Commits for kent

v294_base to v295_preview (2014-01-13 to 2014-01-20) v295

• Making it clean up temp dir when done, but there's a noClean option still. Doing a 'mv' via shell instead of a 'rename' via C library to put files into the warehouse, since it turns out rename doesn't work across devices. Removing some code that was a weak old attempt at making it possible to run this program in parallel. It must be run serially.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 287, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 57, context: html, text, full: html, text
• Utility to look at a job table.
  • src/hg/encode3/encodeDataWarehouse/edwJob/edwJob.c - lines changed 156, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwJob/makefile - lines changed 4, context: html, text, full: html, text
• Utility to look at a job table.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 2, context: html, text, full: html, text
• It's painful enough to reproduce this table I'll put it under source code control. It is a few fields from the encode2 cellType - just sex and organism.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/cellTypeSlim.tab - lines changed 447, context: html, text, full: html, text
• Faking up a biosample table based on term,organism, and sex fields from encode2.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c - lines changed 58, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/makefile - lines changed 3, context: html, text, full: html, text
• telling parasol about our job size. Clarifying name of var.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 15, context: html, text, full: html, text
• Improving exit code handling.
  • src/parasol/parasol/parasol.c - lines changed 15, context: html, text, full: html, text
• Adding -all option to list batches, to see finished ones too.
  • src/parasol/paraHub/paraHub.c - lines changed 18, context: html, text, full: html, text
  • src/parasol/parasol/parasol.c - lines changed 6, context: html, text, full: html, text
• Adding edwBiosample and edwSettings tables.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 137, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 16, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 313, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 22, context: html, text, full: html, text
• New micro start of analyis library.
  • src/hg/encode3/encodeDataWarehouse/lib/eapLib.c - lines changed 15, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/makefile - lines changed 1, context: html, text, full: html, text
• Bumping up analysis jobs since running remotely.
  • src/hg/encode3/encodeDataWarehouse/lib/restartDaemons - lines changed 1, context: html, text, full: html, text
• Fixing time format in a view. Adding hg38 stuff.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 15, context: html, text, full: html, text
• Removing unused eapTempDir variable.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 2, context: html, text, full: html, text
• Bringing in encode2 metadata too.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 72, context: html, text, full: html, text
• Bringing in biosamples from Stanford too.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c - lines changed 117, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/makefile - lines changed 1, context: html, text, full: html, text
• Several changes. This version is tuned to schedule bwa alignments on hg38 mostly.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 254, context: html, text, full: html, text
• Adding delay as a command line parameter.
  • src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c - lines changed 6, context: html, text, full: html, text
• Version 5 - mostly to let Encode2 in with lower standards.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 41, context: html, text, full: html, text
• Making it take constant prefix to license plate from settings table rather than being a hardcoded 'ENCFF'.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 19, context: html, text, full: html, text
• Giving free pass to unknown, idat, rcc,
  • src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c - lines changed 12, context: html, text, full: html, text
• Free pass for idat and rcc. Fixing typo in temp dir.
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 1, context: html, text, full: html, text
• Making paraHost a command line option. Rearranging debugging statements. Adding 1 second sleep. Upping processor use to 3.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 11, context: html, text, full: html, text
• Refactoring to remove fifo and simplify command line. Bypassing stderr file copying which is being flaky since it's trying to go straight from dev to one of the paraNodes.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 128, context: html, text, full: html, text
• Making it so that parasol add job is done serially, just wait for results in parallel.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 33, context: html, text, full: html, text
• Added -printId option, used by edwAnalysisDaemon now. (Wait option no longer used by that daemon.
  • src/parasol/parasol/parasol.c - lines changed 7, context: html, text, full: html, text
• Exporting a few local functions for wider use.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 8, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 3, context: html, text, full: html, text
• Linking in with parasol libraries.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/makefile - lines changed 1, context: html, text, full: html, text
• Handling copy over of stderr from node to db table. Cleaned up a lot of debugging code.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 40, context: html, text, full: html, text
• Got out one more run time kink I think. It was having trouble collecting stderr. I moved the collection to the serial side in hopes that ssh will like it better.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 92, context: html, text, full: html, text
• Removing some debugging statements. Making it schedule only single-end bwa.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 11, context: html, text, full: html, text
• Adding version number to logging. Failing more softly if cant fetch stderr file from parasol node.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 22, context: html, text, full: html, text
• Adding a dry option that just lists command that would get run.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 11, context: html, text, full: html, text
• Creating new library function edwOneLineSystemAttempt
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 11, context: html, text, full: html, text
• Making it retry the ssh to paraHub 6 times over the course of a minute before giving up.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 16, context: html, text, full: html, text
• Changing program so that it can add new tags as well as change existing ones.
  • src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/edwCorrectFileTags.c - lines changed 36, context: html, text, full: html, text
• Continued messing to get pipes reliable. Improving logic that finds matching pair fastq. Deleting some old unused code.
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 69, context: html, text, full: html, text
• Making it sole responsibility of younger member of pair to make edwQaPairedEndFastq record. Creating Record in a single transaction.
  • src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c - lines changed 21, context: html, text, full: html, text
• Removed some debugging.
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 27, context: html, text, full: html, text
• Moving pmSendStringWithRetries and pmHubSingleLineQuery from para application to library, so the edwAnalysisDaemon can use it too.
  • src/parasol/inc/paraMessage.h - lines changed 9, context: html, text, full: html, text
  • src/parasol/lib/paraMessage.c - lines changed 41, context: html, text, full: html, text
  • src/parasol/para/para.c - lines changed 49, context: html, text, full: html, text
• Correcting index on edwQaPairedEndFastq which could not be unique after all. Added parasolId to the edwAnalysisJob table, and added cpusRequested to both edwAnalysisJob and edwAnalysisStep
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 3, context: html, text, full: html, text
• Two steps forward one step back.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 8, context: html, text, full: html, text
• Almost complete reworking that now meshes well with parasol. Only a single copy of the daemon exists, in a boring 2-way polling loop. It looks for new jobs in database table and sends them to paraHub daemon on remote machine. It looks for new lines in a results file to see what jobs parasol has finished. It transports information from the results file back into the database table.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 303, context: html, text, full: html, text
• Improving logging statements.
  • src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c - lines changed 3, context: html, text, full: html, text
• Adding in ChiaPet thresholds.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 18, context: html, text, full: html, text
• Reworking so that it will retry if the most recent attempt at a command failed.
  • src/hg/encode3/encodeDataWarehouse/edwRetryJob/edwRetryJob.c - lines changed 31, context: html, text, full: html, text
• Adding retry and ignoreQa options. Shifting analysis from bam to fastq.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 45, context: html, text, full: html, text
• Adding commented out beta site
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/makk - lines changed 1, context: html, text, full: html, text
• Fixing zero-divide.
  • src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/edwSamPairedEndStats.c - lines changed 8, context: html, text, full: html, text
• Fixing merge conflicts
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 42, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 10, context: html, text, full: html, text
  • src/parasol/parasol/parasol.c - lines changed 4, context: html, text, full: html, text
• Changing human target from hg38 to hg19. Making already scheduled queries sensitive to target.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 45, context: html, text, full: html, text
• Fix to add targets seems to work.
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixTargetSeq/edwFixTargetSeq.c - lines changed 82, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixTargetSeq/makefile - lines changed 4, context: html, text, full: html, text
• Adding targetBaseCount and targetSeqCount fields.
  • src/hg/encode3/encodeDataWarehouse/lib/edwBamFileFromRa.c - lines changed 16, context: html, text, full: html, text
• Adding targetBaseCount and targetSeqCount fields to edwBamFile and seqCount to edwAssembly to help match assemblies to bam files.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 25, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 5, context: html, text, full: html, text
• Tool to parse out sam file run against repeatmasker library.
  • src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/edwSamRepeatAnalysis.c - lines changed 85, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/makefile - lines changed 4, context: html, text, full: html, text
• Utility to convert quality scores in fastqs from Solexa to Sanger style seems to work.
  • src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/edwSolexaToSangerFastq.c - lines changed 123, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/makefile - lines changed 3, context: html, text, full: html, text
• Another fixer. This one for downstream effects of not respecting BAM file ucscDb when running Macs2.
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixTarget2/edwFixTarget2.c - lines changed 115, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixTarget2/makefile - lines changed 4, context: html, text, full: html, text
• Librarified some message-the-hub stuff so can reuse
  • src/parasol/inc/paraMessage.h - lines changed 7, context: html, text, full: html, text
  • src/parasol/lib/paraMessage.c - lines changed 46, context: html, text, full: html, text
  • src/parasol/para/para.c - lines changed 40, context: html, text, full: html, text
• Adding 4 missing directories and alphabetizing.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 6, context: html, text, full: html, text
• Rearranging ifdefs to decide what to schedule.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 38, context: html, text, full: html, text
• Improved comment.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c - lines changed 2, context: html, text, full: html, text
• Adding a level-1 verbose status message, and bumping the version number.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 3, context: html, text, full: html, text
• Added an assert suggested in code review. Matches an assert elsewhere in a similar situation.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c - lines changed 1, context: html, text, full: html, text
• Adding a little logic to make enrichments work in spite of assemblies like 'male.hg19'. Specifically made a routine that returns the root 'hg19' in cases like this.
  • src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c - lines changed 18, context: html, text, full: html, text
• Changed spelling to match database.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 4, context: html, text, full: html, text
• Making dirs on path to the results file.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 5, context: html, text, full: html, text
• Librarifying edwFileFieldsFromTags and edwValidFileUpdateDb. AMaking revalidation an option for edwFileResetTags rather than always happening.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 56, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 11, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 88, context: html, text, full: html, text
• Adding noRevalidate option. Most of work is in library.
  • src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/edwCorrectFileTags.c - lines changed 5, context: html, text, full: html, text
• Fixing bug so cpusRequested actually gets passe to hub. Making it use different queues for different analysis steps.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 58, context: html, text, full: html, text
• Fixer seems to work.
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRepsFromTarballs/edwFixTechRepsFromTarballs.c - lines changed 90, context: html, text, full: html, text
• Making the outputType be 'rejected_reads' in the rejected case.
  • src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRepsFromTarballs/edwFixTechRepsFromTarballs.c - lines changed 7, context: html, text, full: html, text
• Somehow the status demangling slipped out. I put it back in. Also put info on what version we are as first log message.
  • src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c - lines changed 8, context: html, text, full: html, text
• Making pmHubMultilineQuery return a slName list instead of a slRef list with string values. This saves about 8 freez() calls and is a bit tidier overall.
  • src/parasol/inc/paraMessage.h - lines changed 1, context: html, text, full: html, text
  • src/parasol/lib/paraMessage.c - lines changed 5, context: html, text, full: html, text
  • src/parasol/para/para.c - lines changed 40, context: html, text, full: html, text
• When daemon restarts it does a pretty good job of trying to reconnect with exiting running jobs or ones that finished when it was down.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 91, context: html, text, full: html, text
• Improving commenting.
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 8, context: html, text, full: html, text
• Adding looseBed to formats.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 31, context: html, text, full: html, text
• Adding looseBed to formats. Making enrichmentAssembly into a library routine with a more meaningful name.
  • src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c - lines changed 21, context: html, text, full: html, text
• Adding looseBed format
  • src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c - lines changed 1, context: html, text, full: html, text
• Moving encPipe directory to be eap/notes
  • 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/encPipe/sampleBam/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encPipe/sampleBam/sampleBam.c - lines changed 109, context: html, text, full: html, text
• Moving encodeDataWarehouse/edwAnalysisDaemon to eap/eapDaemon
  • src/hg/encode3/eap/eapDaemon/eapDeamon.c - lines changed 375, context: html, text, full: html, text
  • src/hg/encode3/eap/eapDaemon/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c - lines changed 375, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/makefile - lines changed 4, context: html, text, full: html, text
• Renaming edwAnalysisDaemon to eapDaemon
  • src/hg/encode3/eap/eapDaemon/eapDeamon.c - lines changed 7, context: html, text, full: html, text
  • src/hg/encode3/eap/eapDaemon/makefile - lines changed 2, context: html, text, full: html, text
• Easy to misspell daemon.
  • src/hg/encode3/eap/eapDaemon/eapDaemon.c - lines changed 375, context: html, text, full: html, text
  • src/hg/encode3/eap/eapDaemon/eapDeamon.c - lines changed 375, context: html, text, full: html, text
• Refactoring in preparation for moving some code to library.
  • src/hg/encode3/eap/eapDaemon/eapDaemon.c - lines changed 24, context: html, text, full: html, text
• Part of the eap spinning out of the edw.
  • src/hg/encode3/eap/eapFinish/edwFinishAnalysis.c - lines changed 342, context: html, text, full: html, text
  • src/hg/encode3/eap/eapFinish/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/eapSchedule/edwScheduleAnalysis.c - lines changed 747, context: html, text, full: html, text
  • src/hg/encode3/eap/eapSchedule/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c - lines changed 342, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 747, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/makefile - lines changed 4, context: html, text, full: html, text
• adjusting to new position in source tree.
  • src/hg/encode3/eap/eapFinish/edwFinishAnalysis.c - lines changed 2, context: html, text, full: html, text
• simple symbol substitution
  • src/hg/encode3/eap/eapFinish/edwFinishAnalysis.c - lines changed 6, context: html, text, full: html, text
• Renaming edwFinishAnalysis to the more elegant eapFinish
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 342, context: html, text, full: html, text
  • src/hg/encode3/eap/eapFinish/edwFinishAnalysis.c - lines changed 342, context: html, text, full: html, text
  • src/hg/encode3/eap/eapFinish/makefile - lines changed 2, context: html, text, full: html, text
• Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
  • src/hg/encode3/eap/README - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 51, context: html, text, full: html, text
  • src/hg/encode3/eap/eapMonitor/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 743, context: html, text, full: html, text
  • src/hg/encode3/eap/eapSchedule/edwScheduleAnalysis.c - lines changed 747, context: html, text, full: html, text
  • src/hg/encode3/eap/eapSchedule/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/eap/inc/eapLib.h - lines changed 22, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapLib.c - lines changed 29, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/makefile - lines changed 11, context: html, text, full: html, text
  • src/hg/encode3/eap/makefile - lines changed 49, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/eapLib.c - lines changed 15, context: html, text, full: html, text
• Implementing status, chill, and cull commands.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 183, context: html, text, full: html, text
• Added info command. Polishing and extending status command.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 67, context: html, text, full: html, text
• Implementing err and errFile commands.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 194, context: html, text, full: html, text
• Trying to add macs2 chip-seq.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 120, context: html, text, full: html, text
• Implementing steps,errlist, and scrounge commands.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 176, context: html, text, full: html, text
• Changing looseBed to customTrack and allowing track and browser lines
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 45, context: html, text, full: html, text
• Adding code to find control experiment. So far, just the Stanford side.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 37, context: html, text, full: html, text
• Seem to find controls for ChIP-seq on the UCSC side now.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 59, context: html, text, full: html, text
• Removing some debugging.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 2, context: html, text, full: html, text
• Making errList command have optional days and step parameters. Making status command list top three batches sorted by # of jobs running mostly. Making results have a more proper constructor.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 155, context: html, text, full: html, text
• Added -justSchema option, to suppress information depending on contents as opposed to structure of database. Comparing dbSnoop -justSchema output of two databases is an easy way to see if the databases are synchonized (including indexes).
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 25, context: html, text, full: html, text
• Making paraPstat2Job - a parsed version of parasol pstat2 output - public.
  • src/parasol/lib/paraMessage.c - lines changed 13, context: html, text, full: html, text
• Adding mustRemove wrapper around remove.
  • src/inc/portable.h - lines changed 3, context: html, text, full: html, text
  • src/lib/osunix.c - lines changed 8, context: html, text, full: html, text
• Fixing typo in comment.
  • src/inc/common.h - lines changed 1, context: html, text, full: html, text
  • src/lib/common.c - lines changed 1, context: html, text, full: html, text
• Making paraPstat2Job - a parsed version of parasol pstat2 output - public.
  • src/parasol/inc/paraMessage.h - lines changed 16, context: html, text, full: html, text
• Freen counts through some big numbers.
  • src/hg/oneShot/freen/freen.c - lines changed 14, context: html, text, full: html, text
• Trying to avoid using control sets as target sets for peak callers.
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 1, context: html, text, full: html, text
• Moving several things from edw to eap.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 3, context: html, text, full: html, text
• Adding control field to experiment. Adding indexes to several fields.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 13, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 1, context: html, text, full: html, text
• Moving several things from edw to eap.
  • src/hg/encode3/encodeDataWarehouse/lib/makefile - lines changed 1, context: html, text, full: html, text
• Adding edwSimpleAssemblyName.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 17, context: html, text, full: html, text
• Changing looseBed to customTrack.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 1, context: html, text, full: html, text
• Adding a bunch of new linked tables to what gets deleted.
  • src/hg/encode3/encodeDataWarehouse/edwReallyRemoveFiles/edwReallyRemoveFiles.c - lines changed 17, context: html, text, full: html, text
• Changing looseBed to customTrack.
  • src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c - lines changed 2, context: html, text, full: html, text
• Changing looseBed to customTrack.
  • src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c - lines changed 2, context: html, text, full: html, text
• Adding routines to get list of running jobs from Parasol, to put that list intoa a hash, and also a command to extract the 'step' out of a command line.
  • src/hg/encode3/eap/inc/eapLib.h - lines changed 12, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapLib.c - lines changed 61, context: html, text, full: html, text
• Since startTime is now indexed, look for startTime=0 across whole table, not just for recent IDs. Moving some of the parasol interface stuff to eapLib.c
  • src/hg/encode3/eap/eapDaemon/eapDaemon.c - lines changed 55, context: html, text, full: html, text
• Linking with local library.
  • src/hg/encode3/eap/eapDaemon/makefile - lines changed 1, context: html, text, full: html, text
• Added -keepFailing option.
  • src/hg/encode3/eap/eapFinish/eapFinish.c - lines changed 10, context: html, text, full: html, text
• Improving several things. Including node job was run on in errList. Removed nearly useless Youngest Job information item.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 80, context: html, text, full: html, text
• Fixed bug in input tyeps for scheduleMacsChip. Got rid of some uglyfs.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 4, context: html, text, full: html, text
• Adding new argument to edwFileResetTags.
  • src/hg/encode3/encodeDataWarehouse/edwChangeFormat/edwChangeFormat.c - lines changed 1, context: html, text, full: html, text
• QA routines to check alignments against repeat library and save to database.
  • src/hg/encode3/encodeDataWarehouse/edwMakeRepeatQa/edwMakeRepeatQa.c - lines changed 124, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwMakeRepeatQa/makefile - lines changed 4, context: html, text, full: html, text
• Moved to eap.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 6, context: html, text, full: html, text