CVS to Subversion Conversion

CVS to Subversion Conversion Subversion CVS to Subversion Conversion

Rob Buels ran the conversion on September 15, 2009. The conversion finished around 12:45pm, Eastern US. See Subversion for how to access the new repository. We spent the rest of the day locking down CVS access (it is still there, but is read-only), and updating this website to refer to SVN instead of CVS.

Outstanding Issues

We do have a few unfinished items, and we expect a few bumps to pop up over the coming weeks. We’ll keep track of those problems here. Thus far we have identified 2 issues. If you find any more, please add them here, or email them to the GMOD Help Desk.

Issue Name Description Status
Commit Mailing Lists Several GMOD Mailing Lists exist that automatically sent out emails whenever a commit was made to a CVS project. Need to create new lists or modify existing ones to read from SVN instead. Work is under way. GBrowse, Schema, and Apollo have been set up.
GBrowse net installer The GBrowse net install program gets GBrowse from CVS. Needs to now get it from SVN Fixed in the STABLE branch


GMOD’s CVS source code repository will be converted to Subversion (SVN) on September 15, 2009. Rob Buels of Cornell / SGN has generously offered to to do this. The discussion leading up to this decision on the GMOD Developers mailing list.

If you are not a GMOD developer then this will, at most, change how you get pre-release copies of GMOD components. In the future you will do SVN checkouts instead of CVS checkouts. The doc on this web site will be updated to describe how to do this.

If you are a GMOD developer and your project is in GMOD’s CVS repository then this move will significantly affect you.

See SourceForge for a complete list of projects in GMOD CVS. This list is reproduced below. We have contacted all project developers to confirm what projects are still active. All projects will be moved to SVN, but any projects that are no longer active will be placed in a separate archive directory. This will significantly clean up the repository. See below for the future SVN status of each project.

Rob has created a preview version of the repository. Feel free to poke around. This version does not have any projects archived.

Rob will move the projects on September 15. Everyone with uncommitted code changes should commit them to CVS by 3am, Eastern US time, on September 15. Rob will notify folks once the move is complete. After September 15, all CVS checkouts you have should be removed and new checkouts made with SVN. We’ll provide doc on how to do this.

Please let Rob and Dave know if you have any questions.


Dave Clements and Rob Buels


All projects will be moved, but some will be taken out of the active repository and put in an attic, archive, or frozen_projects directory.

This table keeps track of our efforts to identify which of the many projects are still active.

Name Rev Age Last Touch Last Change Asked Response Action
apollo 8803 2 weeks gk_fan + Check to make sure a match has the hit sequence data in case of id …     Keep
argos 8808 5 years dongilbert v0.7 updates Asked Don, Josh Don said keep Keep
balloon-tooltips 8893 5 weeks sheldon_mckay Adding fall through for pre-existing mouseout event handlers. I hope this …     Keep
Bio-Graphics 9120 5 days anonymous This commit was manufactured by cvs2svn to create tag ‘release-1_981’.     Keep
blastGraphic 9133 3 years briano Correct POD Asked Shuai. Had 7 users in 2008 GMOD Community Survey. No response, but keep anyway b/c of users. Keep
bop 9168 4 years nomi Removing this old redundant BOP repository–BOP is now integrated into the … Ed, apollo list Didn’t address bop, but it’s empty with a comment that it has been moved inside Apollo. Archive
Bundle-GMOD 9177 12 days scottcain adding prereqs for DBIx::DBStag, since DBStag’s Makefile.PL doesn’t …     Keep
citrina 9289 4 years jogoodma Various minor bug fixes. Josh Goodman, citrina list Archive it Archive
cmap 692 2 weeks kycl4rk Commit. Asked Ken, CMap list about existing CVS and SVN and what we should do with them. Still under negotiation. The SVN CMap is for CMap 2, while the CVS CMap is CVS 1. These will probably become cmap1 and cma2 in SVN. Keep both
das2 9753 2 years allenday fix to allow 1-column EGR for mas5 call, p-value. still need to make this … Asked Allen Day, Brian O’Connor. Brian said this is done and can be archived. Archive
FlashGViewer 9877 12 months simont updating from laptop     Keep
gbrowse-adaptors 9921 5 days anonymous This commit was manufactured by cvs2svn to create tag ‘release-1_03’.     Keep
gbrowse-tag 9932 5 weeks idavies Updated links for use with login scripts Asked Ian Davies what the future of this is. Yep, it’s his tagging work, but no it won’t be merged by Sept 15 Keep
GBrowse_karyotype 9959 5 months sheldon_mckay Working on Bio::DB::SeqFeature::Store compatibility issues     Keep
gds 10023 5 years jogoodma Latest GDS jar with new sort function. Josh, don Josh said Archive it. Archive
genepages 10131 3 years anonymous This commit was manufactured by cvs2svn to create tag ‘r1’. Asked Josh, don Don said keep. Keep
Generic-Genome-Browser 13464 3 days idavies Better handling of same e-mail user creation, pre-global config     Keep
GenericGenePage 13488 7 months scottcain I think the newer xml schema spec calls for xs: not xsd:     Keep
genogrid 13513 14 months dongilbert genogrid v0.5 updates     Keep
gff-validator 13538 4 months zzgw changed according to latest pod     Keep
gmod 14270 6 years scottcain appended ggb_ to special make targets for gbrowse Asked Scott Scott said this can go away. It was an idea that was never realized. Don’t copy
gmod-home 14152 2 years scottcain pointing to cvs for diagrams in really old website Asked Scott   Archive
gmod-web 14261 5 years scottcain Looks good! Minor fixes, and tt2/custom/feature.tt2 is generated … Asked Allen and Brian Brian responded that the current version of GMODWeb is inside the Turnkey Subversion repository. Archive
goet 14326 7 years jmr39 *** empty log message *** Wrote to John Day-Richter No responses. Drop because of no updates in 7 years. Archive
GOView 14330 4 years anonymous This commit was manufactured by cvs2svn to create tag ‘start’. Asked Shuai. Had 1 user in 2008 survey. No response. Keep b/c of 1 user. Keep
graphbrowse 14349 5 years sletovsky fixed vertical_layout in new forms No idea where Stan is. Asked Ben F and Scott. Scott and Ben said archive it. Work never finished and never used. Archive
imdb 14374 6 years x-pan modified httpd.conf IMDB is already classified as unsupported   Archive
jalview 14452 8 years searle Removed the Jalview source which was mistakenly included with the … Asked Ed, Apollo community. Apollo has its own copy inside Apollo, and the Jalview project (which is quite active, didn’t even know about this copy. Archive
javaSean 14488 3 years smutniak *** empty log message *** Is already flagged as unsupported.   Archive
labdoc 14504 7 years allenday added install file Asked Brian O’Connor and Allen Day and Scott. No response, and no updates for 7 years. Archive
lucegene 14549 15 months dongilbert updates 08june     Keep
nbrowse 710 4 days mgibson handling clusters for khans cytoscape gaggle cluster data     Keep
org.bdgp 14587 4 years nomi ClassLoader?.getSystemClassLoader() doesn’t work from webstart. Need to use … Asked Ed, Apollo list. Apollo has its own copy inside. Chris M says definitive copy is at the GO web site. Archive
pubfetch 14818 4 years simont updated with new version changes Asked Simon, Danny. Pubfetch is already tagged as unsupported. Simon said Pubfetch is inactive and unsupported Archive
pubsearch 17657 4 years dyoo Added note about how our repository is now in Subversion under … Asked Simon, Danny   Keep
pubtrack 17780 4 years vnarayan binary Asked Simon, Danny. PubTrack has no presence on the GMOD web site. Simon said PubTrack is inactive and unsupported. Archive
RestGraph 17784 4 years anonymous This commit was manufactured by cvs2svn to create tag ‘start’. Asked Shuai. There were no users in 2008 survey. No response. No users. Archive.
sample_dbs 17792 3 years anonymous This commit was manufactured by cvs2svn to create tag ‘first’. Asked Scott, schema list. Scott said “sample_dbs is a good idea, but I don’t know that cvs/svn is the right way to do it. In any event, the one db that is in there can go away as it is old” Keep
schema 19460 3 days scottcain adding an option to execute sql after the load of GFF is complete (to, for …     Keep
standard-urls 19465 4 years dongilbert sample genome url soft from flybase Asked Don, Josh Don said keep Keep
SynBrowse 19469 4 years anonymous This commit was manufactured by cvs2svn to create tag ‘initial_import’.     Keep
tripal 695 11 days scottcain initial import of tripal     Keep
XML-XORT 19544 2 years briano Minor edits, correct POD     Keep