MakePushQSql.pl

This script was written by Angie.

It is a script which assists developers in creating a qapushq table for a new genome db's push queue.

Suggested usage: makePushQSql.pl $db > ~/qapushq.$db.sql

It prints SQL commands (that look a lot like hgsqldump output) to stdout. It's best if you redirect the output to a file, edit it to make sure it's all correct, and then hgsql it on hgwbeta. After that point, use the web Push Queue tool to make any further changes.

When it can't figure out where a table belongs, or can't find an expected download file, it prints a message to stderr. When done, it prints more editing suggestions.

It uses trackDb and the joinableFields program to guess which tables belong to which tracks. However, sometimes there are a couple levels of indirection in all.joiner, and sometimes a table might be missing from all.joiner, but again it will alert you.

It does not look very hard for /gbdb/ files that may be associated with a track, but it provides some SQL commands to run on hgwdev to list extFile and wiggle table files in $db, and then you can edit those in.

Other known limitations:

• no concept of composite tracks (but I think those are still somewhat rare in initial releases)
• does not look for goldenPath/ stuff aside from bigZips, database and chromosomes -- I might add something for chains and nets.

This script also makes a single entry in the main pushQ table, which alerts QA to the fact that there is a new assembly sub-pushQ.