admin_overrides.md
... ...
@@ -1,18 +1,22 @@
1
-====== Administrator Software Blacklist ======
2
-Site administrators can prevent the shell initialization files from configuring software on a host by creating an empty file at **/programs/local/conf/disabled-hosts/<hostname>**, where **<hostname>** is the output of the //hostname -s// command. This is useful for encouraging users not to run jobs on bastion hosts, file servers, etc.
1
+### Administrator Software Blacklist
2
+Site administrators can prevent the shell initialization files from configuring software on a host by creating an empty file at
3 3
4
-====== Administrator Software Version Overrides ======
4
+ **/programs/local/conf/disabled-hosts/<hostname>**
5
+
6
+where **<hostname>** is the output of the //hostname -s// command. This is useful for encouraging users not to run jobs on bastion hosts, file servers, etc.
7
+
8
+### Administrator Software Version Overrides
5 9
Most of the software titles installed in the SBGrid Suite have several versions available. Typically, we try to provide at least three versions of each software package, although very old or very new applications may have fewer versions.
6 10
7 11
There are two methods for site admins to configure version overrides using files placed in a **/programs/local/conf/** directory.
8 12
9
-===== Site-wide Version Overrides =====
13
+- Site-wide Version Overrides
10 14
A file named **site.conf** will be read when any SBGrid shell is initialized from the installation.
11 15
12
-===== Per-host Version Overrides =====
16
+- Per-host Version Overrides
13 17
A file named **<hostname.conf>**, where **<hostname>** is the output of the //hostname -s// command, will be read after the site.conf on the host matching that hostname.
14 18
15
-===== Precedence =====
19
+### Precedence
16 20
There are three files that will be examined for version overrides during shell initialization. In order from lowest to highest precedence:
17 21
18 22
* /programs/local/conf/site.conf
... ...
@@ -21,12 +25,10 @@ There are three files that will be examined for version overrides during shell i
21 25
22 26
The overrides are reported during shell initialization:
23 27
24
-<code>
28
+```
25 29
Configuration options in effect for this shell:
26 30
Variable Setting Configuration
27
- SPIDER_L 18.10 site
28
- CNS_L 1.21 machine
29
- CCP4_L 6.1.2 personal
30
-</code>
31
-
32
-See [[Usage::Versions#Overriding Default Versions|this page]] for details on the override syntax.
33 31
\ No newline at end of file
32
+ SPIDER_L 18.10 site
33
+ CNS_L 1.21 machine
34
+ CCP4_L 6.1.2 personal
35
+```
developers.md
... ...
@@ -1,43 +1,26 @@
1
-====== SBGrid Developer Support Program ======
1
+### SBGrid Developer Support Program
2 2
In an effort to show our appreciation for their hard work and to encourage the continuing development and support of cutting edge structural biology software, SBGrid offers a Developer Support Program featuring a wide array of benefits for structural biology software developers.
3 3
4
-\\
4
+### Developer Network
5
+We can provide access to a dedicated development and test network for software developers. As a developer of an SBGrid supported application, you can request an account on this network and use our infrastructure to build and test your application on a wide range of operating systems. Visit the [developer network page](resources) for more details.
5 6
6
-===== Developer Network =====
7
-We can provide access to a dedicated development and test network for software developers. As a developer of an SBGrid supported application, you can request an account on this network and use our infrastructure to build and test your application on a wide range of operating systems. Visit the [[developers::resources|developer network page]] for more details.
7
+### Support Letters
8
+When applying for grants or financial support please let us know! We can provide support letters on behalf of members of SBGrid Consortium. Letters would include details about our membership, number of computers that can access your software, operating systems used by our community, etc. Please use the [contact form](http://sbgrid.org/contact.php|contact) on the SBGrid website.
8 9
9
-\\
10
-
11
-===== Support Letters =====
12
-When applying for grants or financial support please let us know! We can provide support letters on behalf of members of SBGrid Consortium. Letters would include details about our membership, number of computers that can access your software, operating systems used by our community, etc. Please use the [[http://sbgrid.org/contact.php|contact form]] on the SBGrid website.
13
-
14
-\\
15
-
16
-===== Software Beta Testing =====
10
+### Software Beta Testing
17 11
You are welcome to use SBGrid laboratories to beta-test your software. Just let us know when the new beta is available, and we will install it for all participating laboratories or a limited subset that you choose.
18 12
19
-\\
20
-
21
-===== SBGrid Consortium Membership =====
13
+### SBGrid Consortium Membership
22 14
If your application is under active maintenance or development, your development group is entitled to free membership in the consortium. Letting us maintain your general structural biology software environment leaves you with more time to concentrate on your unique software contribution to the community.
23 15
24
-\\
25
-
26
-===== Annual Software Awards =====
16
+### Annual Software Awards
27 17
Members of SBGrid Consortium vote in an annual poll to select their favorite structural biology application. Paul Emsley was the winner of the first poll. He won a Macbook Air laptop for his application Coot.
28 18
29
-\\
30
-
31
-===== Stretch Your Resources =====
19
+### Stretch Your Resources
32 20
First level software support is provided by the SBGrid non-profit center at Harvard Medical School. All members of the consortium communicate with the service center for assistance with software installation, upgrades, and basic troubleshooting. For many of the mundane problems involving installation, operating system portability and environmental set up, SBGrid members will never need to contact you for support. Your expertise with the software be best utilized answering questions and working on problems that directly involve the science behind your application.
33 21
34
-\\
35
-
36
-===== Broad Exposure for Your Software =====
22
+### Broad Exposure for Your Software
37 23
More than 140 structural biology laboratories from 50 institutions in 11 countries participate in the Consortium including the labs of 25 HHMI investigators and 2 Nobel Prize winners. Deployment of your application can be customized to include only non-profit labs or broadened to include industry labs as well. Please visit the Consortium website for the full list of participating groups that can benefit from rapid access to your software. Please note that most SBGrid Consortium laboratories standardize on hardware and operating systems, which simplifies the installation and support process.
38 24
39
-\\
40
-
41
-===== Connect With Users =====
25
+### Connect With Users
42 26
Announcing a new version of your software? We can use webex to broadcast your presentation to all laboratories participating in our consortium. We can also disseminate information about your application to our community in our monthly newsletter. Visiting Boston? Please let us know because we'd love to schedule a seminar for members of our local structural biology community.
43
-
help.md
... ...
@@ -1,16 +1,16 @@
1
-====== Software Help ======
2
-===== Getting Software Help =====
1
+## Software Help
2
+### Getting Software Help
3 3
4
-If you are having a problem with software included in the SBGrid suite or think you've discovered an application bug, please use the [[http://sbgrid.org/bugs|SBGrid Software Bug Report]] to alert us to the problem. You can also email bugs@sbgrid.org with details on the problem, but the web form is the preferred method.
4
+If you are having a problem with software included in the SBGrid suite or think you've discovered an application bug, please use the [SBGrid](http://sbgrid.org/bugs) to alert us to the problem. You can also email bugs@sbgrid.org with details on the problem, but the web form is the preferred method.
5 5
6 6
If the problem with the software started after an update, you can configure your SBGrid environment to [[usage::versions|use an older version of the software]].
7 7
8
-===== New Software and Software Updates =====
9
-To request a new software package or an update to an existing package, please use the [[http://sbgrid.org/req|Software Update/Installation Request form]].
8
+### New Software and Software Updates
9
+To request a new software package or an update to an existing package, please use the [Software](http://sbgrid.org/req) Update/Installation Request form]].
10 10
11 11
We try to accommodate most requests for new software, but we do occasionally run into difficulties. Despite most of our software being free for academics, some developers insist that each lab download and install their own software. We are happy to provide developers with the list of SBGrid members that have access to their software, but that doesn't always satisfy their requirements.
12 12
13
-Even when things go smoothly, license requests and working out licensing details with developers can take some time, so please don't wait until the last minute before requesting software you anticipate you may need for your project.
13
+Even when things go smoothly, license requests and working out licensing details with developers can take some time, so please don't wait until the last minute before requesting software you anticipate you may need for your project.
14 14
15
-===== Newsletter =====
16
-SBGrid sends a monthly newsletter with information concerning software updates, upcoming webinars, talks and other items of interest to our community. The archive of previous newsletters is available online at the [[http://sbgrid.org/news/newsletters|SBGrid Newsletter Archive]].
17 15
\ No newline at end of file
16
+### Newsletter
17
+SBGrid sends a monthly newsletter with information concerning software updates, upcoming webinars, talks and other items of interest to our community. The archive of previous newsletters is available online at the [SBGrid Newsletter Archive](http://sbgrid.org/news/newsletters).
installation_admin.md
... ...
@@ -1,7 +1,9 @@
1
-======Managing Your Software Installation======
2
-====='sbgrid-admin' Utility=====
3
-The //sbgrid-admin// utility used to install the software has a few other uses. There is a download link in the initial site set up email, and it is included in the installation itself at ///programs/share/sbgrid/bin/sbgrid-admin//. It includes built-in help:
4
-<code>
1
+##Managing Your Software Installation
2
+
3
+### *sbgrid-admin* Utility
4
+The *sbgrid-admin* utility used to install the software has a few other uses. There is a download link in the initial site set up email, and it is included in the installation itself at */programs/share/sbgrid/bin/sbgrid-admin*. It includes built-in help:
5
+
6
+```
5 7
$ sbgrid-admin -h
6 8
sbgrid-admin: a tool for administering an SBGrid Software suite installation
7 9
... ...
@@ -15,34 +17,35 @@ Usage: sbgrid-admin [-chirstu]
15 17
-s Install the software branch for SGI IRIX.
16 18
-t Test the configuration file.
17 19
-u Force manual update of an existing installation.
18
-</code>
20
+```
21
+
22
+The most commonly used option is *sbgrid-admin -u* to force a manual update. This will synchronize your local installation with the SBGrid master installation hosted at Harvard Medical School.
19 23
20
-The most commonly used option is //sbgrid-admin -u// to force a manual update. This will synchronize your local installation with the SBGrid master installation hosted at Harvard Medical School.
24
+The SBGrid software configuration files use both static and dynamically generated files. The main shell initialization files, **/programs/sbgrid.cshrc** and **/programs/sbgrid.shrc** are static files, but the operating-system specific configurations are dynamically generated and customized for the packages available at your site. *sbgrid-admin -r* will regenerate the branch-specific configuration files should you accidentally delete or alter them.
21 25
22
-The SBGrid software configuration files use both static and dynamically generated files. The main shell initialization files, **/programs/sbgrid.cshrc** and **/programs/sbgrid.shrc** are static files, but the operating-system specific configurations are dynamically generated and customized for the packages available at your site. //sbgrid-admin -r// will regenerate the branch-specific configuration files should you accidentally delete or alter them.
26
+ Configuration Options
27
+The *sbgrid-admin* script has some additional configuration options to accommodate the installation requirements at different sites.
23 28
24
-===== Configuration Options =====
25
-The //sbgrid-admin// script has some additional configuration options to accommodate the installation requirements at different sites.
29
+The ~sbgrid/.sbgridrc configuration file for the *sbgrid-admin* script must contain a sitename and site key. All other configurations are optional.
26 30
27
-The ~sbgrid/.sbgridrc configuration file for the //sbgrid-admin// script must contain a sitename and site key. All other configurations are optional.
31
+Options take the form of *OPTION_NAME="setting"*.
28 32
29
-Options take the form of //OPTION_NAME="setting"//.
33
+| **Option** |** Example** | **Description** |
34
+|:------------- |:-------------:| :---------------|
35
+| SB_SITENAME | sbgrid-bene | The site name for your installation provided by SBGrid |
36
+| SB_SITEKEY | xyxyxyxyxyxyxy | The installation key for your site provided by SBGrid |
37
+| INSTALL_TARGET| /nfs/programs | The installation directory for the software |
38
+| RSYNC_ARGS | "%%--%%port 8080"| Advanced arguments to rsync. Can be used to workaround blocked rsync ports. |
39
+| HTTP_PROXY | host.name:port | Proxy hostname and port for use by rsync and curl |
40
+| POST_UPDATE_SCRIPT | /absolute/path/to/script|Optional script to be run after a successful software update |
41
+| CRON_SCHEDULE | 5 1 * * * | Set a custom cron schedule |
30 42
31
-|**Option**|**Example**|**Description**|
32
-|SB_SITENAME|sbgrid-bene|The site name for your installation provided by SBGrid|
33
-|SB_SITEKEY|xyxyxyxyxyxyxy|The installation key for your site provided by SBGrid|
34
-|INSTALL_TARGET|/nfs/programs|The installation directory for the software|
35
-|RSYNC_ARGS|"%%--%%port 8080"|Advanced arguments to rsync. Can be used to workaround blocked rsync ports.|
36
-|HTTP_PROXY|host.name:port|Proxy hostname and port for use by rsync and curl|
37
-|POST_UPDATE_SCRIPT|/absolute/path/to/script|Optional script to be run after a successful software update|
38
-|CRON_SCHEDULE|5 1 * * *|Set a custom cron schedule|
39
-\\
40 43
41
-===== Rsync Transaction Logging =====
44
+ Rsync Transaction Logging
42 45
If you want a date-stamped log of all rsync downloads, deletions and updates, you can add a line like this to the ~sbgrid/.sbgridrc file:
43 46
44
-<code>
47
+```
45 48
RSYNC_ARGS="--log-file=$HOME/logs/sbgrid-admin-`date +%Y%m%d`.log"
46
-</code>
49
+```
47 50
48
-This will create a date-stamped log file any time an actual change to the software tree happens. In general this should not be necessary, but for troubleshooting purposes it can be useful.
49 51
\ No newline at end of file
52
+This will create a date-stamped log file any time an actual change to the software tree happens. In general this should not be necessary, but for troubleshooting purposes it can be useful.