All File Changes

v307_preview2 to v307_base (2014-10-06 to 2014-10-13) v307

• src/browserbox/etc/dhcp/dhclient.conf
  • lines changed 62, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 62, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/etc/issue
  • lines changed 4, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/etc/sudoers.d/browserbox
  • lines changed 3, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 2, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/home/browser/.bashrc
  • lines changed 45, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 5, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/home/browser/gbibAddTools
  • lines changed 3, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/home/browser/updateBrowser
  • lines changed 1, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/root/changes.txt
  • lines changed 18, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/root/hg.conf.offline
  • lines changed 437, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/root/updateBrowser
  • lines changed 2, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/root/updateBrowser.sh
  • lines changed 179, context: html, text, full: html, text
    various changes to gbib config files
  • lines changed 101, context: html, text, full: html, text
    more config file changes for gbib
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 9, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/usr/local/apache/cgi-bin/hg.conf.local
  • lines changed 2, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/usr/local/apache/cgi-bin/hgNear
  • lines changed 19, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/usr/local/apache/htdocs/images/title.jpg
  • lines changed 0, context: html, text, full: html, text
    various changes to gbib config files
• src/browserbox/var/spool/cron/crontabs/root
  • lines changed 12, context: html, text, full: html, text
    more config file changes for gbib
• src/hg/hgMirror/hgMirror
  • lines changed 2, context: html, text, full: html, text
    removing tableList syncing from hgMirror on gbib, as it's not on hgdownload
  • lines changed 376, context: html, text, full: html, text
    many changes to hgMirror. I am definitely not proud of this script. Codereview is not critical here, as the script runs only on virtual machines
    and not on the RR.
    This commit changes the way gbib does its post-rsync update, it's now in
    the jobscript, not in the main CGI anymore. It stops/starts the mysql
    server before/after updates and does a mysqlcheck after it.
    The postRsyncUpdates iterate over all DBs now and not only hg19.
    Some redundant code was removed from the file size calculation.
    I am now trying to remove outdated and useless ENCODE files from the download, this
    decreased filesize I believe by 500GB in hg19.
    The whole genome selection menu is build differently now.
    most of the track data is now stored in a pickled file for faster
    loading.
    There is a "please wait" message shown while the track data is built.
    Deactivating the "deflate" apache module allows to show the message in
    the browser (even though there still seems to be some stdout buffering going
    on, somewhere)
    Thanks for reading until here.
    
  • lines changed 48, context: html, text, full: html, text
    fixing broken show subtracks button in hgMirror, refs #14067
  • lines changed 9, context: html, text, full: html, text
    adding a list of links to the track groups to hgMirror, there are toomany tracks in hg19 currently to fit onto a screen.
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 33, context: html, text, full: html, text
    fix bug in mapBox placement when passing in negative numbers
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 6, context: html, text, full: html, text
    fix problem that resulted in base mode not working in maf display iflooking at the very beginning of a sequence.
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 5, context: html, text, full: html, text
    Adding note about using thrid-party tool for windows, refs #12843
  • lines changed 3, context: html, text, full: html, text
    changed gbib internal filenames to make reduce gbib size
  • lines changed 1, context: html, text, full: html, text
    typo in last commit
  • lines changed 2, context: html, text, full: html, text
    Re-wording sentence about ifup command in the GBiB, refs #12843
  • lines changed 10, context: html, text, full: html, text
    changing all gbib command line commands to be prefixed with gbib*.Adding a new command gbibMirrorOff.
    
  • lines changed 3, context: html, text, full: html, text
    adding reference to putty for windows to gbib manual
  • lines changed 1, context: html, text, full: html, text
    fixing typo in gbib manual
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    adding link to blog on homepage left blue bar, adding link to blog at top of News section, adding blog announcement news item plus commented-out short version, and adding blog announcement to news archives
• src/hg/htdocs/inc/ebola.topbar.aux.html
  • lines changed 3, context: html, text, full: html, text
    adding a link to the antibody resources page on the top toolbar
  • lines changed 2, context: html, text, full: html, text
    Removing a link to the current page from the topbar
• src/hg/htdocs/inc/ebola.topbar.html
  • lines changed 2, context: html, text, full: html, text
    adding a link to the antibody resources page on the top toolbar
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Added menu bar link to Blog.
• src/hg/htdocs/index.html
  • lines changed 2, context: html, text, full: html, text
    adding link to blog on homepage left blue bar, adding link to blog at top of News section, adding blog announcement news item plus commented-out short version, and adding blog announcement to news archives
• src/hg/htdocs/indexNews.html
  • lines changed 62, context: html, text, full: html, text
    adding link to blog on homepage left blue bar, adding link to blog at top of News section, adding blog announcement news item plus commented-out short version, and adding blog announcement to news archives
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v307
• src/hg/lib/fileUi.c
  • lines changed 13, context: html, text, full: html, text
    removed my useless function again after code review, refs #14118
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    adding a hg.conf option "isGbib", after gbib meeting
• src/hg/lib/web.c
  • lines changed 9, context: html, text, full: html, text
    allow both alpha and beta binaries to run on gbib
• src/hg/makeDb/doc/hg16.txt
  • lines changed 15, context: html, text, full: html, text
    Built hg16ToHg38 liftOver chains (requested by DGV contributor Jeff MacDonald).
• src/hg/makeDb/doc/hg17.txt
  • lines changed 15, context: html, text, full: html, text
    Built hg17ToHg38 liftOver chains (requested by DGV contributor Jeff MacDonald).
• src/hg/makeDb/doc/hg38.txt
  • lines changed 39, context: html, text, full: html, text
    Two of the three alt sequences for chrX are in PAR1; the other doesn'toverlap either par. Added two chrX_*_alt...PAR1 entries to the par table.
    
  • lines changed 150, context: html, text, full: html, text
    Regenerated most snp141* tables and snp-masked sequences after Matt foundthat MultipleAlignments was assigned incorrectly for a region of PAR1
    that happens to have a couple alt sequences in hg38. In an earlier
    commit I added the chrX_*alts to the par table; then in this commit I
    re-ran the SNP pipeline from snpnNcbiToUcsc (which uses par.bed) onward.
    I also turned a sequence of 3 45-minute commands into a 10-minute cluster
    job followed by one 45-minute sort.
    refs #13309
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    Added bosTau8; refs #13852
  • lines changed 2, context: html, text, full: html, text
    Updated file paths; refs #13852
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
  • lines changed 2, context: html, text, full: html, text
    NCBI changed the ccds tables yet again. Remind me why we're keepingthis table up-to-date?
    
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 9, context: html, text, full: html, text
    NCBI changed the ccds tables yet again. Remind me why we're keepingthis table up-to-date?
    
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • lines changed 30, context: html, text, full: html, text
    NCBI changed the ccds tables yet again. Remind me why we're keepingthis table up-to-date?
    
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 8, context: html, text, full: html, text
    NCBI changed the ccds tables yet again. Remind me why we're keepingthis table up-to-date?
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    changed minCheck per code review #14113
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on Budgerigar (melUnd1), Drosphila (droYak1), Gibbon (nomLeu1), and Nile Tilapia (oreNil2) track description pages
• src/hg/makeDb/trackDb/chainCi2.html
  • lines changed 21, context: html, text, full: html, text
    Chainging links on urchin (strPur2) track description pages
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    adding flyBaseGene experiment track refs #14024
• src/hg/makeDb/trackDb/drosophila/geneMapper.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on Budgerigar (melUnd1), Drosphila (droYak1), Gibbon (nomLeu1), and Nile Tilapia (oreNil2) track description pages
• src/hg/makeDb/trackDb/ebola/eboVir2/pdb.html
  • lines changed 7, context: html, text, full: html, text
    Updating reference on Ebola PDB track description page.
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPan.ra
  • lines changed 543, context: html, text, full: html, text
    adding missing file
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.netMhcPanII.ra
  • lines changed 19, context: html, text, full: html, text
    fixes to netMhcII track
  • lines changed 197, context: html, text, full: html, text
    fixes to netmhc track, after email from david
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fixes to netmhc track, after email from david
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 84, context: html, text, full: html, text
    Adding note about paragraph about differences between 160 Accessions and 160 Strains track. Some white space changes. Removed mentions of phast. Updated references. Changed name of 160 Strains track.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcell.html
  • lines changed 1, context: html, text, full: html, text
    Updating references on eboVir3 track description pages
• src/hg/makeDb/trackDb/ebola/eboVir3/muPIT.html
  • lines changed 8, context: html, text, full: html, text
    Updating references on eboVir3 track description pages
• src/hg/makeDb/trackDb/ebola/eboVir3/pdb.html
  • lines changed 6, context: html, text, full: html, text
    Updating reference on Ebola PDB track description page.
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra
  • lines changed 1, context: html, text, full: html, text
    Adding note about paragraph about differences between 160 Accessions and 160 Strains track. Some white space changes. Removed mentions of phast. Updated references. Changed name of 160 Strains track.
• src/hg/makeDb/trackDb/ebola/gireReferences.html
  • lines changed 7, context: html, text, full: html, text
    Updating references on eboVir3 track description pages
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on Budgerigar (melUnd1), Drosphila (droYak1), Gibbon (nomLeu1), and Nile Tilapia (oreNil2) track description pages
• src/hg/makeDb/trackDb/human/hg17/encodeUtexStage.html
  • lines changed 1, context: html, text, full: html, text
    Changing occurence to occurrence, refs #14062
• src/hg/makeDb/trackDb/human/hg18/encodeUtexStage.html
  • lines changed 1, context: html, text, full: html, text
    Changing occurence to occurrence, refs #14062
• src/hg/makeDb/trackDb/human/hg19/evsEsp6500.html
  • lines changed 1, context: html, text, full: html, text
    Changing occurence to occurrence, refs #14062
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    making gencode v20 visible
• src/hg/makeDb/trackDb/netCi2.html
  • lines changed 15, context: html, text, full: html, text
    Chainging links on urchin (strPur2) track description pages
• src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on Budgerigar (melUnd1), Drosphila (droYak1), Gibbon (nomLeu1), and Nile Tilapia (oreNil2) track description pages
• src/hg/makeDb/trackDb/urchin/strPur2/description.html
  • lines changed 2, context: html, text, full: html, text
    Chainging links on urchin (strPur2) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndPairs.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on zebrafish (danRer4) track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndSingles.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on zebrafish (danRer4) track description pages
• src/hg/near/hgNear/hgNear.c
  • lines changed 7, context: html, text, full: html, text
    refuse to run hgNear on gbib
  • lines changed 1, context: html, text, full: html, text
    fixing typos in last commit
• src/hg/utils/otto/gwas/expectedColumns.txt
  • lines changed 2, context: html, text, full: html, text
    GWAS changed the name of the columns in their database, but the contentseems roughly the same.
    
• src/userApps/fetchKentSource.sh
  • lines changed 1, context: html, text, full: html, text
    adding mafToSnpBed to the utils build refs #14079
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v307 final build refs #14072

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• files changed: 84