File Changes for markd
switch to commits view, user indexv269_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
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