View source for Assembly QA Part 3 BETA Steps

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<span style="color:olive">See also: [[Releasing_an_assembly | Releasing an assembly (old steps)]] </span>

{| class=wikitable width=415 align=right
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<span style="color:darkorange">Navigation Menu</span>
:[[Assembly_Release_QA_Steps | Home Page]]
::[[Assembly QA Part 1 DEV Steps | Assembly QA Part 1: DEV Steps]]
::[[Assembly QA Part 2 Track Steps | Assembly QA Part 2: Track Steps]]
::[[Assembly QA Part 3 BETA Steps | Assembly QA Part 3: BETA Steps]]
::[[Assembly QA Part 4 RR Steps | Assembly QA Part 4: RR Steps]]
|}



====<span style="color:dodgerblue">Beta: Check for Ensembl tracks====
</span>

Before  pushing Ensembl tracks to beta, review the Ensembl wiki page and the [[Ensembl_QA]] script.

====<span style="color:dodgerblue">Beta: Copy redmine table list to hive====
</span>

In Redmine for your assembly, look at the field, "Table List." The engineer should have provided a path to redmine.$db.table.list
E.g.,
/hive/data/genomes/manPen1/redmine5515/redmine.manPen1.table.list

Your file contents should be something like this:
<pre>
head redmine.manPen1.table.list
hg38.chainManPen1
hg38.chainManPen1Link
hg38.netManPen1
manPen1.augustusGene
</pre>

Copy the file list to your assembly directory in hive. 

From hive, copy the file list to your assembly dir:

<pre>
cp /hive/data/genomes/manPen1/redmine5515/redmine.manPen1.table.list .
</pre>

Make a note of which assemblies are listed in this file list by looking at the unique databases/assemblies in column 1. For example:

<pre>
cut -d'.' -f1 redmine.manPen1.table.list | sort -u

hg38
manPen1
mm10
</pre>

====<span style="color:dodgerblue">Beta: Remove trackDb and hgFindSpec tables from your HIVE table list====
</span>

Remove tables from the list that start with trackDb or hgFindSpec:

sed -i.bak '/trackDb/d' cleanTableList

sed -i.bak '/hgFindSpec/d' cleanTableList

You'll be using this cleanTableList when doing your push.

====<span style="color:dodgerblue">Beta: Remove seq and extFile tables from your HIVE table list====
</span>

* Follow the steps above to remove seq or extFile tables from cleanTableList. 
* NOTE: Do not push seq or extFile tables from dev to beta. 
* You must use the copyExtSeqRows.csh script to move only the rows needed. 
* More information can be found [[Conservation_Track_QA#Figure_out_extFile_and_seq_tables| on the conservation track wiki page]].

====<span style="color:dodgerblue">Beta: Make clean table lists for pushing====
</span>

In the example above, the assembly manPen1 has tables in 3 different databases (manPen1, hg38, and mm10). 
It will be helpful to create a file, containing only table names, for each unique database listed in the Table List. These files can then be used for pushing tables in a loop. 

Using the example above, make 3 files with a list of tables to push for each assembly, 
* manPen1 with tables to push
<pre>
cat redmine.manPen1.table.list| grep "mm10." | cut -d'.' -f2 > mm10.push
</pre>
* hg38 with tables to push
<pre>
cat redmine.manPen1.table.list| grep "hg38." | cut -d'.' -f2 > hg38.push
</pre>
* mm10 with tables to push
<pre>
cat redmine.manPen1.table.list| grep "manPen1." | cut -d'.' -f2 > manPen1.push
</pre>

Since the above commands are specific to this example, you could have different patterns in your file list. Be sure to do comparison wc-l counts to be sure you didn't miss any tables.

====<span style="color:dodgerblue">Beta: Compare cleanTableList with dev mySQL table list====
</span>
It's worthwhile to compare the Redmin Table List with the tables that are on dev for your assembly database and also for any other databases listed (e.g., databases that have associated chain net files). 

<pre>
hgsql -Ne "show tables" manPen1 > devTablesAll

cat devTablesAll | grep -v trackDb | grep -v hgFindSpec > devMySqlTableList
</pre>

This command will show a side-by side difference between the tables on dev and the tables you will push. 
<pre>
sdiff -s devMySqlTableList manPen1.push
</pre>
Examine which tables are missing, ask if you have questions.

====<span style="color:dodgerblue">Beta: Push all tables for your assembly to beta====
</span>

Push all tables (EXCEPT seq, extFile, hgFindSpec and trackDb tables)'' from hgwdev to hgwbeta:

'''Option 1: Push 1 table at a time'''

This command will push one table from dev to beta for your database/assembly:

  sudo mypush $db $table mysqlbeta

'''Option 2: Push tables in a loop'''

<pre>
for table in $(cat yourTableList); do sudo mypush $db $table mysqlbeta; done
</pre>

For example:
<pre>

for table in $(cat manPen1.push); do sudo mypush manPen1 $table mysqlbeta; done
</pre>

'''Option 3: Use the bigPush.sh script, list tables in a file'''

List space separated tables in quotes. 

<pre>
hgwdev > bigPush.csh $db myTableList
</pre>

'''Option 4: Use the bigPush.sh script, list tables in quotes'''

List space separated tables in quotes. 

<pre>
hgwdev > bigPush.csh $db "table1 table2 table3 table4" 
</pre>

You can count the number of tables in a database if you want to compare the number of tables listed in your push file to the number of tables that have been pushed to beta. 



FROM HIVE:
<pre>
wc -l manPen1.push
55 manPen1.push
</pre>

FROM MYSQLBETA
<pre>
use manPen1
USE databasename; SHOW TABLES; SELECT FOUND_ROWS();

+--------------+
| FOUND_ROWS() |
+--------------+
|           55 |
+--------------+
</pre>

====<span style="color:dodgerblue">Beta: Push all tables to other assemblies to beta====
</span>
Repeat the push steps for other assemblies listed in your table list (e.g., chain/net tables to other assemblies). For example:

<pre>
for table in $(cat hg38.push); do sudo mypush hg38 $table mysqlbeta; done
</pre>

<pre>
for table in $(cat mm10.push); do sudo mypush mm10 $table mysqlbeta; done
</pre>

====<span style="color:dodgerblue">Beta: Review copyHgcentral steps ====
</span>

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):

<pre>
hgwdev > copyHgcentral test $db all dev beta
</pre>

====<span style="color:dodgerblue">Beta: copyHgcentral test db blatServers dev beta ====

Generates files, run in hive:

</span>
<pre>
hgwdev > copyHgcentral test $db blatServers dev beta
</pre>
<pre>
hgwdev > copyHgcentral execute $db blatServers dev beta
</pre>

You can also check on mysqlbeta:

<pre>
use hgcentralbeta;

select * from blatServers where db='manPen1';
</pre>

====<span style="color:dodgerblue">Beta: copyHgcentral test db dbDb dev beta ====
</span>

Generates files, run in hive:

<pre>
hgwdev > copyHgcentral test $db dbDb dev beta
</pre>
<pre>
hgwdev > copyHgcentral execute $db dbDb dev beta
</pre>

You can also check on mysqlbeta:

<pre>
use hgcentralbeta;

select * from dbDb where name='manPen1' \G;
</pre>

====<span style="color:dodgerblue">Beta: copyHgcentral test db defaultDb dev beta ====
</span>

Generates files, run in hive:

<pre>
hgwdev > copyHgcentral test $db defaultDb dev beta
</pre>
<pre>
hgwdev > copyHgcentral execute $db defaultDb dev beta
</pre>

You can also check on hgsqlbeta
<pre>
use hgcentralbeta;

select * from defaultDb where name="manPen1"limit 1;
</pre>

====<span style="color:dodgerblue">Beta: copyHgcentral test db genomeClade dev beta ====
</span>

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

<pre>
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 |
+-----------------+------------+----------+
</pre>

Generates files, run in hive:

<pre>
hgwdev > copyHgcentral test $db genomeClade dev beta
</pre>
<pre>
hgwdev > copyHgcentral execute $db genomeClade dev beta
</pre>

====<span style="color:dodgerblue">Beta: copyHgcentral: liftOverChain: manual move ====
</span>

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 [http://genomewiki.ucsc.edu/genecats/index.php/Chains_and_Nets_QA Chain and Net QA wiki page].
<pre>
 hgsql -Ne "SELECT * FROM liftOverChain WHERE fromDb = '$db' OR toDb = '$db'" hgcentraltest > chain.dev 
</pre>
Check beta, load if not present and recheck:
<pre>
 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
</pre>

====<span style="color:dodgerblue">Beta: checkMetaData ====
</span>

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.

====<span style="color:dodgerblue">Beta: Double check gbdb files====
</span>

* Double-check that hgnfs1 (which is /gbdb on hgwbeta) has the files listed in Remine file list. 

<pre>
$ /gbdb/manPen1

ls -ld $(find .)
</pre>
*Remove any unnecessary files. 
* If any files were updated on hgwdev in the course of QAing tracks, make sure the correct version is on hgnfs1. 
* To see the timestamps of files with symlinks on hgwdev, use the options "-lL" with ls. 
* The large "L" shows information for a file that a link references, rather than for the link itself. 
* You may notice that hgwdev has TRIX .ix and .ixx files, that is OK. These live on beta in a different location, /data/trix, more information at the at the [http://genomewiki.ucsc.edu/genecats/index.php/Pushing_trackDb TrackDb page]. 

Note: files on hgwdev are double the size as beta, this is not a concern.

====<span style="color:dodgerblue">Beta: Push gbdb files====
</span>

In order to check your assembly on beta, you will need to:
* Request a push of any listed supporting files in''' /gbdb from hgwdev to hgnfs1'''  
* Note that hgwbeta and the RR share the files on hgnfs1, so once these files are in place, there is not another push required when the track is released to the RR. 
* Note that  the gbdb files are sync'd to hgdownload on Sundays. If needed sooner, request a push. 
* If there are images associated with any track description pages, be sure to run a <tt>make beta</tt> from within kent/src/hg/htdocs/ to get the images to beta.
* [https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/push-request/staging$20on$20beta%7Csort:date/push-request/Gt8cRK4eTuw/gPbM5I2SAgAJ Example request]
* They may not be listed in the file list, but you also need to push the /gbdb/$db/trackDb.ixx and /gbdb/$db/trackDb.ix files, as in the example above. 
* After push, you can see files: ssh hgwbeta@qateam ; cd gbdb/$db

====<span style="color:dodgerblue">Beta: Admins pushers completed gbdb push request====
</span>

====<span style="color:dodgerblue">Beta: Do a make beta in trackDb for your assembly====
</span>

Do [http://genomewiki.ucsc.edu/index.php/ThreeStateTrackDb make beta] on hgwdev in kent/src/hg/makeDb/trackDb like so:

  make beta DBS=$db

Example to make beta on more than one db at a time:

  make beta DBS='$db1 $db2 $db3 $db4 etc'


----


'''Running multiple dbs in parallel to save time'''

Multiple assemblies can be run in parallel by using the make -j option (as of 2/10/17, thanks to Mark Diekhans). Updating all dev dbs used to take about 50 minutes, and now it can take about 5 minutes (at 16 in parallel). While Mark has safely run 16 dbs at a time on dev, it is recommended to only run 8 or less at a time on beta or the RR. Use make -j # beta  and make -j # public, where the number (make -j 16 alpha) represents how many parallel processes (16) are running. 

:For example, if you do:

   make -j 8 alpha

:it updates everything, 8 at a time.  If you do:

   make -j 2 DBS="hg19 hg38 mm10 felCat5"

:it updates those 4 databases, 2 at a time .

::Note: the 'make in parallel' process creates and removes temporary files:

::The tmp dirs are found with:
  kent/src/inc/portable.h:
    char *getTempDir(void);
    /* get temporary directory to use for programs.  This first checks TMPDIR environment
     * variable, then /data/tmp, /scratch/tmp, /var/tmp, /tmp.  Return is static and
     * only set of first call */

Examples:

  make beta -j 4 DBS="dm6 ce11 sacCer3 droEre1 droSec1 droSim1 droYak2 droAna2 dp3 droMoj2 droVir2 droGri1 droPer1"
  make public -j 4 DBS="dm6 ce11 sacCer3 droEre1 droSec1 droSim1 droYak2 droAna2 dp3 droMoj2 droVir2 droGri1 droPer1"

====<span style="color:dodgerblue">Beta: Do a make beta in trackDb for chain net organisms====
If your assembly has alignments to other organisms, such as chain/net alignments to hg38 or to the previous assembly version of your organism, be sure to also do a 'make beta' for those assemblies.

[http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_3_BETA_Steps#Beta:_Do_a_.27make_beta.27_in_trackDb_for_your_assembly See details in above section]


----

====<span style="color:dodgerblue">Beta: Do a make public in trackDb for your assembly====
</span>

Make your track public by using the "make public" command on hgwdev while in the trackDb directory (src/hg/makeDb/trackDb):

    [user@hgwdev trackDb]$ make public DBS=$db

Example to make beta on more than one db at a time:

  make beta DBS='$db1 $db2 $db3 $db4 etc'

Your track should now be visible on the [http://hgwbeta-public.cse.ucsc.edu/cgi-bin/hgTracks hgwbeta-public server].

If your track is not visible, you may want to check that your track has the correct release tag. Also see [[http://genomewiki.ucsc.edu/index.php/ThreeStateTrackDb Three State TrackDb]] for more information.

====<span style="color:dodgerblue">Beta: Do a make public in trackDb for chain net organisms====
</span>

If your assembly has alignments to other organisms, such as chain/net alignments to hg38 or to the previous assembly version of your organism, be sure to also do a 'make public' for those assemblies. 

[http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_3_BETA_Steps#Beta:_Do_a_.27make_public.27_in_trackDb_for_your_assembly See details in above section]



<pre>
cat ~/kent/src/hg/makeDb/genbank/etc/align.dbs | grep manPen
manPen1
</pre>
If your assembly is missing from align.dbs , check with Brian Raney.

====<span style="color:dodgerblue">Beta: Check that your assembly is listed in align:dbs====
</span>

The new assembly should already be listed in the files align.dbs and hgwdev.dbs in the source tree at ~/kent/src/hg/makeDb/genbank/etc/.

<pre>
cat ~/kent/src/hg/makeDb/genbank/etc/align.dbs | grep $db
</pre>


====<span style="color:dodgerblue">Beta: Turn on GenBank updates add:commit:push====
</span>
* Once your assembly is listed in align.dbs, turn on GenBank updates on hgwbeta before 4:30 p.m.
* Add the new assembly to ~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs in alphabetical order.  
* Be sure to save, git add, git commit, and git push the file. 
* Do not yet edit the rr.dbs, this comes later when the assembly is on the RR.

====<span style="color:dodgerblue">Beta: GenBank updates: make libs and run make====
</span>
After committing the change, make sure your libs are up to date:
 cd ~/kent/src ; make libs

then go ahead and run the make: 
 
 cd ~/kent/src/hg/makeDb/genbank/ 
 git pull 
 make install-rr install-server

To see whether updates have run (at least a day after the *.dbs files were updated), check the update times of the table 'gbLoaded':

====<span style="color:dodgerblue">Beta: GenBank updates: check Genbank update times====
</span>
 hgwdev > updateTimes.csh $db gbLoaded verbose

For example, you'll see updates for dev and beta (but not yet for the rr/euro/asia):

<pre>
updateTimes.csh manPen1 gbLoaded verbose

gbLoaded
=============
dev  2017-04-18 11:40:07
beta 2017-04-18 11:40:07

rr
euro
asia
</pre>

The update times will be out of sync between machines, but not by more than 24 hours or so if updates are running. The gbLoaded table will be updated regardless of whether changes to other GenBank tables were picked up. More genbank update instructions are available at [[Genbank updates]].

The etc-update-server part of the make will cause the downloads mentioned below in the "Verify downloads" section to be created.

====<span style="color:dodgerblue">Beta: joinerCheck common keys====
</span>
Check that common keys between tables are in sync:

<pre>
 hgwdev > cd ~/kent/src/hg/makeDb/schema 

 hgwdev > joinerCheck -database=$db -keys all.joiner
</pre>
If there are errors related to genbank identifiers, it is likely because of the genbank load process, and not an issue with your database. Run joinerCheck once the tables are on beta to confirm:
<pre>
 hgwdev > HGDB_CONF=~/.hg.conf.beta joinerCheck -keys -identifier=$identifier all.joiner
</pre>

====<span style="color:dodgerblue">Beta: joinerCheck table times====
</span>

Check table update times:
<pre>
hgwdev > cd ~/kent/src/hg/makeDb/schema 

hgwdev > joinerCheck -database=$db -times all.joiner
</pre>

====<span style="color:dodgerblue">Beta: joinerCheck tableCoverage====
</span>
Check that all tables in this database are mentioned/referenced in all.joiner
<pre>
 hgwdev > joinerCheck -database=$db -tableCoverage all.joiner 
</pre>
If not all of the tables are listed, email the developer asking him to add those tables to the tablesIgnored $db. According to Hiram it is probably ok for us to edit all.joiner ourselves.

====<span style="color:dodgerblue">Beta: Check release tags: compare dev and beta tracks side by side====
</span>

Compare your tracks by bringing up a dev and a beta browser window side-by-side. If some beta tracks can't be seen, you may need to edit the release tag.
See this page for more information:
http://genomewiki.ucsc.edu/index.php/ThreeStateTrackDb

Where are your release tags? You can do a recursive search, like this:

<pre>
find . -name '*ra' | xargs grep "manPen1"
</pre>

====<span style="color:dodgerblue">Beta: Remove release tag for big vcf track types====
</span>

Once you verify that the track looks good on hgwbeta, remove the release tag from trackDb.ra.

====<span style="color:dodgerblue">Beta: Check Tools: LiftOver ====
</span>

Check LiftOver on beta and beta public.

====<span style="color:dodgerblue">Beta: Check Tools: BLAT: dna====
</span>
Copy some dna and check BLAT for a DNA search on beta and beta public.

====<span style="color:dodgerblue">Beta: Check Tools: BLAT: protein ====
</span>

Copy some protein and check BLAT for a protein search on beta and beta public.

====<span style="color:dodgerblue">Beta: Check Tools: PCR ====
</span>

Check PCR on beta and beta public.
See [http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_1_DEV_Steps#Dev:_isPCR_test how to test PCR details from DEV steps]

====<span style="color:dodgerblue">Beta: Review chain net track QA wiki ====
</span>
* Review the Chain/Net QA wiki page, see the section [http://genomewiki.ucsc.edu/genecats/index.php/Chains_and_Nets_QA#QAing_on_hgwbeta QAing on hgwbeta]
* See also [http://genomewiki.ucsc.edu/genecats/index.php/Editing_the_human_trackDb.ra_file Editing the human trackDb.ra file]

Your assembly may have chain/nets for a composite chain/net track. For example, you may have a 'turkey' assembly that belongs in the "Vertabrate  Chain/Net" composite track on hg38. If your chain/nets appear next to the composite track, rather than within the composite track, you may need to create separate chainNetMelGal1.ra and chainNetMelGal5.ra files in trackDb/human. Once you have those files created then you will need to add the appropriate includes to the trackDb/human/hg38/trackDb.ra and trackDb/human/hg19/trackDb.chainNet.ra files.

====<span style="color:dodgerblue">Beta: Do chain net quick qa or full qa ====
</span>

Details in Chain/Net QA wiki page, section [http://genomewiki.ucsc.edu/genecats/index.php/Chains_and_Nets_QA#QAing_on_hgwbeta QAing on hgwbeta]

Full QA, run:
<pre>
chainNetTrio.csh  [database] [other database]
</pre>

Quick QA, run

<pre>
getChainLines.csh [database] [other database]
</pre>

<pre>
getMatrixLines.csh [database] [other database]
</pre>

====<span style="color:dodgerblue">Beta: Re push any tables if needed after checking updateTimes====
</span>

* Make sure no tables need to be repushed from hgwdev to hgwbeta.
* Note that if at any point you need to re-push some genbank tables, you must push ALL genbank tables together.

You can use 
<pre> 
hgwdev > updateTimesDb.sh -d $db
</pre>

to compare table update times between hgwdev and hgwbeta. Everything but hgFindSpec, history, tableDescriptions, trackDb and the genbank tables should have the same update times. 

To see all of the tables in the assembly that are related to genbank do this:
 hgwdev > hgsql -Ne 'show tables' $db | egrep -f /cluster/data/genbank/etc/genbank.tbls




🔵  Done with BETA steps? Go to [[Assembly QA Part 5 RR Steps | Assembly QA Part 5: RR Steps]]



















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