All File Changes
v300_preview2 to v300_base (2014-05-12 to 2014-05-19) v300
- src/browserbox/README.txt
- lines changed 6, context: html, text, full: html, text
removed my symlinks as they tend to confuse everyone, including myself
- src/browserbox/usr/local/apache/htdocs/folders
- lines changed 1, context: html, text, full: html, text
removed my symlinks as they tend to confuse everyone, including myself
- src/browserbox/usr/local/apache/trash
- lines changed 1, context: html, text, full: html, text
removed my symlinks as they tend to confuse everyone, including myself
- src/browserbox/usr/local/apache/userdata
- lines changed 1, context: html, text, full: html, text
removed my symlinks as they tend to confuse everyone, including myself
- src/browserbox/var/lib/mysql
- lines changed 1, context: html, text, full: html, text
removed my symlinks as they tend to confuse everyone, including myself
- src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
- lines changed 2, context: html, text, full: html, text
Consistent sort order for replicates. Refs Stanford #1372
- lines changed 14, context: html, text, full: html, text
1. Show EDW submission on browse page while uploading. 2. Minor layout changes for readability. refs Stanford #1372
- lines changed 4, context: html, text, full: html, text
1. Switch to new URL for encodedcc site. 2. Restore 'No files submitted' message (found by QA). 3. Remove now-superflous message about start time. refs Stanford #1372
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
- lines changed 4, context: html, text, full: html, text
Drop the sentence "or someone you know who already does have an "ENCODE Data Warehouse account, and have them create an account for you with
http://%s/cgi-bin/edwWebCreateUser" error message from edwWebSubmit when
a non-existent user tries to submit a validated.txt.
- src/hg/encode3/encodeDataWarehouse/lib/resetEdw
- lines changed 6, context: html, text, full: html, text
Using edwAddQaEnrichTarget add introns, exons, and promoter regionsas enrichment targets for dm3 (flyBasegene) and ce10 (ensGene)
- src/hg/hgGene/domains.c
- lines changed 1, context: html, text, full: html, text
update hgGene to use new SCOP URL format
- src/hg/hgGene/geneReviews.c
- lines changed 1, context: html, text, full: html, text
When display geneReviews related article on refGene and UCSC gene detail page,Associated the NBKid link to gr-short name only, for example, for SOD1, display
GeneReviews article(s) related to gene SOD1:
als-overview (Amyotrophic Lateral Sclerosis Overview)
/|\ /|\
| |
NBKid link No Link
- src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
- lines changed 1, context: html, text, full: html, text
some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
- src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
- lines changed 1, context: html, text, full: html, text
some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
- src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
- lines changed 1, context: html, text, full: html, text
some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
- src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
- lines changed 1, context: html, text, full: html, text
some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
- src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer3/otherOrgs.ra
- lines changed 1, context: html, text, full: html, text
some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 96, context: html, text, full: html, text
adding the ability to search hubs for content.
- src/hg/hgLogin/makefile
- lines changed 2, context: html, text, full: html, text
Don't override HG_WARN that is set in inc/common.mk .
- src/hg/hgMirror/makefile
- lines changed 2, context: html, text, full: html, text
fixing makefile after feedback from Hiram
- lines changed 2, context: html, text, full: html, text
fixing makefile after feedback from Braney
- src/hg/hgTracks/cds.c
- lines changed 4, context: html, text, full: html, text
Mac OS X Mavericks gcc -Wall complained about the parentheses in this "if"condition split up by #ifdef/#else/#endif. Fix: simplify the syntax so the
"if" condition is not split.
- src/hg/hgc/geneReviewsClick.c
- lines changed 2, context: html, text, full: html, text
When display geneReviews related article on refGene and UCSC gene detail page,Associated the NBKid link to gr-short name only, for example, for SOD1, display
GeneReviews article(s) related to gene SOD1:
als-overview (Amyotrophic Lateral Sclerosis Overview)
/|\ /|\
| |
NBKid link No Link
- src/hg/hgc/hgc.c
- lines changed 2, context: html, text, full: html, text
fix bug with crashing hgc pages #13262
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 35, context: html, text, full: html, text
added news announcement for hg38 ucsc genes release
- src/hg/htdocs/indexNews.html
- lines changed 78, context: html, text, full: html, text
added news announcement for hg38 ucsc genes release
- src/hg/htdocs/style/encode3Ucsc.css
- lines changed 4, context: html, text, full: html, text
1. Show EDW submission on browse page while uploading. 2. Minor layout changes for readability. refs Stanford #1372
- src/hg/inc/hubConnect.h
- lines changed 2, context: html, text, full: html, text
adding the ability to search hubs for content.
- src/hg/inc/trackHub.h
- lines changed 2, context: html, text, full: html, text
adding the ability to search hubs for content.
- src/hg/inc/versionInfo.h
- src/hg/js/edwPersona.js
- src/hg/js/encodeDataSummary.js
- lines changed 3, context: html, text, full: html, text
jshint doesn't like global variables used in iterators. refs #13255
- src/hg/lib/bacEndPairs.sql
- lines changed 1, context: html, text, full: html, text
hg38 has longer chrom names for the bacEnds track sql file
- src/hg/lib/cart.c
- lines changed 8, context: html, text, full: html, text
Mac OS X Mavericks gcc -Wall detects unused INLINE functions;getting rid of the one it found.
- src/hg/lib/hubPublic.as
- lines changed 1, context: html, text, full: html, text
adding the ability to search hubs for content.
- src/hg/lib/hubPublic.sql
- lines changed 1, context: html, text, full: html, text
adding the ability to search hubs for content.
- src/hg/lib/hui.c
- lines changed 15, context: html, text, full: html, text
fix pennantIcon code to reflect the documentation.
- src/hg/lib/trackHub.c
- lines changed 19, context: html, text, full: html, text
adding the ability to search hubs for content.
- src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh
- lines changed 8, context: html, text, full: html, text
load Vidal, Wanker, and P2P gene sorter tables
- src/hg/makeDb/trackDb/apis/apiMel2/brhInparalog.html
- lines changed 1, context: html, text, full: html, text
Changing links on bee (apiMel2) description page
- src/hg/makeDb/trackDb/apis/apiMel2/description.html
- lines changed 2, context: html, text, full: html, text
Changing links on bee (apiMel2) description page
- src/hg/makeDb/trackDb/apis/apiMel2/gold.html
- lines changed 1, context: html, text, full: html, text
Changing links on bee (apiMel2) description page
- src/hg/makeDb/trackDb/apis/apiMel2/modelRefGene.html
- lines changed 2, context: html, text, full: html, text
Changing links on bee (apiMel2) description page
- src/hg/makeDb/trackDb/blastHg17KG.html
- lines changed 6, context: html, text, full: html, text
Changes to opossum (monDom1) description pages
- src/hg/makeDb/trackDb/drosophila/dm3/description.html
- lines changed 3, context: html, text, full: html, text
Removing broken link, noted by user, refs #13272
- src/hg/makeDb/trackDb/human/hg38/knownGene.html
- lines changed 3, context: html, text, full: html, text
a few tweaks to the hg38 knownGene page
- lines changed 8, context: html, text, full: html, text
some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
- src/hg/makeDb/trackDb/mostConserved.html
- lines changed 35, context: html, text, full: html, text
Changes to opossum (monDom1) description pages
- src/hg/makeDb/trackDb/opossum/monDom1/description.html
- lines changed 1, context: html, text, full: html, text
Changes to opossum (monDom1) description pages
- src/hg/makeDb/trackDb/opossum/multiz5way.html
- lines changed 38, context: html, text, full: html, text
Changes to opossum (monDom1) description pages
- src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
- src/hg/near/hgNear/hgNearData/Human/acc.html
- lines changed 2, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/columnDb.ra
- lines changed 27, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg17/columnDb.ra
- lines changed 28, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg17/orderDb.ra
- lines changed 19, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg18/acc.html
- lines changed 2, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg18/columnDb.ra
- lines changed 28, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg18/orderDb.ra
- lines changed 19, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg19/acc.html
- lines changed 2, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg19/columnDb.ra
- lines changed 27, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/hg19/orderDb.ra
- lines changed 19, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/near/hgNear/hgNearData/Human/orderDb.ra
- lines changed 19, context: html, text, full: html, text
clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
for Wanker, Vidal, and P2P.
- src/hg/utils/hubPublicCheck/hubPublicCheck.c
- lines changed 14, context: html, text, full: html, text
adding the ability to search hubs for content.
- lines changed 4, context: html, text, full: html, text
Mac OS X Mavericks gcc -Wall found a use of uninitialized variablethat had been missed by earlier versions, probably because the
uninitialized variable was never used. Got rid of the unused variable.
- src/hg/utils/otto/geneReviews/buildGeneReviews.sh
- lines changed 70, context: html, text, full: html, text
Feature #5522geneReviews track automatic update
- lines changed 3, context: html, text, full: html, text
Track #13281 GeneReviews for hg38Add hg38 to the otto geneReviews party
- src/hg/utils/otto/geneReviews/checkGeneReviews.sh
- lines changed 55, context: html, text, full: html, text
Feature #5522geneReviews track automatic update
- lines changed 2, context: html, text, full: html, text
Track #13281 GeneReviews for hg38Add hg38 to the otto geneReviews party
- src/hg/utils/otto/geneReviews/geneReviews.tables
- lines changed 2, context: html, text, full: html, text
Feature #5522geneReviews track automatic update
- src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
- lines changed 8, context: html, text, full: html, text
Feature #5522geneReviews track automatic update
- src/hg/utils/otto/geneReviews/validateGeneReviews.sh
- lines changed 36, context: html, text, full: html, text
Feature #5522geneReviews track automatic update
- src/inc/common.mk
- lines changed 1, context: html, text, full: html, text
Mac OS X Mavericks gcc -Wall complains that openssl is deprecated(Apple wants everyone to use its Common Crypto lib instead).
Suppress those warnings by adding -Wno-deprecated-declarations
to HG_WARN for Mac (Darwin).
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
v300 final build refs #13064
- lines changed: 838
- files changed: 75