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KryoEM / AAProject

Accelerate and automate the RELION 2.0 workflow
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Create template Relion submission script #35

Closed darthweider closed 7 years ago

darthweider commented 7 years ago

Template submission script should be OpenMPI compatible and export a CUDA-8.0 environment.

See: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install#Set-up_queue_job_submission especially this example script: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Manual_machinefile_script_example

The Biowulf submission script to sbatch: /usr/local/apps/RELION2.0/2.0.1/relion_sbatch.sh

kuybeda commented 7 years ago

As discussed, this script will set the environment first, then call the actual program.

Maybe, it would be a good idea first to source /etc/profile.d from this script as well. This will avoid the need to change global /etc/bashrc for setting environment for non-interactive shells.

If sourcing /etc/profile.d doesn't work, because there are unrelated scripts that interfere with our project, all our script might be moved to a separate location in /etc/aaproject.d and sourced from there

darthweider commented 7 years ago

See #41 and #45

kuybeda commented 7 years ago

Is resolved by adding "bash -l " to each relion command.