sites/sbgrid-qv2016/$ARCH/*** $target/programs/$ARCH
125
-
126
-printf "\n"
127
-printf "Be sure to create a symlink to $HOME/programs after this script completes with this command:\n"
128
-printf "\n"
129
-printf " ln -s $HOME/programs /programs \n"
130
-printf "\n"
131
-printf "This will likely require sudo/admin priveleges and cannot be completed by the script.\n"
132
-printf "\n"
133
-printf "\n"
134
-
135
-#Build environment
136
-$target/programs/share/sbgrid/bin/createrc -f -t $target/programs
137
-if [ $? -eq 21 ] ; then
138
- printf " Environment created successfully\n\n"
139
- printf " Source /programs/sbgrid.shrc (bash) or /programs/sbgrid.cshrc (tcsh) to get started !\n\n"
140
-fi
141
-
142
-if [ ! -L /programs ] ; then
143
- printf "A symlink to $HOME/programs is required. \n"
144
- printf 'Run "sudo ln -s $HOME/programs /programs" \n'
145
- printf "\n"
146
- printf "This command will require sudo/admin priveleges\n"
147
-fi
sbgrid-qv2016-installation.md
... ...
@@ -1,47 +0,0 @@
1
-## SBGrid Quo Vadis 2016
2
-
3
-Looking forward to seeing you next week for QuoVadis 2016.
4
-
5
-We will be using CCP4, COOT, DIALS, iMosflm, XDS, and XDSGUI during the workshop.
6
-The script below will install these applications on your mac or linux laptop.
7
-
8
-SBGrid builds on CentOS 6, though these applications should work on any modern Linux distro.
9
-For Mac, we support 10.9 and higher, but this subset will likely work on older macs as well.
10
-
11
-### Step 1. Download the script.
12
-
13
-[[download|sbgrid-qv2016]]
14
-
15
-### Step 2. Make the script execuatable
16
-
17
- chmod +x sbgrid-qv2016
18
-
19
-### Step 3. Run the script
20
-
21
- ./sbgrid-qv2016
22
-
23
-The script will use rsync to download the software to $HOME/programs. A symlink is required at / programs, the script will provide more info.
24
-
25
-### Step 4. Set up the environment
26
-
27
-For BASH users:
28
-
29
- source /programs/sbgrid.shrc
30
-
31
-For TCSH users:
32
-
33
- source /programs/sbgrid.cshrc
34
-
35
-
36
-Please report any issues to bugs@sbgrid.org, See you next week.
37
-
38
-
39
-## Intro to linux slides
40
-[[slides|QV2016-intro_to_linux.pdf]]
41
-
42
-## MTZ for for dataset 117
43
-[[117.mtz|d117_mr01_hl.mtz]]
44
-
45
-### Maps for COOT
46
-https://www.dropbox.com/sh/0s8kev2jxxxvp4g/AADHWTJ73Fszaah6BH9WM0yqa?dl=0
47
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