All File Changes

v307_preview to v307_preview2 (2014-09-29 to 2014-10-06) v307

• src/browserbox/README.txt
  • lines changed 7, context: html, text, full: html, text
    gbib update to ubuntu 14 , refs #11957
  • lines changed 10, context: html, text, full: html, text
    gbib admin readme update
• src/browserbox/etc/apache2/sites-available/001-browser.conf
  • lines changed 41, context: html, text, full: html, text
    gbib update to ubuntu 14 , refs #11957
• src/browserbox/packages-ubuntu13.txt
  • lines changed 394, context: html, text, full: html, text
    gbib update to ubuntu 14 , refs #11957
• src/browserbox/packages-ubuntu14.txt
  • lines changed 451, context: html, text, full: html, text
    gbib update to ubuntu 14 , refs #11957
• src/browserbox/packages.txt
  • lines changed 394, context: html, text, full: html, text
    gbib admin readme update
• src/browserbox/root/updateBrowser.sh
  • lines changed 175, context: html, text, full: html, text
    gbib update to ubuntu 14 , refs #11957
• src/hg/hgLogin/hgLogin.c
  • lines changed 2, context: html, text, full: html, text
    fixing a memory error that become apparent only on the new gbib, refs #14067 note 86
• src/hg/hgTables/identifiers.c
  • lines changed 5, context: html, text, full: html, text
    deactivate sample identifiers on gbib, cannot use hgTemp database, refs #14067
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    Adding announcemnts and release info for eboVir3 release
• src/hg/htdocs/ebolaPortal/antibodyResources.html
  • lines changed 1, context: html, text, full: html, text
    Grammatical err, tnx Luvina
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 5, context: html, text, full: html, text
    Add virion cartoon image and launcher to ViralZone
  • lines changed 66, context: html, text, full: html, text
    Added a new page, zoonotic infections, updated the 'about virus' and 'treatment' panels
  • lines changed 19, context: html, text, full: html, text
    fixing a merge conflict
  • lines changed 8, context: html, text, full: html, text
    added NEJM Ebola Resource
  • lines changed 20, context: html, text, full: html, text
    Removing the zoonotic infections page (too controversial) added a entry to the therapies section
• src/hg/htdocs/ebolaPortal/zoonoticInfections.html
  • lines changed 38, context: html, text, full: html, text
    Creating a zoonoitc infection page for the ebola portal
  • lines changed 120, context: html, text, full: html, text
    fixing a merge conflict
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 66, context: html, text, full: html, text
    Adding announcemnts and release info for eboVir3 release
  • lines changed 9, context: html, text, full: html, text
    Small corrections to Ebola credits
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 6, context: html, text, full: html, text
    explained license better
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 37, context: html, text, full: html, text
    Adding announcemnts and release info for eboVir3 release
  • lines changed 17, context: html, text, full: html, text
    Made a few edits.
  • lines changed 1, context: html, text, full: html, text
    Changing Ebola date to Jun. 2014.
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling error in Ebola announcement
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 11, context: html, text, full: html, text
    Added cgHub pub, per David.
• src/hg/htdocs/images/Filovirus_virion.jpg
  • lines changed 0, context: html, text, full: html, text
    Adding a new image for the Ebola Portal page
• src/hg/htdocs/images/Filovirus_virion_small.png
  • lines changed 0, context: html, text, full: html, text
    Add virion cartoon image and launcher to ViralZone
• src/hg/htdocs/images/fruitBat.jpg
  • lines changed 0, context: html, text, full: html, text
    An image for the Ebola Portal: Zoonosis page
• src/hg/htdocs/index.html
  • lines changed 3, context: html, text, full: html, text
    adding (back) the link to the Ebola Portal from the left-side blue nav bar on the home page
• src/hg/htdocs/indexNews.html
  • lines changed 64, context: html, text, full: html, text
    Adding announcemnts and release info for eboVir3 release
  • lines changed 18, context: html, text, full: html, text
    Made a few edits.
  • lines changed 3, context: html, text, full: html, text
    Changing Ebola date to Jun. 2014.
  • lines changed 1, context: html, text, full: html, text
    Fixing spelling error in Ebola announcement
• src/hg/lib/fileUi.c
  • lines changed 15, context: html, text, full: html, text
    fixing gbib bug due to rsync 3.1, refs #14091
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    fixing gbib error on assembly hubs, refs #11957
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    fixing null pointer error that occurs in gbib using angie's suggested code changes in refs #14067, note 58, refs #11957
• src/hg/makeDb/doc/eboVir3/gbkToGp.pl
  • lines changed 172, context: html, text, full: html, text
    scanning genbank records for genePred construction, works only on Ebola records refs #10411
• src/hg/makeDb/doc/eboVir3/ordinaryTracks.txt
  • lines changed 21, context: html, text, full: html, text
    adding joinerCheck and making download files refs #10411
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    modified minCheck to resolve errors reported by runJoiner.csh, refs #13593
  • lines changed 42, context: html, text, full: html, text
    adding eboVir3 refs #10411
• src/hg/makeDb/trackDb/ebola/eboVir2/ncbiGene.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on Code Review, refs #14073
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPanII.ra
  • lines changed 403, context: html, text, full: html, text
    adding more netMhc prediction tracks
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    reactivating the iedb predictions, as table should be dropped ongenome-preview by now, so should only be live on hgwdev
    
  • lines changed 1, context: html, text, full: html, text
    adding more netMhc prediction tracks
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 9, context: html, text, full: html, text
    indented bulleted list. moved Ebola reference out of Phylo section. Limited Ebola reference to 10 authors.
  • lines changed 20, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
• src/hg/makeDb/trackDb/ebola/eboVir3/description.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on gateway page. Adding downloads links to bottom of page
• src/hg/makeDb/trackDb/ebola/eboVir3/gap.html
  • lines changed 2, context: html, text, full: html, text
    Removed last line about gap type since it was empty.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcell.html
  • lines changed 9, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 21, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
  • lines changed 25, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels. Some git merge conflict resolutions.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcellNeg.html
  • lines changed 10, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 18, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
  • lines changed 22, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels. Some git merge conflict resolutions.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellI.html
  • lines changed 5, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 14, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
  • lines changed 15, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels. Some git merge conflict resolutions.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellII.html
  • lines changed 7, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 17, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
  • lines changed 16, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels. Some git merge conflict resolutions.
• src/hg/makeDb/trackDb/ebola/eboVir3/muPIT.html
  • lines changed 56, context: html, text, full: html, text
    adding MuPIT click locations refs #10411
  • lines changed 10, context: html, text, full: html, text
    update credits and references refs #10411
• src/hg/makeDb/trackDb/ebola/eboVir3/pdb.html
  • lines changed 10, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 16, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
  • lines changed 16, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels. Some git merge conflict resolutions.
• src/hg/makeDb/trackDb/ebola/eboVir3/spAnnot.html
  • lines changed 8, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 1, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
• src/hg/makeDb/trackDb/ebola/eboVir3/spMut.html
  • lines changed 5, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 1, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
• src/hg/makeDb/trackDb/ebola/eboVir3/spStruct.html
  • lines changed 5, context: html, text, full: html, text
    Fixed a few minor typos and grammar issues, edited a few references.
  • lines changed 1, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra
  • lines changed 2, context: html, text, full: html, text
    trying out full frame annotations on 160way refs #10411
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made a few edits for consistency in capitalization and hyphenation.
  • lines changed 4, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
  • lines changed 8, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels. Some git merge conflict resolutions.
  • lines changed 2, context: html, text, full: html, text
    adding URL link to MuPIT protein structures
  • lines changed 9, context: html, text, full: html, text
    adding MuPIT click locations refs #10411
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra
  • lines changed 2, context: html, text, full: html, text
    trying out full frame annotations on 160way refs #10411
• src/hg/makeDb/trackDb/ebola/gireIntraHost.html
  • lines changed 4, context: html, text, full: html, text
    Changes based on Code Review, refs #14073
• src/hg/makeDb/trackDb/ebola/gireMethods.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on Code Review, refs #14073
• src/hg/makeDb/trackDb/ebola/gireReferences.html
  • lines changed 16, context: html, text, full: html, text
    Alphabetized refs.
  • lines changed 1, context: html, text, full: html, text
    Changes based on Code Review, refs #14073
• src/hg/makeDb/trackDb/ebola/gireZebov.html
  • lines changed 32, context: html, text, full: html, text
    Changes to various ebola (eboVir3) description pages. Change to B/T cell short and long labels.
• src/hg/makeDb/trackDb/human/hg19/genomicSuperDups.html
  • lines changed 13, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 30, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • lines changed 122, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/hg19/targetScanS.html
  • lines changed 23, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/hg19/wgRna.html
  • lines changed 58, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/ntSssSnps.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/ntSssZScorePMVar.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/phastBias.html
  • lines changed 62, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/placentalChainNet.html
  • lines changed 19, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/polyA.html
  • lines changed 15, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/primateChainNet.html
  • lines changed 19, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/rgdQtl.html
  • lines changed 7, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/sestanBrainAtlas.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/stsMap.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/switchDbTss.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/vertebrateChainNet.html
  • lines changed 19, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/human/vistaEnhancers.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/mouse/mm7/description.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm7/knownGene.html
  • lines changed 26, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
  • lines changed 103, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm7/picTar.html
  • lines changed 22, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm8/NIAGene.html
  • lines changed 18, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm8/broadChromatinChIPSeq.html
  • lines changed 28, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm8/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm8/knownGene.html
  • lines changed 34, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm8/miRNA.html
  • lines changed 37, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
  • lines changed 81, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/mm8/wssdCoverage.html
  • lines changed 25, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/phastConsElements17way.html
  • lines changed 50, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/regPotential7X.html
  • lines changed 22, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/rikenCageCtss.html
  • lines changed 18, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/rikenCageTc.html
  • lines changed 18, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/mouse/rinnSex.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on mouse (mm7 and mm8) track description pages
• src/hg/makeDb/trackDb/rat/stsMapRat.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/recombRate.html
  • lines changed 33, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/rgdRatQtl.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/sibGene.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    scoreMin does work with bigBed, must have been forgotten in tagTypes.tab
• src/hg/makeDb/trackDb/uniGene_3.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on Human (hg19) track description pages. Changes to phastBias.html were primarily whitespace changes
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    adding mafToSnpBed to the utils build refs #14079
• src/inc/common.mk
  • lines changed 5, context: html, text, full: html, text
    adding a makefile flag COREDUMP=1 to make the CGIs create coredumps instead of showing errors
• src/lib/annoAssembly.c
  • lines changed 2, context: html, text, full: html, text
    taking back commit bd1c185f86d1b6cd77570bc5583c87ad27c791ba
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    fixing null pointer error that occurs in gbib using angie's suggested code changes in refs #14067, note 58, refs #11957
• src/lib/errAbort.c
  • lines changed 3, context: html, text, full: html, text
    adding a makefile flag COREDUMP=1 to make the CGIs create coredumps instead of showing errors
• src/userApps/fetchKentSource.sh
  • lines changed 6, context: html, text, full: html, text
    adding mafToSnpBed to the utils build refs #14079
• src/utils/pslScore/pslScore.pl
  • lines changed 1, context: html, text, full: html, text
    remove STDERR printout of intermediate values refs #10478
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v307 preview2 refs #14072
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 4, context: html, text, full: html, text
    Changes based on Code Review, refs #14073

• lines changed: 4108
• files changed: 132