Transition to new deepdive release about dd-genomics

[netj]

This should be straightforward if you look at the DeepDive app structure doc and the rewritten examples in the DeepDive source tree, but do let me know if you need any help or advice!

[ajratner]

Thanks!
On Tue, Jul 14, 2015 at 4:59 PM Jaeho Shin [email protected] wrote:

This should be straightforward if you look at the DeepDive app structure
doc http://deepdive.stanford.edu/doc/advanced/deepdiveapp.html and the
rewritten examples in the DeepDive source tree
https://github.com/HazyResearch/deepdive/tree/master/examples/spouse_example/postgres/tsv_extractor,
but do let me know if you need any help or advice!

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[ajratner]

Marking as low priority for now... @Colossus next time we do a big code cleanup / re-org we can do this too

[Colossus]

This is straightforward. You need to do only a few things:

• Prepend deepdive/util to your path, if you haven't done so already

• in env_local.sh, add the following:
  export DBPASSWORD=
  export DEEPDIVE_JDBC_DRIVER=org.postgresql.Driver
  export DEEPDIVE_JDBC_URL="jdbc:postgresql://"${PGHOST}":"${PGPORT}"/"${DBNAME}

• In deepdive/util, execute one of the following commands:

  ln -s format_converter_mac format_converter && ln -s sampler-dw-mac sampler-dw
  

or the same for -linux.

If you get a strange error like n_vars == n_factors or something like that during inference, you forgot to do the last step. Please repeat it until success.

I'm running DD0.7 exclusively now. @ajratner feel free to close this when you're done with the transition too.

[netj]

@Colossus your changes shouldn't be necessary if you just replace the sbt command with deepdive env java .... See http://deepdive.stanford.edu/doc/changelog/0.7.0-alpha.html

[Colossus]

@netj OK sounds cool thanks!