This repository contains a collection of files and scripts that will be useful in almost all cases of making a specialisation for cerise-mdstudio. It is built into Docker image mdstudio/cerise-mdstudio-base:.
To make a Cerise specialisation of the mdstudio project for machine mymachine, create a Docker image cerise-mdstudio-mymachine, starting from cerise-mdstudio-base, and adding the following files (paths relative to /home/cerise):
This file sets up the environment for running Gromacs. Note that it is not Gromacs' own gmxrc, but a cerise-mdstudio specific one. It should:
- Load any modules needed to run Gromacs
- Define the GMXRC_MDSTUDIO environment variable, containing the path to Gromacs' GMXRC.bash
This is the Cerise installation script. If you have it call $CERISE_PROJECT_FILES/install_base.sh, miniconda will be installed at $CERISE_PROJECT_FILES/miniconda, a Conda environment will be set up inside of it, and the necessary dependencies for running getEnergies.py will be installed.
The mdstudio/energies.cwl and mdstudio/decompose.cwl steps depend on this to work.
This is the Cerise machine configuration file, in which you specify how to connect to the machine, and how to run jobs on it. You can use api/config.yml in this repository as a starting point for yours.
This software is Copyright 2017-2018, VU University Amsterdam and Netherlands eScience Center.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.