Commits for markd

v269_preview to v269_preview2 (2012-06-12 to 2012-06-19) v269

• use less error prone shell syntax
  • src/hg/makeDb/genbank/etc/align-genbank - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/build-genbank - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/ccds-import - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/dbload - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/euronode-copy - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgdownload-copy - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgnfs1-copy - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwbeta-dbload - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev-dbload - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/mkdownload - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/rr-dbload - lines changed 1, context: html, text, full: html, text
• reduced number of parallel genbank alignments in an attempt to reduce GPFS impact
  • src/hg/makeDb/genbank/etc/align-genbank - lines changed 1, context: html, text, full: html, text
• added not on Ensembl convergence with GENCODE
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.html - lines changed 7, context: html, text, full: html, text
• Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
  implementation used an approach that some arbitrarily and unintuitively
  capped the number of scaffolds that were batched.
  - Eliminate the flag files that were created per-partation, which
  we required during migration. Instead create one file that
  lists the partations that needed to aligned or migrated.
  
  • src/hg/makeDb/genbank/doc/config.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignFinish - lines changed 197, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignGet.c - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignSetup - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/inc/gbDefs.h - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbCommon.pm - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbDefs.c - lines changed 23, context: html, text, full: html, text
• Updated CCDS import to reflect changes in the schema.
  • src/hg/makeDb/doc/encodeDccHg19/gencodeV11.txt - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/ccds/createKeys.sql - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/ccds/createTables.sql - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql - lines changed 10, context: html, text, full: html, text
• include maf header in output to prevent downstream programs from crashing on empty mafs
  • src/hg/mouseStuff/mafFetch/mafFetch.c - lines changed 2, context: html, text, full: html, text
• remove explictly MAILTO to work around SOE google move
  • src/hg/makeDb/genbank/etc/euronode.crontab - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgnfs1.crontab - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwbeta.crontab - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.crontab - lines changed 1, context: html, text, full: html, text