Commits for ceisenhart

v325_base to v326_preview (2015-11-16 to 2015-11-23) v326

• Changing the defaul makefile target from normal to all at Kate's advice, refs# 16352
  
  • src/utils/newPythonProg/newPythonProg.c - lines changed 1, context: html, text, full: html, text
• Added new javascript code to the c program, refs #16341 and #16216
  
  • src/hg/expMatrixToJson/expMatrixToJson.c - lines changed 31, context: html, text, full: html, text
• finishing up the program, making it more general and added in a function to change the corresponding .html file. refs #16182
  
  • src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson - lines changed 43, context: html, text, full: html, text
• Changing the condense to a sum rather than an average, refs #16182
  
  • src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix - lines changed 6, context: html, text, full: html, text
• Adding a mouse test data set for the rna seq pipeline, it should be very small. refs #16244
  
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/tests/mouse/README - lines changed 10, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/tests/mouse/fastqFiles/fq1-R1-001.fastq.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/tests/mouse/fastqFiles/fq1-R2-001.fastq.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/tests/mouse/fastqFiles/fq2-R1-001.fastq.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/tests/mouse/fastqFiles/fq2-R2-001.fastq.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/tests/mouse/manifest.txt - lines changed 5, context: html, text, full: html, text
• Adding changes to a suprogram in the rna seq pipeline, the one that handles Kallisto. refs #16244
  
  • src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani - lines changed 49, context: html, text, full: html, text
• Adding in some changes to make the pipeline more universal, refs #16244
  
  • src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/rnaSeqToClustersPipeline - lines changed 91, context: html, text, full: html, text
• Adding the tRNA track to the non-coding RNA supertrack refs #11694
  
  • src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.ra - lines changed 10, context: html, text, full: html, text