Commits for kent

v295_base to v296_preview (2014-02-03 to 2014-02-10) v296

• Fixed typo in comment.
  • src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c - lines changed 1, context: html, text, full: html, text
• Renaming eapAnalysis structure to eapRun and eapAnalysisJson to eapRunAddJson
  • src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c - lines changed 231, context: html, text, full: html, text
  • src/hg/encode3/eap/eapAnalysisJson/eapRunAddJson.c - lines changed 231, context: html, text, full: html, text
  • src/hg/encode3/eap/eapAnalysisJson/makefile - lines changed 1, context: html, text, full: html, text
• Renaming eapAnalysis back to eapRun.
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 7, context: html, text, full: html, text
• Renaming analysisId to runId
  • src/hg/encode3/eap/eapAnalysisJson/eapRunAddJson.c - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 2, context: html, text, full: html, text
• Adding a bunch of missing utils and renaming eapAnalysisJson to eapRunAddJson.
  • src/hg/encode3/eap/eapAnalysisJson/eapRunAddJson.c - lines changed 231, context: html, text, full: html, text
  • src/hg/encode3/eap/eapAnalysisJson/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c - lines changed 231, context: html, text, full: html, text
  • src/hg/encode3/eap/eapRunAddJson/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/makefile - lines changed 6, context: html, text, full: html, text
• Moving sampleBam from notes to oneShot
  • src/hg/encode3/eap/notes/sampleBam/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/eap/notes/sampleBam/sampleBam.c - lines changed 109, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/sampleBam/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/sampleBam/sampleBam.c - lines changed 109, context: html, text, full: html, text
• Adding version number to usage statement.
  • src/utils/bigWigMerge/bigWigMerge.c - lines changed 1, context: html, text, full: html, text
• Reworking it so that inputs (or outputs) of same name get bundled together in JSON list
  • src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c - lines changed 78, context: html, text, full: html, text
• Adding back old table defs since have to rerun this and they are gone. Fixing bug in eapStepSwVersion table where it was using the edw version of the swVersion, not the eap one.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.as - lines changed 58, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.c - lines changed 941, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.h - lines changed 302, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwToEap1.c - lines changed 15, context: html, text, full: html, text
• Adding in separate module for old style tables.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/makefile - lines changed 1, context: html, text, full: html, text
• Fixing usage message to reflect what is, rather than what we want.
  • src/hg/encode3/encodeDataWarehouse/oneShot/sampleBam/sampleBam.c - lines changed 2, context: html, text, full: html, text
• Fixed a place where data was sent to stdout instead of specified file.
  • src/lib/jsonParse.c - lines changed 1, context: html, text, full: html, text
• Moving several routines from edwMakeValidFile to the library where they could be used by others, routines required to generate a license plate name. Added convenience wrapper to get an edwAssembly from it's ID.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 16, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 53, context: html, text, full: html, text
• Disengaging old style analysis daemon.
  • src/hg/encode3/encodeDataWarehouse/lib/restartDaemons - lines changed 2, context: html, text, full: html, text
• Moving several routines from edwMakeValidFile to the library where they could be used by others, routines required to generate a license plate name.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 17, context: html, text, full: html, text
• Improving comment.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c - lines changed 1, context: html, text, full: html, text
• Mostly improving commenting. Favoring 'Input' controls over other controls per Eurie's suggestion, but there aren't input controls to test it on, so I'm not sure if this part works yet.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 27, context: html, text, full: html, text
• Adding sum_bigWig step.
  • src/hg/encode3/eap/eapAddStep/eapAddStep.c - lines changed 8, context: html, text, full: html, text
• Coping with change from eapParaQueues constant to eapParaDirs() function call needed as part of separating the ENC/TST/DEV versions of the parasol dirs. Minor rejiggering of how tags are transfered from inputs to output including adding the technical_replicate and paired_end field, and making the experiment field robust in the presence of a control input.
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 6, context: html, text, full: html, text
• Coping with change from eapParaQueues constant to eapParaDirs() function call needed as part of separating the ENC/TST/DEV versions of the parasol dirs.
  • src/hg/encode3/eap/eapDaemon/eapDaemon.c - lines changed 4, context: html, text, full: html, text
• Quite a number of changes combined here. Implementing a new column to show the average job length in minutes of a step. Coping with change from eapParaQueues constant to eapParaDirs() function call needed as part of separating the ENC/TST/DEV versions of the parasol dirs. Moving step count from status to lesser used info sub-command.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 77, context: html, text, full: html, text
• Fairly large scale changes here. It now just produced a json file rather than attaching json to a row in the database. It also generates json for the software and step objects as well as the run object and some versioning objects.
  • src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c - lines changed 254, context: html, text, full: html, text
• Implementing first cut at wig pooler step that gets called at the replicate matching stage.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 192, context: html, text, full: html, text
• Changing from eapAnalysis to eapRun.
  • src/hg/encode3/eap/inc/eapDb.h - lines changed 40, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.as - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.c - lines changed 49, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.sql - lines changed 6, context: html, text, full: html, text
• Replacing eapParaQueues constant with calls to eapParaDirs(conn).
  • src/hg/encode3/eap/inc/eapLib.h - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapLib.c - lines changed 17, context: html, text, full: html, text
• Good enough for a one shot job.
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixTstToTstff/edwFixTstToTstff.c - lines changed 82, context: html, text, full: html, text
• Fixing crash on empty message sent to main message queue.
  • src/parasol/paraHub/paraHub.c - lines changed 6, context: html, text, full: html, text
• Moving a check on commands against message size to library since in fact it was already implemented twice, and I needed it a third time.
  • src/parasol/inc/paraMessage.h - lines changed 5, context: html, text, full: html, text
  • src/parasol/lib/paraMessage.c - lines changed 13, context: html, text, full: html, text
  • src/parasol/para/para.c - lines changed 5, context: html, text, full: html, text
  • src/parasol/parasol/parasol.c - lines changed 5, context: html, text, full: html, text
• Bumping version and adding note to version.doc.
  • src/parasol/inc/paraVersion.h - lines changed 1, context: html, text, full: html, text
  • src/parasol/version.doc - lines changed 1, context: html, text, full: html, text
• Worked well enough for something just to make test database prettier....
  • src/hg/encode3/eap/fix/eapDepricateUntracked/eapDepricateUntracked.c - lines changed 104, context: html, text, full: html, text
  • src/hg/encode3/eap/fix/eapDepricateUntracked/makefile - lines changed 4, context: html, text, full: html, text
• This is far from working, but there's enough good work here to be worth protecting under source control.
  • src/hg/encode3/eap/eapToHub/eapToHub.c - lines changed 503, context: html, text, full: html, text
• Needs more testing, but works in at least three cases.
  • src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/edwReplicatedPeaks.c - lines changed 299, context: html, text, full: html, text
• Added replicated peaks steps and removing some debugging uglies.
  • src/hg/encode3/eap/eapAddStep/eapAddStep.c - lines changed 17, context: html, text, full: html, text
• Starting to build collection of queries that take like half an hour to build.
  • src/hg/encode3/eap/hardQueries/notFromMyBam - lines changed 30, context: html, text, full: html, text
• Added edwSubmitFromId function. Revised edwLicensePlateHead to cope with TST->TSTFF change for Stanford compatibility. Added edwSubmitIsValidated. Improved some comments.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 9, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 21, context: html, text, full: html, text
• Added version to usage message.
  • src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/edwReplicatedPeaks.c - lines changed 1, context: html, text, full: html, text
• Coping with edwLicensePlateHead(conn)/edwLicensePlatePrefix change.
  • src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c - lines changed 3, context: html, text, full: html, text
• Put in a first draft, currently ifdefed out, of routine to mail user when validation finishes. Coping with edwLicensePlateHead(conn)/edwLicensePlatePrefix change.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 71, context: html, text, full: html, text
• Coping with edwLicensePlateHead(conn)/edwLicensePlatePrefix change.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 1, context: html, text, full: html, text
• Making program able to deal with things like 'male.hg19' that have crept into the ucscDb field in addition to plain 'hg19'
  • src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c - lines changed 2, context: html, text, full: html, text
• Added function to get email of pipeline daemon. Shortened a number of directories as a weak attempt to improve my carpel tunnel outlook, and also to make it so that can have more files mentioned in a command line without it overflowing parasol limits. The wig pooling command still has one case that overflows though.
  • src/hg/encode3/eap/inc/eapLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapLib.c - lines changed 9, context: html, text, full: html, text
• Moved 'edwUserFOrPipeline' to library, but to eap library.
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 8, context: html, text, full: html, text
• Making it so a command can be 4 chars wider without disrupting spacing.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 2, context: html, text, full: html, text
• Fixing small issue in seconds field of timestamp where it would show :1 instead of the :01 that was wanted.
  • src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c - lines changed 1, context: html, text, full: html, text
• A lot of new code written to attempt to find the best replicates to use when creating replicated peaks, and also just to run the new program, edwReplicatedPeaks, that does the careful intersection plus data transfer from the individual replicates to the replicated peaks. I think the best-two-replicates code may take some tweaking still. The current logic is to pick the most recent file in either replicate as the file used for that replicate, and then to use enrichments and depth of coverage to pick the best file from all other replicates.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 148, context: html, text, full: html, text
• Added a few more fields to the composite track, and starting to generate track stanzas for views and subtracks. Still a ways to go before it generates a working trackDb though!
  • src/hg/encode3/eap/eapToHub/eapToHub.c - lines changed 104, context: html, text, full: html, text