Biogrids and HMSGrid installer update

+## BioGrids installation client CLI

+

+This page is for the BioGrids 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.

+

+Looking to get started with the BioGrids installation client? First, set up an account by registering here : [BioGrids registration](https://biogrids.org/registration/register)

+

+A GUI version is also available for MacOS / OSX - [installation instructions can be found here](client_install).

+[GUI usage info is here](client_usage).

+

+### Pre-installation requirements

+

+**Admin access required on your computer.**

+ The BioGrids installation client will install the software tree to /opt/hmsgrid 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/hmsgrid and /programs .

+

+**Existing BioGrids installations must be renamed or removed.**

+ If you have previously installed BioGrids software on your computer at /programs or at /opt/hmsgrid, these directories should be removed or renamed. The client will create these on first run.

+

+**Hard Drive Space**

+ Depending on what you install, ensure you have enough free hard drive space on your machine.

+

+**For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended.**

+ Some packages are quite large and can be slow to download, especially over WiFi.

+

+**pip**

+ 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.

+

+### pip - Mac Installation

+

+ 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.

+

+ $ sudo easy_install pip

+

+###pip - Linux Installation

+

+ 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/)

+

+## CLI client - Installation and activation

+**1. Download the latest BioGrids installation client from here.**

+

+[Latest build : 1.0.555, 2017-02-17](downloads/hmsgrid-1.0.555-py2-none-any.whl)

+

+**2. Install / Upgrade with pip**

+

+ $ sudo pip install HMS_Installer-1.0.555-py2-none-any.whl

+

+ Which should produce output similar to :

+

+```

+Unpacking ./BioGrids_Installer-1.0.555-py2-none-any.whl

+Requirement already satisfied (use --upgrade to upgrade): pyasn1 in /nfs/programs-dev/i386-mac/python/2.7.5/lib/python2.7/site-packages (from BioGrids-Installer==1.0.488)

+Downloading/unpacking requests (from BioGrids-Installer==1.0b2.dev412)

+ Downloading requests-2.11.1.tar.gz (485kB): 485kB downloaded

+ Running setup.py egg_info for package requests

+

+ warning: no files found matching 'test_requests.py'

+Installing collected packages: BioGrids-Installer, requests

+ Running setup.py install for requests

+

+ warning: no files found matching 'test_requests.py'

+Successfully installed BioGrids-Installer requests

+Cleaning up...

+```

+

+The *hmsgrid* command will produce this usage info :

+

+ $ hmsgrid

+

+```

+usage:

+hmsgrid <command> [<command_args>]

+

+Available commands are:

+ activate Activate new installation

+ list List available packages

+ info Print package metadata

+ install Install single package

+ install-all Install all packages from collection

+ installed List installed packages

+ remove Remove installed package

+ resume Resume interrupted installations

+ upgrades List available upgrades for installed packages

+ upgrade Upgrade package to latest version

+ upgrade-all Upgrade all packages to latest version

+ version Print package version string

+hmsgrid: error: too few arguments

+

+```

+

+**4. Activate the installation**

+Enter your site and key which you should have received these by email.

+

+ $ hmsgrid activate <site name> <user name> <activation key>

+

+You may be prompted for your sudo password to create /programs and /opt/hmsgrid.

+

+**5. On successful activation, list software titles.**

+

+ $ hmsgrid list

+

+ If activation continues to fail, you may have an old BioGrids installation at /programs or /opt/hmsgrid. 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)

+

+For help, email *bugs@sbgrid.org.*

+

+### Installation on an external drive or USB key

+Currently the installer application installs the software tree in /opt/hmsgrid and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/hmsgrid. This functionality is not yet included in the BioGrids application, but can be set up manually with a symlink.

+

+An installation can be made on an external drive if you first do an install (into /opt/hmsgrid), then move it and symlink to the new location.

+

+**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/hmsgrid_client_install*. Then, using the BioGrids installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.

+

+Next move */opt/hmsgrid* to the USB key at */Volumes/hmsgrid_client_install*. You will likely need sudo for this.

+

+ $ sudo mv /opt/hmsgrid /Volumes/hmsgrid_client_install/.

+

+Now we have */Volumes/hmsgrid_client_install/sbgrid*. Create a symlink from */opt/hmsgrid* to */Volumes/hmsgrid_client_install/sbgrid*.

+

+ $ sudo ln -s /Volumes/hmsgrid_client_install/sbgrid /opt/hmsgrid

+

+The symlink at */programs* still points to */opt/hmsgrid*, 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.

+

+[BioGrids install client -- Usage info](client_usage)

+

+### Known issues

+

+* **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.

+

+* **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.

+## BioGrids installation client

+

+This page is for the BioGrids GUI installation client for Apple OSX computers running MacOSX v10.9 - 10.12 .

+

+

+

+Looking to get started with the BioGrids installation client? First, set up an account by registering here : [BioGrids registration](https://sbgrid.org/registration/register/hms)

+

+A command line version is also available for mac and linux - installation instuctions can be found here : [CLI installation](HMSclient_CLI_install).

+

+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.

+

+### Pre-installation

+

+**1. Admin access required.**

+ The BioGrids installation client will install the software tree to */opt/hmsgrid* 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/hmsgrid* and */programs* .

+

+**2. Existing installations must be renamed or removed.**

+ If you have previously installed BioGrids software on your computer at */programs* or at */opt/hmsgrid*, these directories should be removed or renamed. The client will create these on first run.

+

+**3. Hard Drive Space**

+ Depending on what you install, ensure that you have enough free hard drive space on your machine.

+

+**4. For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended.**

+ Some packages are quite large and can be slow to download, especially over WiFi.

+

+### Installation and activation

+

+**1. Download the latest BioGrids installation client from here.**

+

+ [Latest build : 1.0.555, 2017-02-17](downloads/BioGrids_Installer-1.0.555.dmg)

+

+**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.

+

+**3. Enter your site, user name, and key.** You should have received these by email.

+

+

+

+On activation you will be prompted to provide admin credentials for your mac. This is to create the */opt/hmsgrid* directory and */programs* symlink.

+

+

+

+**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/hmsgrid*. 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)

+For help, email *bugs@sbgrid.org.*

+

+### Installation on an external drive or USB key

+Currently the installer application installs the software tree in */opt/hmsgrid* 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/hmsgrid* 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/hmsgrid*), then move it to the desired localtion. Then symlink to the new location from */opt/hmsgrid*.

+

+**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/hmsgrid_client_install*. Then, using the BioGrids installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.

+

+Next move **/opt/hmsgrid** to the USB key at */Volumes/hmsgrid_client_install*. You will likely need sudo for this.

+

+ sudo mv */opt/hmsgrid* /Volumes/hmsgrid_client_install/.

+

+Now we have */Volumes/hmsgrid_client_install/sbgrid*. Create a symlink from **/opt/hmsgrid** to */Volumes/hmsgrid_client_install/sbgrid*.

+

+ sudo ln -s /Volumes/hmsgrid_client_install/sbgrid */opt/hmsgrid*

+

+The symlink at **/programs** still points to **/opt/hmsgrid**, 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.

+

+[BioGrids install client -- Usage info](client_usage)

+

+### Known issues

+

+* **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.

+

+* **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.

+Looking to get started with the BioGrids installation client? First, set up an account by registering here : [BioGrids registration](https://biogrids.org/registration/register/)

+ The BioGrids installation client will install the software tree to /opt/biogrids 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/biogrids and /programs .

+ If you have previously installed BioGrids software on your computer at /programs or at /opt/biogrids, these directories should be removed or renamed. The client will create these on first run.

+[Latest build : 1.0.555, 2017-02-17](downloads/BioGrids_Installer-1.0.555-py2-none-any.whl)

+The *biogrids* command will produce this usage info :

+ $ biogrids

+biogrids <command> [<command_args>]

+You may be prompted for your sudo password to create /programs and /opt/biogrids.

+ $ biogrids list

+ If activation continues to fail, you may have an old BioGrids installation at /programs or /opt/biogrids. These should be removed.

+Currently the installer application installs the software tree in /opt/biogrids and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/biogrids. This functionality is not yet included in the BioGrids application, but can be set up manually with a symlink.

+An installation can be made on an external drive if you first do an install (into /opt/biogrids), then move it and symlink to the new location.

+**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/biogrids_client_install*. Then, using the BioGrids installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.

+Next move */opt/biogrids* to the USB key at */Volumes/biogrids_client_install*. You will likely need sudo for this.

+ $ sudo mv /opt/biogrids /Volumes/biogrids_client_install/.

+Now we have */Volumes/biogrids_client_install/sbgrid*. Create a symlink from */opt/biogrids* to */Volumes/biogrids_client_install/sbgrid*.

+ $ sudo ln -s /Volumes/biogrids_client_install/sbgrid /opt/biogrids

+The symlink at */programs* still points to */opt/biogrids*, 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.