Do a fresh merge from master for genome.

[sakoht]

This will entail getting a bunch of new software related to workflow, nessy, and other things.

[malachig]

Known or expected sources of issues

• schema changes
• genome-snapshot-deps, stuff added to lucid but not precise
• workflow/ptero transition
• config of environment variables needed by GMS
• sometime missing tools that have not been packaged

[jasonwalker80]

Reposting here for @mkiwala-g "Nessy is the new locking service, and Ptero is the replacement for workflow. GMS is not dependent on either of these systems at this time, so merging in the latest master should not make sGMS dependent on these new systems."

[sakoht]

Ah interesting.

So "genome model build start" won't run into any problems in a world
without them?

I won't claim to understand, but glad if it's going to be that easy.

On Fri, Feb 20, 2015 at 9:02 AM, Jason Walker [email protected]
wrote:

Reposting here for @mkiwala-g https://github.com/mkiwala-g "Nessy is
the new locking service, and Ptero is the replacement for workflow. GMS is
not dependent on either of these systems at this time, so merging in the
latest master should not make sGMS dependent on these new systems."

—
Reply to this email directly or view it on GitHub
#160 (comment).

[sakoht]

The gms-pub branch now with has the latest master merged.

The changes were pretty minimal. I made gms-pub-before-plos-merge-from-master to track the pre-merge point for convenience.

I also merged the latest UR and tagged it as gms-pub-2015.02.22, but there are no actual differences with UR, so it effectively just puts on on the latest master, but it won't change.

Workflow is a little more weird. The latest master has Oracle passwords in it. I'm presuming Oracle isn't being used anymore, and that if it is these aren't real. Is the workflow repo that is actually used somewhere else now?

[sakoht]

I pushed up a new gms-pub branch for workflow. It keeps some of the changes I made from master from last time, but merges all other changes. The merge went well, so we'll see if it builds.

[malachig]

Since the sGMS installer, automatically pulls from gms-pub it seems likely that this might break the installer and various analyses in our example tutorials until we have a chance to work through all the unexpected issues/dependencies. In the past there were at least ~10 of these each time we did a merge after a while. I think in those cases we started by creating a gms-pub-merge branch for each repo, and then a gms repo that installed from these branches. Tested and flipped the switch once everything was working. Doing it this way will certainly motivate us to work through the issues quickly though ... ;)

[sakoht]

We can rename those branches. I'll do that.

Sent from my iPhone

On Feb 22, 2015, at 5:45 PM, Malachi Griffith [email protected] wrote:

Since the sGMS installer, automatically pulls from gms-pub it seems likely that this might break the installer and various analyses in our example tutorials until we have a chance to work through all the unexpected issues/dependencies. In the past there were at least ~10 of these each time we did a merge after a while. I think in those cases we started by creating a gms-pub-merge branch for each repo, and then a gms repo that installed from these branches. Tested and flipped the switch once everything was working. Doing it this way will certainly motivate us to work through the issues quickly though ... ;)

—
Reply to this email directly or view it on GitHub.

[malachig]

There does seem to be an error related to resource locking on attempt to prime the database now: #162

[sakoht]

So I renamed the branches. The old regular gms-pub branches are back where they were.

The new install in the gms repo is on branch gms-pub-2015.02.22.
When it uses genome, ur and workflow, it uses the branch/tag gms-pub-2015.02.22 for each of them.

So to test the new hypothetical merge:

git clone [email protected]:genome/gms -b gms-pub-2015.02.22
make

[gatoravi]

These branches are still being tested, to test this branch do the same as above,

git clone [email protected]:genome/gms -b gms-pub-2015.02.22
make