Commits for ceisenhart

v324_preview2 to v324_base (2015-10-19 to 2015-10-26) v324

• Finishing this program up, refs #16182
  
  • src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix - lines changed 80, context: html, text, full: html, text
• fixing a bug that causes the extTbl and seq tables to get out of sync, refs #16034
  
  • src/hg/makeDb/hgLoadSeq/hgLoadSeq.c - lines changed 11, context: html, text, full: html, text
• Removed a bunch of cruft, two useless files and added some documentation. Refs #16216
  
  • src/hg/expMatrixToJson/expMatrixToJson.c - lines changed 248, context: html, text, full: html, text
  • src/hg/expMatrixToJson/forceLayout.json - lines changed 247, context: html, text, full: html, text
  • src/hg/expMatrixToJson/radialDend.html - lines changed 109, context: html, text, full: html, text
• Finishing up this program, refs #16182
  
  • src/hg/cirm/cdw/wrangle/makeExpMatrix/makeExpMatrix - lines changed 47, context: html, text, full: html, text
• The first version of this program. Relatively complete still, refs #16244
  
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/rnaSeqToClustersPipeline - lines changed 176, context: html, text, full: html, text
• This program is also known as maniMani, were using it on CIRM. refs #16113
  
  • src/hg/cirm/cdw/wrangle/addToStepTables/addToStepTables - lines changed 164, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/addToStepTables/makefile - lines changed 6, context: html, text, full: html, text
• Changing the makefile produced to not be cluster dependent. Refs #16156
  
  • src/utils/newPythonProg/newPythonProg.c - lines changed 1, context: html, text, full: html, text
• Changing the makefile so it is not cluster dependent. Refs #16182
  
  • src/hg/cirm/cdw/wrangle/addMetaDataToJson/makefile - lines changed 2, context: html, text, full: html, text
• Changing the makefile so it is not cluster dependent. Refs #16113
  
  • src/hg/cirm/cdw/wrangle/addToStepTables/makefile - lines changed 2, context: html, text, full: html, text
• Changing the makefile so it is not cluster dependent. Refs #16182
  
  • src/hg/cirm/cdw/wrangle/condenseMatrix/makefile - lines changed 2, context: html, text, full: html, text
• Changing the makefile so it is not cluster dependent. Refs #16182
  
  • src/hg/cirm/cdw/wrangle/makeExpMatrix/makefile - lines changed 2, context: html, text, full: html, text
• Changing the makefile so it is not cluster dependent. Refs #16244
  
  • src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/makefile - lines changed 6, context: html, text, full: html, text
• Adding a check to the argparse module that causes the program to spit help with no arguments. This replicates the C code style. Refs #16156
  
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/newPythonProg/newPythonProg.c - lines changed 2, context: html, text, full: html, text
• Adding a makefile for the cirm wrangle directory. Incorporates python and C flawlessly using the new python framework! No ref for this, general CIRM thing.
  
  • src/hg/cirm/cdw/wrangle/makefile - lines changed 22, context: html, text, full: html, text
• Finishing the program kallistoOnFastqMani and adding some dependencies. Refs #16244
  
  • src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallisto - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani - lines changed 114, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/runKallisto.sh - lines changed 56, context: html, text, full: html, text
• Finishing this program and adding it to the pipeline, refs #16244
  
  • src/hg/cirm/cdw/wrangle/makeExpMatrix/makeExpMatrix - lines changed 5, context: html, text, full: html, text
• Finishing up the pipeline and making it a bit more universal, refs #16244
  
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/rnaSeqToClustersPipeline - lines changed 78, context: html, text, full: html, text