All File Changes

v343_base to v344_preview (2017-01-09 to 2017-01-16) v344

• confs/hgwbeta.hg.conf
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    05a7268d74bfe3d74f633b1bc1123d6bf1d418c0 Sun Jan 15 01:11:32 2017 -0800
    Installing updated hg.conf files from UCSC servers
• confs/preview.hg.conf
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    05a7268d74bfe3d74f633b1bc1123d6bf1d418c0 Sun Jan 15 01:11:32 2017 -0800
    Installing updated hg.conf files from UCSC servers
• python/lib/ucscGb/qa/qaUtils.py
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    c3aa94b6be83af4de2e755eaaf1e1294b795963e Tue Jan 10 09:46:49 2017 -0800
    Adding two new functions to qaUtils. Both are intended to be used to run various commands and manipulate the output beyond the original runCommand function. runCommandMergedOutErr combines both stdout and stderr into a single output and returns this. runCommandNoAbort skips the returncode check of the other versions of runCommand and instead returns the returncode to the user alongside the stdout and stderr of the command. Both added at the recommendation of Jonathan in CR, refs #18564
• python/lib/ucscGb/qa/tables/factory.py
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    853fb0e2d808a14d43a223ae7f19fdfd63e18869 Tue Jan 10 10:02:12 2017 -0800
    Changes to positionalQa.py include having it call new runCommandMergedOutErr function when running runBits. Also includes new runCommandNoAbort to replace Popen calls. Similar things was done in factory.py and genePredQa.py, Popen call were replaced with calls to new function runCommandNoAbort. Work to runBits done at Jonathan's request in CR, but other changes were made for the sake of consistency. refs #18564
• python/lib/ucscGb/qa/tables/genePredQa.py
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    853fb0e2d808a14d43a223ae7f19fdfd63e18869 Tue Jan 10 10:02:12 2017 -0800
    Changes to positionalQa.py include having it call new runCommandMergedOutErr function when running runBits. Also includes new runCommandNoAbort to replace Popen calls. Similar things was done in factory.py and genePredQa.py, Popen call were replaced with calls to new function runCommandNoAbort. Work to runBits done at Jonathan's request in CR, but other changes were made for the sake of consistency. refs #18564
• python/lib/ucscGb/qa/tables/positionalQa.py
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    853fb0e2d808a14d43a223ae7f19fdfd63e18869 Tue Jan 10 10:02:12 2017 -0800
    Changes to positionalQa.py include having it call new runCommandMergedOutErr function when running runBits. Also includes new runCommandNoAbort to replace Popen calls. Similar things was done in factory.py and genePredQa.py, Popen call were replaced with calls to new function runCommandNoAbort. Work to runBits done at Jonathan's request in CR, but other changes were made for the sake of consistency. refs #18564
• python/lib/ucscGb/qa/tables/pslQa.py
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    5b4eab4fd242caef8f8dd352d8f7f82b18cd4dba Tue Jan 10 09:55:40 2017 -0800
    Fixed error where qaGbTracks would crash if output from tdbQuery was empty. Included new runCommondNoAbort in the script. Instead of deleting db.sizes file created during process, will instead keep this and utilize it if it already exists which prevents the file from being created and deleted multiple times if qaGbTracks is run on multiple psl tracks. All added at Jonathan's recommendation in CR, refs #18564
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    e69aa3d527905a950a684ffc450ceed65b52368c Tue Jan 10 10:19:26 2017 -0800
    Correcting indentation on a few lines, no redmine
• src/hg/hgTracks/bigBedTrack.c
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    c10fd16316fab8dfd1f823c5bc6e10ef55dadf84 Wed Jan 11 13:51:14 2017 -0800
    fix bug #18657, by closing an open bigBed file
• src/hg/hgc/hgc.c
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    2f262ebebd76067ea983cfeb7454ed626a450c61 Fri Jan 6 15:45:54 2017 -0800
    In mysql 5.7 with the default configuration, it is now an error if a SELECT list using DISTINCT does not include all ORDER BY fields. The solution is to add the ORDER BY fields to the end of the SELECT list if they're not already included. The extra columns returned by the query are ignored. refs #18626, #18597
• src/hg/htdocs/images/Parus_major.jpg
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    c26bea0c9dd5b61a617482c7f350e9d659c5695b Mon Jan 9 13:39:56 2017 -0800
    Great tit birds male and female Luc Viatour and Francis C. Franklin wikimedia commons refs #18629
• src/hg/lib/ensGene.as
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    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/genePred.as
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    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/genePredExt.as
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    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/hAnno.c
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    6072cb04b34e57ebdef620512124c4d8722b79df Fri Jan 13 11:09:48 2017 -0800
    hAnnoGetAssembly assumed that db.2bit would be found in hDbDbNibPath(db) but for old nib/ assemblies it is one level up in /gbdb/db/. Similar to hdb's hNibForChrom, test file existence and look in ../ as a backup. fixes #18445
• src/hg/lib/hdb.c
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    2f262ebebd76067ea983cfeb7454ed626a450c61 Fri Jan 6 15:45:54 2017 -0800
    In mysql 5.7 with the default configuration, it is now an error if a SELECT list using DISTINCT does not include all ORDER BY fields. The solution is to add the ORDER BY fields to the end of the SELECT list if they're not already included. The extra columns returned by the query are ignored. refs #18626, #18597
• src/hg/lib/knownGene.as
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    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/refFlat.as
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    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/sangerGene.as
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    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/web.c
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    2f262ebebd76067ea983cfeb7454ed626a450c61 Fri Jan 6 15:45:54 2017 -0800
    In mysql 5.7 with the default configuration, it is now an error if a SELECT list using DISTINCT does not include all ORDER BY fields. The solution is to add the ORDER BY fields to the end of the SELECT list if they're not already included. The extra columns returned by the query are ignored. refs #18626, #18597
• src/hg/makeDb/doc/melGal5/initialBuild.txt
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    674c373d41c24a782250680d5d7a05efd4c37e36 Thu Jan 12 14:14:40 2017 -0800
    running up melGal5 assembly for rn6 conservation track refs #18656
• src/hg/makeDb/doc/rn6.txt
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    4fac872bbc8f95a8b0e8c20b78060f904616d788 Wed Jan 11 13:17:34 2017 -0800
    starting pair wise alignments for conservation track refs #18656
• src/hg/makeDb/genbank/etc/align-genbank
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    7954e70503f29182076239317f5ceecf76fe676b Wed Jan 11 17:23:18 2017 -0800
    fixes #18627
• src/hg/makeDb/schema/all.joiner
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    d8c373a4f759373703b194c65b89efa763282e71 Tue Jan 10 13:07:25 2017 -0800
    fix up some problems in all.joiner that resulted from the Great Genbank Migration
• src/hg/makeDb/trackDb/alpaca/vicPac1/description.html
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    1386a89441229b67baa984cc8bfe2e9728858c69 Thu Jan 12 16:43:07 2017 -0800
    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/alpaca/vicPac2/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
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• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
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• src/hg/makeDb/trackDb/baboon/papHam1/description.html
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• src/hg/makeDb/trackDb/balAcu/balAcu1/description.html
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• src/hg/makeDb/trackDb/bats/rouAeg1/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/birds/amaVit1/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/birds/aptMan1/description.html
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• src/hg/makeDb/trackDb/birds/aquChr2/description.html
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• src/hg/makeDb/trackDb/birds/geoFor1/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/bison/bisBis1/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/bonobo/panPan1/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/bonobo/panPan2/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
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    2516bdd7c30a701809caed89993ea908dc214b02 Fri Jan 13 13:25:48 2017 -0800
    correct breaks after bioproject and biosample links refs #16036
• src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
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    1386a89441229b67baa984cc8bfe2e9728858c69 Thu Jan 12 16:43:07 2017 -0800
    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/calMil/calMil1/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/cat/felCat5/description.html
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    Changing label from GenBank accession ID to Accession ID, #refs 18190
• src/hg/makeDb/trackDb/cat/felCat8/description.html
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• src/hg/makeDb/trackDb/chicken/galGal4/description.html
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• src/hg/makeDb/trackDb/chicken/galGal5/description.html
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• src/hg/makeDb/trackDb/chimp/panTro4/description.html
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• src/hg/makeDb/trackDb/chimp/panTro5/description.html
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• src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html
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• src/hg/makeDb/trackDb/chlorocebus/chlSab2/description.html
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• src/hg/makeDb/trackDb/ciliate/oxyTri2/description.html
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• src/hg/makeDb/trackDb/cow/bosTau7/description.html
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• src/hg/makeDb/trackDb/cow/bosTau8/description.html
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• src/hg/makeDb/trackDb/cow/snp148.shared.html
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    ca2d8076cac8fdc1bec0e6399f9d8fe8b255517d Wed Jan 11 13:37:53 2017 -0800
    edited shared.html pages per refs #17960
• src/hg/makeDb/trackDb/criGri/criGri1/description.html
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• src/hg/makeDb/trackDb/dog/canFam3/description.html
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• src/hg/makeDb/trackDb/drosophila/dm6/description.html
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• src/hg/makeDb/trackDb/drosophila/droSim2/description.html
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• src/hg/makeDb/trackDb/ebola/bunEbo1/description.html
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• src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
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• src/hg/makeDb/trackDb/gorilla/gorGor4/description.html
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    1386a89441229b67baa984cc8bfe2e9728858c69 Thu Jan 12 16:43:07 2017 -0800
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    2432c31310796c29d4cdb2f878320871cd4f66d4 Fri Jan 13 15:25:49 2017 -0800
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    db3a935a53d2763ecdc3b6840c277396ff006ab0 Mon Jan 9 10:43:01 2017 -0800
    Adding quotes around link to minimal.hg.conf so it properly prints
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• src/utils/qa/checkMachineName.csh
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    9b1eb09e57cf432a1efe4fae3a240c66babfc2cc Tue Jan 10 13:06:05 2017 -0800
    Adding genome-asia to machine name list. Part of work to make genome-asia show up in updateTimes output, refs #18617
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    Adding exception for genome-asia to and if statement. Part of work to make genome-asia show up in updateTimes output, refs #18617
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    Making script aware of genome-asia, refs #18646
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    Adding helper script that runs qaAutoTrack.sh for all current autopushed tracks. Updating makefile so that this new script will be copied when make is run. refs #12561
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    df0b2815a68268581da0984e2de1d718a9dcb661 Wed Jan 11 15:54:16 2017 -0800
    Changes based on CR. Added new variables for previous log time and current runtime. Changed log file name format, now includes current runtime in name. Changed way previous log file was found, now can compare to previous logs from the same day. Simplified checks for newLogDir and overwriteLogUrl. refs #18632
• src/utils/qa/realTime.csh
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    d3f13ad7ba599c99681f0c5924eff738971ea97e Tue Jan 10 13:51:08 2017 -0800
    Adding genome-asia to output for both scripts, refs #18617
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    22341d9f9e935e2adb290488f5321fee77e770c3 Fri Jan 13 11:18:00 2017 -0800
    Adding helper script that runs qaAutoTrack.sh for all current autopushed tracks. Updating makefile so that this new script will be copied when make is run. refs #12561
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    Minor tweak to usage message for runQaAutoTrack.sh, refs #12561
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    d3f13ad7ba599c99681f0c5924eff738971ea97e Tue Jan 10 13:51:08 2017 -0800
    Adding genome-asia to output for both scripts, refs #18617
• src/utils/qa/weeklybld/buildEnv.csh
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