8f9914e3e7b315e85f00c6e3cb6b9d0d9b631e8b brianlee Wed Apr 24 15:16:17 2013 -0700 Changing comments in script to match Ensemble QA wiki notes, adding lnk to wiki reminder diff --git src/utils/qa/qaEnsGenes.csh src/utils/qa/qaEnsGenes.csh index 1faf399..d681a7a 100755 --- src/utils/qa/qaEnsGenes.csh +++ src/utils/qa/qaEnsGenes.csh @@ -215,36 +215,35 @@ echo "\n\n----------------------" echo "A few tracks have another table or two associated with them. For" echo "example, when Ensembl uses different scaffold names than we do, there" echo "should be a translation table called: ensembleGeneScaffold. This" echo "table supports a separate track called: Ensembl Assembly." echo "Assemblies with a UCSC Gene track should also have a table called:" echo "knownToEnsembl. Here's what this assembly has:" echo hgsql -Ne "SHOW TABLES LIKE 'ensemblGeneScaffold'" $db hgsql -Ne "SHOW TABLES LIKE 'knownToEnsembl'" $db end # huge loop through each database # remember the hgFixed.trackVersion table echo "\n\n----------------------" -echo "Don't forget to also push (to beta and then to the RR) the appropriate" -echo "rows from the trackVersion table in the hgFixed database." -echo "These rows allow the correct version number to be displayed in hgTrackUi." -echo "\nEdit the following pseudo-SQL statement to include only those" -echo "assemblies you will be pushing:" -echo 'hgsql -Ne "SELECT * FROM trackVersion WHERE version = ensGeneUpdateVersion AND db like 'dbsYouWillPush'" hgFixed' +echo "Don't forget to also push (to beta and then to the RR)" +echo "the trackVersion table in the hgFixed database." +echo "There are rows to allow the correct version number to be displayed in hgTrackUi." +echo "Before you push the table, check the differences with compareWholeTable.csh hgFixed trackVersion" +echo "See Wiki for more details: http://genomewiki.cse.ucsc.edu/genecats/index.php/Ensembl_QA" # make sure the date column has been updated echo "\n\n----------------------" echo "the dateReference column in the hgFixed.trackVersion table" echo "should say 'current' for your database (or all):" hgsql -Ne "SELECT db, dateReference FROM trackVersion WHERE version = $ver AND name = 'ensGene' ORDER BY db" hgFixed # check that the corresponding upstream MAF files have been updated echo "\n\n----------------------" echo "In conjunction with an Ensembl Gene update, some upstream MAF files need" echo "to be rebuilt. Specifically those for: ornAna1, fr2, gasAcu1, oryLat2" echo "Check for them here (look for new dates) there should be 3 for each db:" echo "hgwdev:/data/apache/htdocs-hgdownload/goldenPath/<db>/multiz*way/maf/ensGene.upstream?000.maf.gz" echo