Chains and Nets QA

Prior to QAing on hgwbeta: Pushing from hgwdev

1) Use sudo mypush to push chain/net tables from hgwdev to hgwbeta if this isn't part of a new assembly (the files have most likely been pushed). This will include 3 tables: a chain, net and chain link table. Syntax for this command is: sudo mypush [from database] [tableName] mysqlbeta. See the example below:

• hgwdev: sudo mypush danRer6 chainMm9 mysqlbeta
• hgwdev: sudo mypush danRer6 netMm9 mysqlbeta
• hgwdev: sudo mypush danRer6 chainMm9Link mysqlbeta

2) "Make beta" on beta so that trackDb is updated to include the tables just pushed. Syntax for this command is: make strict DBS=[from database].

• ex: hgwbeta: make beta DBS=danRer6

3) Email a push request to copy /gbdb/[from database]/liftOver/[from database]To[to database].over.chain.gz from hgwdev to hgnfs1. Note that the liftover file will now be available on both beta and RR as it is on hgnfs1. However, because the hgcentral database on the RR doesn't have an entry pointing to this file, it will only be visible on beta. Check to see if the push is needed first by clicking on the convert navigation link and checking if the other assembly is in the drop down.

• ex: email: Please push /gbdb/danRer6/liftOver/danRer6ToMm9.over.chain.gz from hgwdev to hgnfs1.

• note that the to database is capitalized as shown above in bold.

4) Add a line from hgcentraltest database to hgcentralbeta so that file pushed in step 3 is visible on beta (this is similar to the same way that tables are not visible until trackDb is updated). To do this you first find the line on hgcentraltest.liftOverChain, copy it and then insert it into hgcentralbeta.liftOverChain. Note that it is very easy to make a mistake that can bring down hgcentral so make sure that your syntax and mysql statements are correct. See the example below:

• hgwdev: hgsql hgcentraltest

mysql> select * from liftOverChain where fromDb=“danRer6” and toDb=“mm9”;

• (copy the output into a text editor for later use)
• (go to hgwbeta)

ssh hgwbeta

hgwbeta: hgsql hgcentralbeta

• Repeat the previous mysql statement to make sure that this line isn't already on hgcentralbeta (duplicate lines are hard to remove):

mysql> select * from liftOverChain where fromDb=“danRer6” and toDb=“mm9”;

• (put the values copied from hgcentral test into this statement. please note that the formatting must be followed exactly or output it to a file to be loaded in the next step)

mysql (on hgwbeta)> insert into liftOverChain values ("danRer6","mm9","/gbdb/danRer6/liftOver/danRer6ToMm9.over.chain.gz","0.1","0","0","Y","1","N");

or hgwbeta> hgsql -e "load data local infile 'fileName' into table liftOverChain" hgcentralbeta

• (checking your work)

mysql> select * from liftOverChain where fromDb=“danRer6” and toDb=“mm9”;