Chains and Nets QA

Nets/Chains: The primary thing is to run this script: chainNetTrio.csh [database] [other database]

ex: chainNetTrio.csh tetNig2 GasAcu1

I recommend making a separate directory as the script generates a bunch of files. Ann said she changed the script to tell you which files to look at, but in case it doesn't for whatever reason, you want to look at

• .chain.* , *.chain2.* , *.net.*

Just read through making sure all the checks went okay and doing the few manual checks

If you're QAing, for example, chainNet from tetNig2 to hg19, you will also see, in the file section of the pushQ entry, some files listed:

/usr/local/apache/htdocs/goldenPath/tetNig2/vsHg19/*.txt /usr/local/apache/htdocs/goldenPath/tetNig2/vsHg19/*.gz /usr/local/apache/htdocs/goldenPath/tetNig2/vsHg19/axtNet/* /usr/local/apache/htdocs/goldenPath/tetNig2/liftOver/tetNig2ToHg19.over.chain.gz /gbdb/tetNig2/liftOver/tetNig2ToHg19.over.chain.gz

You can read about liftOver here (if you don't already know about it). [1]

And you can test your liftOver chains in two CGIs: hgLiftOver and hgConvert. [2] [3]

To get to the hgConvert CGI, start from your assembly (that your chains/nets are on -- tetNig2 in this example) and press the "Convert" link in the top blue navigation bar.

To get the to hgLiftOver CGI, start from the home page and cick on "utilities" link, then click on "Batch Coordinate Conversion (liftOver)".

Not that you will need to stage these on beta, but just FYI, files that start with /usr/local/apache/htdocs/goldenPath get pushed from hgwdev to hgwbeta and the RR machines. Files that start with /gbdb/ get pushed from hgwdev to hgnfs1.

To push the files gbdb to hgwbeta: cd /gbdb cd “assembly” cd liftover

Check on hgwbeta to see if that directory is there.

If it isn’t you need to send a push-request with the following info: Please push file path/filename from hgwdev to hgnfs1

Reason: staging liftOver file on hgwbeta.

Additionally, the hgcentral database contains a line that needs to be edited in order to enable the liftOvers to work on beta and on the RR. To do this:

Hgdev:

   1)	hgsql hgcentraltest;
   2)	show tables;
   3)	desc liftOverChain;
   4)	select * from liftOverChain where fromDb like “assembly” and toDb like “assembly%”;
   5)	check on hgcentralbeta using the same sql statements above.
   6)	Find the line on dev and copy without the pipes at the front and end.
   7)	Paste in a text editor.
      a. In the text editor surround the newly pasted text in ( ).  
      b. Add the statement: insert into liftOverChain values);
      c. Revmove spaces and pipes. Place all text into quotes.
      d. Statement should look like this: insert into liftOverChain values (“ “,” “);
   8) In hgwbeta:
      a. Paste this statement in the terminal (must in database) place your hands under your legs and make sure it is correct,   press enter
   9) Do this statement again to make sure that it has been inserted: select * from liftOverChain where fromDb like “assembly” and toDb like “assembly%”;
  10)	Look at covert and liftover dropdowns on beta to confirm push. 
  11)	Repeat when ready to release to RR (hgcentral)

Here is some old documentation: [4]

Testing Liftovers:

  1) Pick a top level short net and zoom in.
  2) Paste in browser search position in hgliftover 
  3) Click submit
  4) Compare output back to the net in the browser. It should be the same.

Testing Convert:

  1) Convert with the same net chosen
  2) Check to make sure that it matches the net. 

Moving files to RR:

  1) Push tables from hgwbeta to RR with push request.
  2) Push trackDb from mysqlbeta to mysqlrr.
  3) Test

Add line to hgcentral see above.

Push file sections of pushQ (liftOver file and vs directory)

Moving files to hgdownload:

  1) Compare http://hgwdev.cse.ucsc.edu/downloads.html with http://hgdownload.cse.ucsc.edu/downloads.html
  2) Check for liftOver files and if yours is missing on hgdownloads you will need to ask for a push of the corresponding .over.chain.gz to be moved to the download server.
  3) You will then need to add the link to to the downloads page:
     a. To get to downloads on hgwdev:
       From your home directory 
        1. cd browser
        2. cvsup
        3. vi downloads.htm
        4. Go to the line that has the previous version of the chains and hit yy p (this copies and pastes the text below) 
        5. Correct the links and names and save.
        6. cvs commit 
        7. make alpha in browser tree.
        8. and push-request this file to be move to RR