8428ee7683872fe2a83626437d7e79be2879825e
_Sidebar.md
... | ... | @@ -4,12 +4,10 @@ Installing Software |
4 | 4 | |
5 | 5 | * [Installation: Overview](installation_overview) |
6 | 6 | * [Downloads](downloads) |
7 | -* [Supported Operating Systems](operatingsystems) |
|
8 | 7 | * [Installation: 'Site' installation](installation_admin) |
9 | 8 | * [Installation: MacOS GUI](client_install) |
10 | 9 | * [Installation: CLI Installer](client_CLI_install) |
11 | 10 | * [Available Packages](https://biogrids.org/software/) |
12 | -* [R Packages](r_packages) |
|
13 | 11 | |
14 | 12 | Using the BioGrids Environment |
15 | 13 | * [Getting Started with BioGrids](getting_started) |
catalina.md
... | ... | @@ -15,7 +15,7 @@ First, [download](downloads) the latest Installation Manager. |
15 | 15 | You can use *curl* to download the tarball directly in your terminal. |
16 | 16 | This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the *xattr* step below. |
17 | 17 | ``` |
18 | -curl -LO https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/biogrids-cli_2.4.5-macos.tar.gz |
|
18 | +curl -LO https://biogrids-installation-manager.s3.amazonaws.com/2.4.8/biogrids-cli_2.4.8-macos.tar.gz |
|
19 | 19 | ``` |
20 | 20 | |
21 | 21 | |
... | ... | @@ -23,7 +23,7 @@ curl -LO https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/biogrids-c |
23 | 23 | Untar and run the application to test. |
24 | 24 | Untar : |
25 | 25 | ``` |
26 | -tar -zxf biogrids-cli_2.4.5-macos.tar.gz |
|
26 | +tar -zxf biogrids-cli_2.4.8-macos.tar.gz |
|
27 | 27 | ``` |
28 | 28 | |
29 | 29 | then run : |
client_CLI_install.md
... | ... | @@ -6,11 +6,7 @@ This page is for the BioGrids CLI (command line interface) software installation |
6 | 6 | |
7 | 7 | - BioGrids Installation Manager - Downloads |
8 | 8 | - [Requirements](https://biogrids.org/wiki/client_downloads#requirements) |
9 | - - [BioGrids Command-line Installation Manager for MacOS and Linux, v2.4.0](https://biogrids.org/wiki/client_downloads#biogrids-command-line-installation-manager-for-macos-and-linux-v240) |
|
10 | - |
|
11 | - |
|
12 | - |
|
13 | - |
|
9 | + - [Installation Manager Downloads](https://biogrids.org/wiki/downloads) |
|
14 | 10 | |
15 | 11 | Step 1 : [BioGrids registration](https://biogrids.org/registration/register/) |
16 | 12 | |
... | ... | @@ -34,20 +30,15 @@ Step 1 : [BioGrids registration](https://biogrids.org/registration/register/) |
34 | 30 | |
35 | 31 | There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location. |
36 | 32 | |
37 | -The latest version of the command line interface BioGrids Installation Manager, v2.4.0, is now available for Linux and MacOS computers: |
|
38 | - |
|
39 | - |
|
40 | -Linux : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-linux.tar.gz) |
|
41 | - |
|
42 | -macOS : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-macos.tar.gz) |
|
33 | +The latest versions of the BioGrids Installation Manager are available on the [downloads page](https://biogrids.org/wiki/downloads) |
|
43 | 34 | |
44 | 35 | |
45 | 36 | |
46 | 37 | ``` |
47 | -$ tar zxf ./wbiogrids-cli_2.4.0-macos.tar.gz |
|
38 | +$ tar zxf ./wbiogrids-cli_2.4.8-macos.tar.gz |
|
48 | 39 | $ ./biogrids-cli -h |
49 | 40 | |
50 | - BioGrids Installer 2.4.0 01da16b7bf — |
|
41 | + BioGrids Installer 2.4.8 01da16b7bf — |
|
51 | 42 | _______ _____ _ __ |
52 | 43 | / __/ _ )/ ___/___(_)__/ / |
53 | 44 | _\ \/ _ / (_ / __/ / _ / |
client_usage.md
... | ... | @@ -1,95 +1,65 @@ |
1 | -## Using BioGrids Installer |
|
1 | +## Using BioGrids Installation Manager |
|
2 | 2 | |
3 | 3 | |
4 | 4 | **Download and activate here** : [Installation Instructions](client_install) |
5 | 5 | |
6 | 6 | ### General |
7 | -The BioGrids Installer client is a GUI-based installer for the BioGrids software collection. Install software titles with just a few clicks. |
|
7 | +The BioGrids Installation Manager is a GUI-based installer for the BioGrids software collection. |
|
8 | 8 | |
9 | - ![installed](images/client_install.png) |
|
9 | +All install or remove operations in the Installation Manager are a two step process. First, we add a software title for installation or removal to the "Tasks" list, then carry out the tasks by clicking the "Apply all tasks" button. |
|
10 | 10 | |
11 | -The client GUI lists software titles in the left panel with folder icons under the Packages and BioGrids headings. These control the list of titles displayed in the center panel. |
|
11 | + ![installed](images/gui_client_installed.png) |
|
12 | 12 | |
13 | -Under Packages: |
|
14 | 13 | |
15 | -**Installed**: currently installed titles |
|
16 | 14 | |
17 | -**Updates**: updates available from BioGrids |
|
15 | +List all available software title by clicking the "Programs" icon in the left panel. |
|
18 | 16 | |
19 | -**Pending**: pending installs and removals |
|
17 | +See already installed titles by clicking the "Installed" icon. |
|
20 | 18 | |
21 | -**All**: Every available package |
|
22 | 19 | |
23 | -Below the Packages folders titles are grouped by primary scientific use to aid in exploring available software.. |
|
24 | 20 | |
25 | 21 | |
26 | -Clicking on a title shows details in the right panel. |
|
22 | +### Example : Installing FastQC |
|
27 | 23 | |
28 | -![FastQC Main](images/fastqc_main.png) |
|
24 | +Search for FastQC by typing in the Search box or click on the "Programs" icon and scroll to find it. |
|
29 | 25 | |
30 | 26 | |
31 | -### Example : Installing FastQC |
|
32 | 27 | |
33 | -Search for FastQC by typing in the Search box or click on the All package list and scroll to find it. |
|
28 | +Two versions are available. Click on the "+install" link to add that version for installation. |
|
34 | 29 | |
35 | 30 | |
36 | -Check the box to select FastQC, then click the 'Apply Changes' button. |
|
37 | 31 | |
38 | -Notice the text turns green for pending installations. |
|
39 | -![Install FastQC](images/client_apply2.png) |
|
32 | +![Install FastQC](images/install_fastqc.png) |
|
40 | 33 | |
41 | -Click the Apply Changes button and FastQC will be installed. |
|
42 | 34 | |
43 | -Notice that a version of Java is also installed. FastQC depends on Java. |
|
44 | 35 | |
45 | -After installation is complete, click on the Installed list to see FastQC listed. |
|
36 | +The software title is added to the "Tasks" list. To complete installation, click on the "Tasks" icon and then the "Apply all tasks" button. |
|
46 | 37 | |
38 | +After installation is complete, click on the Installed list to see FastQC listed. |
|
47 | 39 | |
48 | -### Example : Removing FastQC |
|
49 | 40 | |
50 | -In the Installed list, uncheck the box for FastQC. Notice the title turns red indicating it will be removed. |
|
51 | -Click Apply Changes. FastQC will be removed. |
|
52 | 41 | |
53 | -![Remove FastQC](images/remove_fastqc.png) |
|
42 | +![FastQC Installed](images/fastqc_installed.png) |
|
54 | 43 | |
55 | -### Version selection |
|
56 | 44 | |
57 | -Default versions are installed for each application. |
|
58 | 45 | |
59 | -To select a different version choose **"Show all package versions"** from the **"View"** menu. Then, in the bottom right, select a desired version with the check boxes. |
|
60 | 46 | |
61 | -Multiple versions of a given title can be installed and are indicated in the main panel. |
|
47 | +### Removing FastQC |
|
62 | 48 | |
63 | -![Version Selection](images/version_select.png) |
|
49 | +In the Installed list, click on the "Remove" link next to a title. This will add the remove task to the "Tasks" list. To compete removal, click on the "Tasks" icon and then "Apply all tasks" button. |
|
64 | 50 | |
65 | 51 | |
66 | 52 | |
67 | 53 | ### Versions and the BioGrids environment |
68 | 54 | If you have a single version of an application installed, explicit version selection in your environment will not be needed. In the case of multiple installed versions, the *BioGrids Default* version will be the version available at the terminal when installed, unless configured otherwise in *~/.sbgrid.conf*. |
69 | 55 | |
70 | -If you have multiple non-default versions installed, the *latest release* will be the 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 BioGrids environment. |
|
71 | - |
|
72 | -**Version priority in the shell** |
|
73 | - 1. *~/.sbgrid.conf* |
|
74 | - 2. Installed Default version |
|
75 | - 3. Latest installed release |
|
76 | - |
|
77 | -You can open the configuration file by selecting the *"Edit Configuration File"* from the *"BioGrids Installer"* menu. |
|
78 | - |
|
79 | -![Edit Configuration](images/edit_configuration.png) |
|
80 | - |
|
81 | -This will open a text editor with a sample configuration file, or your *~/.sbgrid.conf* file if you have one already. |
|
82 | - |
|
83 | - |
|
56 | +If you have multiple non-default versions installed, the *latest release* will be the 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 either set this explicitly in your *~/.sbgrid.conf* file as in the standard BioGrids environment or set an overrides version variable in the shell where you are running the application. |
|
84 | 57 | |
85 | 58 | There is more info on how to do that here --> [BioGrids Version Overrides](versions) |
86 | 59 | |
87 | 60 | |
88 | 61 | ### Running the software |
89 | 62 | |
90 | -To run the software, you can click the "BioGrids Shell" button for an initialized bash shell. |
|
91 | - |
|
92 | -You may also run the software from another terminal on your machine. |
|
93 | 63 | To use the software at the terminal in bash, open a new terminal and run |
94 | 64 | |
95 | 65 | source /programs/biogrids.shrc |
... | ... | @@ -99,8 +69,9 @@ or in tcsh |
99 | 69 | source /programs/biogrids.cshrc |
100 | 70 | |
101 | 71 | ### Questions, Problems and Known Issues |
102 | -For questions or problems, the Help menu will direct to the BioGrids help page. Or just email *bugs@biogrids.org*. |
|
103 | -If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/biogrids.log file with your report. |
|
72 | +For questions or problems email *help@biogrids.org*. |
|
73 | + |
|
74 | +If relevant, please include a screenshot of the GUI. |
|
104 | 75 | |
105 | 76 | **Known issues** |
106 | 77 |
getting_started.md
... | ... | @@ -29,7 +29,7 @@ For Bash, in **~/.bashrc**, add : |
29 | 29 | For tcsh, in **~/.tcshrc** or **~/.cshrc**, add : |
30 | 30 | |
31 | 31 | if ( -e /programs/biogrids.cshrc) then |
32 | - source /programs/biogrids.cshrc |
|
32 | + source /programs/biogrids.cshrc |
|
33 | 33 | endif |
34 | 34 | |
35 | 35 | ### Setting an alias |
images/fastqc_installed.png
images/gui_client_installed.png
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images/install_fastqc.png
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templates/wiki_content.mustache
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