Svn migration to git

Migration of the ontology respository from svn to git

Motivation

After much discussion with Chris Mungall, it was decided to migrate all relevant files from the POC svn repo to a new planteome repository in [github http://github.com].

Not all files are needed to be moved. Most notably, the association files are too large to be hosted on github, so we are looking for a solution for this.

Also, ontology files besides the plant_ontology.obo file were stored in a collaborators_ontology folder. We decided to restructure the repo to make these at the same level

Dumping the svn repo

To keep the revision info for the files, we need to dump all of that from svn and then filter it out for the specific files we need to move to git.

On Palea

cd /data/svnrepos/Poc
svn admin dump . > /lemma/justin/Poc_svn_migration/Poc_svn_dump

This will dump all repo information including revision info and commit messages to a file named Poc_svn_dump. I stored this on lemma as the file is large (>25GB).

Filtering the dump

Note: the following was run on one of cluster compute nodes because I didn't want to swamp palea working on it.

I decided to test this out with trait.obo first as a proof of concept. Other files should be similar with changes to the include statement

cd /lemma/justin/Poc_svn_migration
cat Poc_svn_dump | svndumpfilter include trunk/ontology/collaborators_ontology/gramene/traits/trait.obo --drop-empty-revs --renumber-revs > trait.obo_filtered_dump

The

svndumpfilter

command will go through the dump file and only output revision info for trait.obo, in this case. The full path needs to be in the include argument, otherwise it output an empty repo. The other arguments will reset the revision numbers so that they start at 1 and have no empty revisions.