Assembly QA Part 4 RR Steps

This page is currently a draft in progress. For now, use Releasing an assembly instead.

Navigation Menu Home Page Assembly QA Part 1: DEV Steps Assembly QA Part 2: Track Steps Assembly QA Part 3: BETA Steps Assembly QA Part 4: RR Steps Assembly QA Part 5: Post Release Steps

RR: Populate spreadsheet steps

• We need to create a checklist for your RR steps.
• You can add a new tab to track RR steps, or you can pick up where you left off on the same tab as your "dev" and "beta" steps.

To populate the "wiki link" for each step, add this formula to cell A2 (or the row after your last "dev" step) in your new "track checklist" spreadsheet and drag the formula down:

A2 (or the row after your last "beta" step)

=HYPERLINK("http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_4_RR_Steps#"&SUBSTITUTE(B2," ", "_"),"link")

IMPORTANT: Drag the formula for "A" down the spreadsheet to populate the other rows.

To populate the "track checklist steps," add this formula to cell B2 ((or the row after your last "dev" step) in your new "track checklist" spreadsheet. Do NOT drag the formula down.

B2

=IMPORTXML("http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_4_RR_Steps#", "/html/body/div/div/div/div/div/h4/span/span")

This formula will populate all the rows below it with the wiki section titles. You do no need to drag this formula down.

RR: Push Request: rsync complete database

• Request an rsync of the entire database from mysqlbeta to mysqlrr/euro/asia.
• Request drop of trackDb_public and hgFindSpec_public from mysqlrr/euro/asia
• Request push of trackDb and friends
• See an example push request

RR: Push Downloads

If there are files associated with the track that are to be pushed to hgdownload, check to see that there is a README that makes sense and the files have an md5sum.txt file that goes with them and is correct. Check the file itself to make sure it is not corrupted and that it contains what is expected. If it is a gzipped file, you can do "zcat file.gz | head" and "zcat file.gz | tail" to look at it. Looking at the last part of the file can sometimes catch corruption that can't be seen by only looking at the first part.

Data files destined for hgdownload are organized on hgwdev at:

/usr/local/apache/htdocs-hgdownload/goldenPath/*

and can be viewed in a browser from http://hgdownload-test.cse.ucsc.edu/downloads.html. Non-data files (such as downloads.html) are in the "hgdownload" git repository. See the Static_Page_Protocol for instructions on checking out that repository. Push requests for downloads should look like something like this:

Please push files from here on hgwdev:
    /usr/local/apache/htdocs-hgdownload/goldenPath/$db/file
To here on hgdownload:
    /usr/local/apache/htdocs/goldenPath/$db/file
(in the path, "htdocs-hgdownload" should become "htdocs") 

RR: Push Request: start dump/autodump

• Database rsync should be complete before doing this.
• Request start of dump/autodump for your assembly on rr/euro/asia.

See this example push request.

Beta: Review copyHgcentral steps

You can copy items from hgcentraltest to hgcentralbeta with the copyHgcentral script. For the usage statement, run:

hgwdev > copyHgcentral -h

• The copyHgcentral script must be run in test mode first.
• Test mode will show you the state of hgcentraltest, hgcentralbeta and hgcentral.
• Once test mode has been run and reviewed, run execute mode to copy from hgcentraltest to hgcentralbeta.
• Note that test mode generates output files which must be manually deleted afterward. Be sure to run copyHgcentral in hive or your home directory and not in a directory where temp files should not be.
• Note that copyHgcentral can be run for "all" (blatServers, dbDb, defaultDb, genomeClade):

hgwdev > copyHgcentral test $db all dev beta

Beta: copyHgcentral test $db blatServers dev beta

Generates files, run in hive:

hgwdev > copyHgcentral test $db blatServers dev beta

hgwdev > copyHgcentral execute $db blatServers dev beta

You can also check on mysqlbeta:

use hgcentralbeta;

select * from blatServers where db='manPen1';

Beta: copyHgcentral test $db dbDb dev beta

Generates files, run in hive:

hgwdev > copyHgcentral test $db dbDb dev beta

hgwdev > copyHgcentral execute $db dbDb dev beta

You can also check on mysqlbeta:

use hgcentralbeta;

select * from dbDb where name='manPen1' \G;

Beta: copyHgcentral test $db defaultDb dev beta

Generates files, run in hive:

hgwdev > copyHgcentral test $db defaultDb dev beta

hgwdev > copyHgcentral execute $db defaultDb dev beta

You can also check on hgsqlbeta

use hgcentralbeta;

select * from defaultDb where name="manPen1"limit 1;

Beta: copyHgcentral test $db genomeClade dev beta

NOTE: This table probably will not need to be updated. It contains records like this:

mysql> select * from genomeClade order by rand() limit 5;
+-----------------+------------+----------+
| genome          | clade      | priority |
+-----------------+------------+----------+
| GRCh38.p2       | haplotypes |      134 |
| C. japonica     | worm       |       70 |
| Atlantic cod    | vertebrate |      125 |
| D. melanogaster | insect     |       10 |
| D. persimilis   | insect     |       55 |
+-----------------+------------+----------+

Generates files, run in hive:

hgwdev > copyHgcentral test $db genomeClade dev beta

hgwdev > copyHgcentral execute $db genomeClade dev beta

Beta: copyHgcentral: liftOverChain (manual move)

liftOverChain is not copied with the copyHgcentral script, it needs to be copied manually.

• Only copy lines from liftOverChain on hgcentraltest to hgcentralbeta if there are liftOver files listed in the pushQ and if the assemblies they go to/from exist on the RR.
• Check for lines in liftOverChain that should be in the pushQ, but aren't (e.g., the liftOver from a previous assembly).
• Add lines related to your assembly, any previous versions of your organism, and any other organisms that are associated with liftOver files and your assembly.
• More details on the Chain and Net QA wiki page.

 hgsql -Ne "SELECT * FROM liftOverChain WHERE fromDb = '$db' OR toDb = '$db'" hgcentraltest > chain.dev 

Check beta, load if not present and recheck:

 hgsql -h mysqlbeta -Ne "SELECT * FROM liftOverChain WHERE fromDb = '$db' OR toDb = '$db'" hgcentralbeta 

 hgsql -h mysqlbeta -e "LOAD DATA LOCAL INFILE 'chain.dev' INTO TABLE liftOverChain" hgcentralbeta

Beta: checkMetaData

After completing copyHgcentral steps, run checkMetaData.csh $db

• This checks that all of the metadata is the same on hgwdev and on hgwbeta.
• Run this script in a temporary folder or hive; it creates some comparison files that can be deleted after the check.

RR: Check all tracks on the RR

Check your track on the RR. Check that searches work (if not, you probably need to push the hgFindSpec_public table). Also check that all default tracks still display. If you filled in the "Release Log URL" field in the push queue, check the next day to be sure that the link from the release log works as expected.

RRs: Edit downloads.html

Check to see if the downloads files ought to have a link from downloads.html. If so, add the link and push downloads.html (after the files are already pushed!). NOTE: If you are pushing ENCODE tracks, when using a second/third/fourth version of the data there is often a "releaseLatest" directory that has the latest files. Be sure that you are not pushing the entire releaseLatest directory, only the files from there. Be sure to add a helpful sentence in your push-request to tip off the admin about this unusual push.

RR: Push chain/nets for other assemblies

• At the start of the RR steps, you asked for an rsync of your database from beta>rr/euro/asia, so you have already pushed the chain/nets within your database. Now we need to do this for any other databases (aka, other assemblies that your assembly has chain/net alignments to).
• Push trackDb & friends for any other databases
• Push chain/chainLink/net tables for each database.
• See this example push request .

RR: Chain chain/nets tracks for other assemblies

QA chain/nets for the other assemblies.

RR: Write Google Groups announcement

See announcement example.

RR: Write release log text in Redmine & close

🔵 Done with RR steps? Go to Assembly QA Part 5: Post Release Steps