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| Nets/Chains:
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| The primary thing is to run this script:
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| chainNetTrio.csh [database] [other database]
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| ex: chainNetTrio.csh tetNig2 GasAcu1
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| I recommend making a separate directory as the script generates a bunch
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| of files. Ann said she changed the script to tell you which files to
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| look at, but in case it doesn't for whatever reason, you want to look at
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| *.chain.* , *.chain2.* , *.net.*
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| Just read through making sure all the checks went okay and doing the few
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| manual checks
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| If you're QAing, for example, chainNet from tetNig2 to hg19, you will also
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| see, in the file section of the pushQ entry, some files listed:
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| /usr/local/apache/htdocs/goldenPath/tetNig2/vsHg19/*.txt
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| /usr/local/apache/htdocs/goldenPath/tetNig2/vsHg19/*.gz
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| /usr/local/apache/htdocs/goldenPath/tetNig2/vsHg19/axtNet/*
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| /usr/local/apache/htdocs/goldenPath/tetNig2/liftOver/tetNig2ToHg19.over.chain.gz
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| /gbdb/tetNig2/liftOver/tetNig2ToHg19.over.chain.gz
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| You can read about liftOver here (if you don't already know about it).
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| [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert]
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| And you can test your liftOver chains in two CGIs: hgLiftOver and hgConvert.
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| [http://hgwdev.cse.ucsc.edu/cgi-bin/hgLiftOver]
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| [http://hgwdev.cse.ucsc.edu/cgi-bin/hgConvert]
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| To get to the hgConvert CGI, start from your assembly (that your chains/nets
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| are on -- tetNig2 in this example) and press the "Convert" link in the top blue
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| navigation bar.
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| To get the to hgLiftOver CGI, start from the home page and cick on
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| "utilities" link, then click on "Batch Coordinate Conversion (liftOver)".
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| Not that you will need to stage these on beta, but just FYI, files that start
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| with /usr/local/apache/htdocs/goldenPath get pushed from hgwdev to hgwbeta and
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| the RR machines. Files that start with /gbdb/ get pushed from hgwdev to hgnfs1.
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| To push the files gbdb to hgwbeta:
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| cd /gbdb
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| cd “assembly”
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| cd liftover
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| Check on hgwbeta to see if that directory is there.
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| If it isn’t you need to send a push-request with the following info:
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| Please push file path/filename
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| from hgwdev to hgnfs1
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| Reason: staging liftOver file on hgwbeta.
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| Additionally, the hgcentral database contains a line that needs to be edited
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| in order to enable the liftOvers to work on beta and on the RR. To do this:
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| Hgdev:
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| 1) hgsql hgcentraltest;
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| 2) show tables;
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| 3) desc liftOverChain;
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| 4) select * from liftOverChain where fromDb like “assembly” and toDb like “assembly%”;
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| 5) check on hgcentralbeta using the same sql statements above.
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| 6) Find the line on dev and copy without the pipes at the front and end.
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| 7) Paste in a text editor.
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| a. In the text editor surround the newly pasted text in ( ).
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| b. Add the statement: insert into liftOverChain values);
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| c. Revmove spaces and pipes. Place all text into quotes.
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| d. Statement should look like this: insert into liftOverChain values (“ “,” “);
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| 8) In hgwbeta:
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| a. Paste this statement in the terminal (must in database) place your hands under your legs and make sure it is correct, press enter
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| 9) Do this statement again to make sure that it has been inserted: select * from liftOverChain where fromDb like “assembly” and toDb like “assembly%”;
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| 10) Look at covert and liftover dropdowns on beta to confirm push.
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| 11) Repeat when ready to release to RR (hgcentral)
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| Here is some old documentation: [http://hgwdev.cse.ucsc.edu/qa/test-protocols/tracks/liftover.html]
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| Testing Liftovers:
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| 1) Pick a top level short net and zoom in.
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| 2) Paste in browser search position in hgliftover
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| 3) Click submit
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| 4) Compare output back to the net in the browser. It should be the same.
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| Testing Convert:
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| 1) Convert with the same net chosen
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| 2) Check to make sure that it matches the net.
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| Moving files to RR:
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| 1) Push tables from hgwbeta to RR with push request.
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| 2) Push trackDb from mysqlbeta to mysqlrr.
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| 3) Test
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| Add line to hgcentral see above.
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| Push file sections of pushQ (liftOver file and vs directory)
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| Moving files to hgdownload:
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| 1) Compare http://hgwdev.cse.ucsc.edu/downloads.html with http://hgdownload.cse.ucsc.edu/downloads.html
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| 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.
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| 3) You will then need to add the link to to the downloads page:
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| a. To get to downloads on hgwdev:
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| From your home directory
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| 1. cd browser
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| 2. cvsup
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| 3. vi downloads.htm
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| 4. Go to the line that has the previous version of the chains and hit yy p (this copies and pastes the text below)
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| 5. Correct the links and names and save.
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| 6. cvs commit
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| 7. make alpha in browser tree.
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| 8. and push-request this file to be move to RR
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