_Sidebar.md
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@@ -4,12 +4,10 @@ Installing Software
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* [Installation: Overview](installation_overview)
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* [Downloads](downloads)
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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 Installer](client_CLI_install)
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* [Available Packages](https://biogrids.org/software/)
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-* [R Packages](r_packages)
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Using the BioGrids Environment
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* [Getting Started with BioGrids](getting_started)
catalina.md
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@@ -15,7 +15,7 @@ First, [download](downloads) the latest Installation Manager.
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You can use *curl* to download the tarball directly in your terminal.
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This approach has the added benefit of not triggering the macOS "unidentified developer" Gatekeeper response which requires the *xattr* step below.
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```
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-curl -LO https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/biogrids-cli_2.4.5-macos.tar.gz
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+curl -LO https://biogrids-installation-manager.s3.amazonaws.com/2.4.8/biogrids-cli_2.4.8-macos.tar.gz
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```
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Untar and run the application to test.
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Untar :
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```
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-tar -zxf biogrids-cli_2.4.5-macos.tar.gz
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+tar -zxf biogrids-cli_2.4.8-macos.tar.gz
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```
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then run :
client_CLI_install.md
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@@ -6,11 +6,7 @@ This page is for the BioGrids CLI (command line interface) software installation
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- BioGrids Installation Manager - Downloads
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- [Requirements](https://biogrids.org/wiki/client_downloads#requirements)
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- - [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)
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-
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-
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-
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-
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+ - [Installation Manager Downloads](https://biogrids.org/wiki/downloads)
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Step 1 : [BioGrids registration](https://biogrids.org/registration/register/)
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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.
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-The latest version of the command line interface BioGrids Installation Manager, v2.4.0, is now available for Linux and MacOS computers:
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-
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-
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-Linux : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-linux.tar.gz)
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-
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-macOS : [biogrids-cli-2.4.0](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/biogrids-cli_2.4.0-macos.tar.gz)
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+The latest versions of the BioGrids Installation Manager are available on the [downloads page](https://biogrids.org/wiki/downloads)
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```
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-$ tar zxf ./wbiogrids-cli_2.4.0-macos.tar.gz
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+$ tar zxf ./wbiogrids-cli_2.4.8-macos.tar.gz
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$ ./biogrids-cli -h
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- BioGrids Installer 2.4.0 01da16b7bf —
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+ BioGrids Installer 2.4.8 01da16b7bf —
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_______ _____ _ __
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/ __/ _ )/ ___/___(_)__/ /
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_\ \/ _ / (_ / __/ / _ /
client_usage.md
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-## Using BioGrids Installer
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+## Using BioGrids Installation Manager
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**Download and activate here** : [Installation Instructions](client_install)
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### General
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-The BioGrids Installer client is a GUI-based installer for the BioGrids software collection. Install software titles with just a few clicks.
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+The BioGrids Installation Manager is a GUI-based installer for the BioGrids software collection.
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- ![installed](images/client_install.png)
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+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.
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-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.
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+ ![installed](images/gui_client_installed.png)
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-Under Packages:
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-**Installed**: currently installed titles
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-**Updates**: updates available from BioGrids
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+List all available software title by clicking the "Programs" icon in the left panel.
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-**Pending**: pending installs and removals
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+See already installed titles by clicking the "Installed" icon.
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-**All**: Every available package
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-Below the Packages folders titles are grouped by primary scientific use to aid in exploring available software..
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-Clicking on a title shows details in the right panel.
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+### Example : Installing FastQC
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-![FastQC Main](images/fastqc_main.png)
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+Search for FastQC by typing in the Search box or click on the "Programs" icon and scroll to find it.
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-### Example : Installing FastQC
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-Search for FastQC by typing in the Search box or click on the All package list and scroll to find it.
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+Two versions are available. Click on the "+install" link to add that version for installation.
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-Check the box to select FastQC, then click the 'Apply Changes' button.
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-Notice the text turns green for pending installations.
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-![Install FastQC](images/client_apply2.png)
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+![Install FastQC](images/install_fastqc.png)
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-Click the Apply Changes button and FastQC will be installed.
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-Notice that a version of Java is also installed. FastQC depends on Java.
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-After installation is complete, click on the Installed list to see FastQC listed.
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+The software title is added to the "Tasks" list. To complete installation, click on the "Tasks" icon and then the "Apply all tasks" button.
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+After installation is complete, click on the Installed list to see FastQC listed.
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-### Example : Removing FastQC
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-In the Installed list, uncheck the box for FastQC. Notice the title turns red indicating it will be removed.
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-Click Apply Changes. FastQC will be removed.
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-![Remove FastQC](images/remove_fastqc.png)
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+![FastQC Installed](images/fastqc_installed.png)
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-### Version selection
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-Default versions are installed for each application.
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-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.
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-Multiple versions of a given title can be installed and are indicated in the main panel.
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+### Removing FastQC
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-![Version Selection](images/version_select.png)
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+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.
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### Versions and the BioGrids environment
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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*.
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-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.
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-**Version priority in the shell**
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- 1. *~/.sbgrid.conf*
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- 2. Installed Default version
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- 3. Latest installed release
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-You can open the configuration file by selecting the *"Edit Configuration File"* from the *"BioGrids Installer"* menu.
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-![Edit Configuration](images/edit_configuration.png)
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-This will open a text editor with a sample configuration file, or your *~/.sbgrid.conf* file if you have one already.
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+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.
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There is more info on how to do that here --> [BioGrids Version Overrides](versions)
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### Running the software
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-To run the software, you can click the "BioGrids Shell" button for an initialized bash shell.
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-You may also run the software from another terminal on your machine.
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To use the software at the terminal in bash, open a new terminal and run
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source /programs/biogrids.shrc
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source /programs/biogrids.cshrc
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### Questions, Problems and Known Issues
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-For questions or problems, the Help menu will direct to the BioGrids help page. Or just email *bugs@biogrids.org*.
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-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.
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+For questions or problems email *help@biogrids.org*.
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+If relevant, please include a screenshot of the GUI.
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**Known issues**
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getting_started.md
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For tcsh, in **~/.tcshrc** or **~/.cshrc**, add :
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if ( -e /programs/biogrids.cshrc) then
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- source /programs/biogrids.cshrc
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+ source /programs/biogrids.cshrc
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endif
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### 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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<div id="wiki-content">
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- <h1 class="pt-4">{{page_header}}</h1>
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<div class="breadcrumb">{{{breadcrumb}}}</div>
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