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Migration from Scipion 1.0 to 1.1

yaizar edited this page Jun 13, 2017 · 3 revisions

This page will guide users that are already using Scipion v1.0 or v1.0.1 to minimize the effort of migrating from version 1.0 to 1.1. There are different scenarios for the migration from the point of view of a sysadmin in charge of a central Scipion installation (later we will explain changes from a user point of view):

Installation from binaries

In this case the normal procedure is to download the compressed binaries here, extract them in a different location and run scipion config. You should then verify configuration files on $SCIPION_HOME/config/, in particular scipion.conf and hosts.conf, comparing them with the old ones.

Installation from source

Follow the same procedure as above and compile Scipion by running scipion install -j N (where N is the number of threads for compilation).

In both cases you also need to install the required EM packages, please run scipion install --help to see the list of available packages. If you wish to use already installed packages then you should create the appropriate symlinks taking into account that they should be named package-version (again, running scipion install --help can help with that).

Update using git

If your current Scipion was installed from the git repository you should follow the next steps: First update your code by doing git pull Then run scipion config --update to update Scipion configuration files. This will add new variables and give you some useful warning on possible changes or conflicts. A copy of your previous file will be kept on the backups directory. After you have reviewed and maybe changed the configuration files you can execute scipion install -j N. The last step is to upgrade existing EM packages to follow the new name convention (package-version). To facilitate this step there is a script, scripts/, that will create symbolic links with the correct naming.

Additional step for users

From the point of view of a user the only thing to do is running scipion config --update, which will update the user scipion.conf file. This will warn the user of existing changes and manual intervention on the file might be needed to adapt location of packages to the new name convention.

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