File Changes for markd

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

• src/hg/makeDb/doc/encodeDccHg19/gencodeV11.txt
  • lines changed 41, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/doc/config.html
  • lines changed 9, 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/etc/align-genbank
  • lines changed 3, context: html, text, full: html, text
    use less error prone shell syntax
  • 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/build-genbank
  • lines changed 2, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/ccds-import
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/dbload
  • lines changed 4, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 2, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/euronode.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 3, 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/etc/hgdownload-copy
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgnfs1-copy
  • lines changed 2, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgnfs1.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/hgwbeta-dbload
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgwbeta.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/hgwdev-dbload
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgwdev.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/mkdownload
  • lines changed 3, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/rr-dbload
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/src/align/gbAlignFinish
  • lines changed 197, 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/src/align/gbAlignGet.c
  • lines changed 30, 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/src/align/gbAlignSetup
  • lines changed 73, 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/src/ccds/createKeys.sql
  • lines changed 2, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 10, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • lines changed 37, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 10, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/inc/gbDefs.h
  • lines changed 6, 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/src/lib/gbCommon.pm
  • lines changed 3, 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/src/lib/gbDefs.c
  • lines changed 23, 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/trackDb/human/hg19/wgEncodeGencodeV12.html
  • lines changed 7, context: html, text, full: html, text
    added not on Ensembl convergence with GENCODE
• src/hg/mouseStuff/mafFetch/mafFetch.c
  • lines changed 2, context: html, text, full: html, text
    include maf header in output to prevent downstream programs from crashing on empty mafs