Setting everything up

Under development

Users:

Each user needs to have the appropriate permissions & keypair created for them.

• Keypair
• Access ID & Secret ID
• Access to EC2 & S3: IAM=AmazonEC2FullAccess & AmazonS3FullAccess

In the home directory of the user, create a directory:

/home/[user]/.aws/

Place * path to AWS code directory into .aws/aws_init.sh

Into this directory, place aws_init.sh.

Edit aws_init.sh to include:

• Absolute path to key pair

• Access & secret ID

• research group name

Installing relion on a mac:

• Install cmake: https://cmake.org/download/ --> cmake-3.8.0-rc1-Darwin-x86_64.dmg ; drag to Applications folder

• Install openmpi: https://wiki.helsinki.fi/display/HUGG/Open+MPI+install+on+Mac+OS+X

• Download link: http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.5.tar.gz

• untar file

• $ cd openmpi-1.6.5

• $ ./configure

• $ make all install

• A lot of text printed to screen

• Download relion from github

• $ cd relion/

• $ mkdir build

• $ cd build

• $ /Applications/CMake.app/Contents/bin/cmake ..

• $ make

Minimally set: export PATH={pathToRelionRepo}/build/bin:$PATH export LD_LIBRARY_PATH={pathToRelionRepo}/build/lib:$LD_LIBRARY_PATH

Install Fabric

• pip install --upgrade pip
• pip install fabric

For mac, replace rclone in AWS with http://downloads.rclone.org/rclone-v1.35-osx-amd64.zip