Easy install: Download link for Linux and Mac OS X

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(Sorry - no Windows support at this moment)

Important: We are currently Alpha testing right now, so we appreciate any feedback that you might have regarding the instructions and execution of the code.


Instructions for Mac OSX:

Compatible Mac OSX versions: 10.12+

Incompatible Mac OSX versions: 10.9.5 (and older)

  1. Unzip file
  2. Navigate to unzipped file, and then execute by double clicking on icon OR via the command line:
    • $ ./install_cloud_tools_macOSX

Follow the instructions to include your AWS credentials into the text file indicated. These credentials are generated during AWS setup, more information here.

When installation script finishes, you will see the following message printed:

Installation complete! Software can be found in /Users/michael/CloudSoftwareTools
Only a few more steps to finish: 

1.) Please add the following line to the file /Users/michael/.bash_profile

source /Users/michael/CloudSoftwareTools/aws_init.sh

2.) Download AWS keypair and put it in a secure location (e.g. /Users/michael/CloudSoftwareTools/)

3.) Open and edit the file /Users/michael/CloudSoftwareTools/aws_init.sh

Place your information for AWS into the lines indicated: #INPUT REQUIRED

Instructions for Linux:

  1. Unzip file
  2. Navigate to unzipped file, and then execute by double clicking on icon OR via the command line:
    • $ ./install_cloud_tools_Linux

Follow the instructions to include your AWS credentials into the text file indicated. These credentials are generated during AWS setup, more information here.

When installation script finishes, you will see the following message printed:

Installation complete! Software can be found in /home/user/CloudSoftwareTools

Only a few more steps to finish: 

1.) Please add the following line to the file /home/ubuntu/.bashrc or /home/ubuntu/.cshrc

source /home/ubuntu/CloudSoftwareTools/aws_init.sh

2.) Download AWS keypair and put it in a secure location (e.g. /home/ubuntu/CloudSoftwareTools/)

3.) Open and edit the file /home/ubuntu/CloudSoftwareTools/aws_init.sh

Place your information for AWS into the lines indicated: #INPUT REQUIRED

4.) Install AWSCLI: $ pip install awscli

5.) Install Relion-2.0:

For Ubuntu:

$ sudo apt-get update

$ sudo apt-get install openmpi-bin build-essential libx11-dev libextutils-f77-perl libopenmpi-dev libcr-dev mpich mpich-doc build-essential git cmake libqt4-dev libphonon-dev python2.7-dev libxml2-dev libfltk-gl1.3 libfftw3-double3

$ git clone https://github.com/3dem/relion.git

$ cd relion/

$ mkdir build

$ cd build/

$ cmake -DCMAKE_INSTALL_PREFIX=/home/user/CloudSoftwareTools/cryoem-cloud-tools/external_software/relion-2.0-linux/ ..

$ make -j4

$ make install

NOTE: If you do not put Relion software into directory listed above, update the software environment paths in the file /home/user/CloudSoftwareTools/external_software.sh

Test that everything works

Type the following into your command line:

$ awsls

This should produce an output like this:

If you see any errors, such as /bin/sh: aws: command not found, the installation did not complete successfully.


Expert install: Manual installation

  1. Install the following software:
    • fabric
    • awscli
    • git
    • Relion-2.0
  2. Clone git repository:
    • https://github.com/cianfrocco-lab/cryoem-cloud-tools
  3. Edit file cryoem-cloud-tools/aws/aws_init.sh to include AWS credentials. Consider moving out of cryoem-cloud-tools folder so that it does not get over written when you update the git repo.
  4. Source aws_init.sh file in .bashrc / .bash_profile for user

For MacOSX users:

  • We compiled all python code into the directory aws_build_osx so that users do not need to install fabric (which sometimes can be a hassle)
  • If you use this library on your Mac, use file aws_aliases_osx.sh instead of aws_aliases.sh
  • This repo also comes with Relion-2.0 pre-compiled for Mac (see below)

External software included in repo:

  • AWS CLI:
    • We have included AWS CLI into the git repo that you can use by including cryoem-cloud-tools/external_software/aws in your $PATH and  cryoem-cloud-tools/external_software/aws/lib/python2.7/site-packages/ into your $PYTHONPATH
  • Relion-2.0:
    • We also included a compiled Relion-2.0 version compatible for Mac OSX that can be found in cryoem-cloud-tools/external_software/relion-2.0-mac