Home.md
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# BioGrids GUI Installation Manager
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-The latest version of the BioGrids Installation Manager, v2.4.0, is now available for Linux and MacOS computers. The GUI installation Manager will also install the CLI (command line interface) version:
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-
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-
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-Linux : [BioGrids_Installation_Manager-2.4.0.AppImage](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/BioGrids-installation-manager-2.4.0.AppImage)
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-
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-macOS : [BioGrids_Installation_Manager-2.4.0.dmg](https://biogrids-installation-manager.s3.amazonaws.com/2.4.0/BioGrids-installation-manager-2.4.0.dmg)
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-
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-
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-# BioGrids CLI Installation Manager
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-
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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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+[Download the BioGrids Installation Manager](downloads.md), GUI or CLI.
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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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-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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_Sidebar.md
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![BioGrids](images/BioGrids_small_logo.png) **[BioGrids Wiki](Home)**
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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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* [Software Help and Requests](help)
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* [Tutorials](tutorials)
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* [Workshops](workshops)
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-* [Preworkshop Setup](pre_workshop)
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Support for Site Administrators
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* [Preparing Workstations to run the Software](workstation_setup)
biogrids_sbgrid.md
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* [Download](downloads) the Installation Manager (IM)
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* Use your SBGrid Installation Manager credentials to launch.
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-* If you don't have an existing IM account [register for one](https://biogrids.org/registration/register/).
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-
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-https://biogrids.org/registration/register/
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+* If you don't have an existing IM account [register for one](https://biogrids.org/registration/register/)
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### Full site installations
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catalina.md
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Activation with our latest command-line install client is possible in 3 steps, but a reboot is required to add the '/programs' path.
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### 1. Download the client, biogrids-cli :
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-First, download the latest install client from here
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-
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-[biogrids-cli version 2.0.43](downloads/biogrids_cli_2.0.43_mac.tar.gz)
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+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.org/wiki/downloads/biogrids_cli_2.0.43_mac.tar.gz
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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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```
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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_2.0.43_mac.tar.gz
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+tar -zxf biogrids-cli_2.4.5-macos.tar.gz
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```
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then run :
client_install.md
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-## BioGrids installation client
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-
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-This page is for the BioGrids GUI installation client for Apple OSX computers running MacOSX v10.11 - 10.13.
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-
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-![](images/client_all.png)
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+## BioGrids Installation Manager
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Looking to get started with the BioGrids installation client? First, set up an account by registering here : [BioGrids registration](https://biogrids.org/registration/register/)
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**3. Hard Drive Space**
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Depending on what you install, ensure that you have enough free hard drive space on your machine.
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-**4. For large packages (R, Bioconductor), a wired connection is recommended.**
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+**4. For large packages a wired connection is recommended.**
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Some packages are quite large and can be slow to download, especially over WiFi.
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### Installation and activation
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-**1. Download the latest BioGrids installation client from here.**
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-
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- [Latest build : 1.0.695, 2020-05-31](downloads/Biogrids_Installer-1.0.695.dmg)
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+**1. Download the latest BioGrids installation client from [here](download).**
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**2. Mount the .dmg disk image on your Mac.** Copy the 'BioGrids 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.
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**3. Enter your site, user name, and key.** You should have received these by email.
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-![activation](images/client_activation.png)
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+![activation](images/gui_client_activate.png)
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On activation you will be prompted to provide admin credentials for your mac. This is to create the */opt/biogrids* directory and */programs* symlink.
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-![activation](images/client_permissions.png)
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-
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-During installation the application may need to restart. You will be prompted with a simple message and should select Restart application.
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-
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-![restart](images/client_restart.png)
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-
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**4. 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 BioGrids installation at */programs* or */opt/biogrids*. These should be removed. You may also be blocked from accessing BioGrids 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)
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-For help, email *bugs@biogrids.org.*
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+For help, email *help@biogrids.org.*
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### Installation on an external drive or USB key
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Currently the installer application installs the software tree in */opt/biogrids* 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/biogrids* to the desired installation point. This functionality is not yet included in the BioGrids application, but can be set up manually post-install with a symlink. First do an install (into */opt/biogrids*), then move it to the desired localtion. Then symlink to the new location from */opt/biogrids*.
downloads.md
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+# Downloads
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+## Version 2.4.5
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+
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+GUI
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+<hr/>
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+Linux : [BioGrids_Installation_Manager-2.4.5.AppImage](https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/BioGrids-installation-manager-2.4.5.AppImage)
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+macOS : [BioGrids_Installation_Manager-2.4.5.dmg](https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/BioGrids-installation-manager-2.4.5.dmg)
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+CLI
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+<hr/>
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+
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+Linux : [biogrids-cli-2.4.5](https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/biogrids-cli_2.4.5-linux.tar.gz)
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+macOS : [biogrids-cli-2.4.5](https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/biogrids-cli_2.4.5-macos.tar.gz)
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images/gui_client_activate.png
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installation_overview.md
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-[ GUI Installation Manager](client_install)
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+[ GUI Installation Manager](downloads)
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The BioGrids GUI Installation Manager client allows users to select the applications through a graphical client. This client also allows users to search for titles or browse all available titles.
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Installing the GUI Installation Manager also installs the CLI Installation Manager as a BioGrids application located under the /programs tree.
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-[CLI Installation Manager](client_CLI_install)
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+[CLI Installation Manager](downloads)
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The BioGrids CLI Installation Manager 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. This client can be made automatic or used in manual mode.
pre_workshop.md
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-## BioGrids Workshops
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-Before attending a workshop, register for a BioGrids account then download and activate the BioGrids Installer software.
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-### 1: Register for BioGrids
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-[![BioGrids Registration](images/BioGrids_Account_Registration.png)](https://biogrids.org/registration/register/)
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-### 2: Install BioGrids
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-
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-<table style="border: none;">
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-<tr style="border: none;">
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- <td style="border: none;">
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- <a href="downloads/Biogrids_Installer-1.0.694.dmg"><img src="images/biogrids_osx_gui_download.png" /></a>
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- </td>
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- <td style="border: none;">&nbsp;</td>
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- <td style="border: none;">
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- <a href="downloads/biogrids-1.0.694-Darwin.tgz"><img src="images/biogrids_osx_cli_download.png"/></a>
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- </td>
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- <td style="border: none;">&nbsp;</td>
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- <td style="border: none;">
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- <a href="downloads/biogrids-1.0.694-Linux.tgz"><img src="images/biogrids_linux_cli_download.png" /></a>
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- </td>
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-</tr>
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-</table>
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-
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-```
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-OSX CLI:
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-curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz
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-
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-Linux CLI:
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-curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz
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-```
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-### 3: Activate BioGrids
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-**CLI**
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-Substitute your sitename, user name and activation key:
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-./biogrids activate [site name] [user name] [activation key]
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-
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-Example:
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-```
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-./biogrids activate biogrid-production jvin1 70rYFBTDnr93VUklfbf1s3M4jdyC9bFVYHew==
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-```
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-**GUI**
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-Fill in the form when prompted upon first start of the BioGrids application.
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-
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-
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-
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- <style>
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- .blue {
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- color: blue;
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- font-weight: bold;
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- }
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- .bold {
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- }
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- </style>
tutorials.md
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As a simple example, here is the command to install samtools
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on your OS X based Mac:
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+`biogrids-cli install samtools`
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This same command can be used to install
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on an AWS EC2 instance. Here is a brief
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Get the BioGrids CLI installer
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```
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-wget https://biogrids.org/wiki/downloads/biogrids-1.0.695-Linux.tgz
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-tar zxf biogrids-1.0.695-Linux.tgz
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-cd biogrids-1.0.695-Linux
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+wget https://biogrids-installation-manager.s3.amazonaws.com/2.4.5/biogrids-cli_2.4.5-linux.tar.gz
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+tar zxf biogrids-cli_2.4.5-linux.tar.gz
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```
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Activate the installer
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```
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-./biogrids activate <your_site> <your_name> <your_key>
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+./biogrids-cli activate <your_site> <your_name> <your_key>
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```
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Install your tools
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```
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-./biogrids install samtools
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-./biogrids install trimmomatic
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+./biogrids-cli install tophat
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+./biogrids-cli install trimmomatic
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```
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Verify versions of installed tools:
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```
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-./biogrids installed
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Installed packages:
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samtools (1.5)
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tophat (2.1.1)
workshops.md
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Learn how to use the BioGrids Installer with practical science applications.
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-Before attending a workshop, register for a BioGrids account then download and activate the BioGrids Installer software --> [Preworkshop Setup](pre_workshop)
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### Upcoming Workshops
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Use the login you were assigned in class:
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https://sbgrid.signin.aws.amazon.com/console
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username: workshop21
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password: Biogrids_Workshop1
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