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| Go to [[New_Assembly_Release_Process_Details | New Assembly Release Process Details]] page.
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| {| border="1" cellpadding="2" width=800px
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| |width="10%"|'''Start'''
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| |width="10%"|'''Complete'''
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| |width="60%"|'''Step'''
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| |width="20%"|'''Link to details doc'''
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| |If the organism has an existing assembly, check to see if chroms have changed in size considerably since the last release of an assembly.
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| |Check to see if anyone has given WUStL the heads-up so they can begin doing their N-Scan predictions. Send email to markd and Jeltje van Baren: jeltje at cse.wustl.edu.
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| |Ask admins to add your assembly to the exclude list (both the gbdb and mysql rsync download targets) at: hgdownload:/opt/csw/etc/rsyncd.conf. This should be done before syncing /gbdb data to hgnfs1 (i.e., before testing on beta).
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| |Complete staging of assembly on hgwbeta.
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| |[[New_Assembly_Release_Process_Details#Stage_and_test_on_hgwbeta | details]]
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| |Check assembly details on hgwbeta, including: BLAT/PCR, GenBank updates, .nib file, default position/tracks, orderKey, gateway page, joinerCheck, indices, makedoc, featureBits.
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| |[[New_Assembly_Release_Process_Details#Stage_and_test_on_hgwbeta | details]]
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| |Complete testing of all tracks in sub-pushQ
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| |Check that .2bit file on blat servers is the same as the one in /gbdb/<db>/ and /usr/local/apache/htdocs-hgdownload/goldenPath/<db>/bigZips using md5sum.
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| |[[New_Assembly_Release_Process_Details#2bit | details]]
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| |Warn Donna K. that the release is imminent so she can update docs. Read everything and test links in downloads, gateway, credits, currentGenomes.
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| |[[New_Assembly_Release_Process_Details#Push_Static_Content_from_hgwdev_to_hgwbeta_and_Round_Robin | details]]
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| |Send email to genome-mirror letting them know that there is a new assembly (and exactly how much data) and when it will be released for rsync. Give 24 hours notice.
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| |[[New_Assembly_Release_Process_Details#Push_Data_to_Round_Robin_from_hgwbeta | details]]
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| |Adjust Release Log in main pushQ
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| |[[ New_Assembly_Release_Process_Details#release_log| details]]
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| |Check that all of the MySQL tables are in good repair: hgwbeta> sudo dbCheck.sh $db
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| |[[New_Assembly_Release_Process_Details#Stage_and_test_on_hgwbeta | details]]
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| |Request rsync of database: hgwbeta -> RR (email to push-request)
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| |[[New_Assembly_Release_Process_Details#Push_Data_to_Round_Robin_from_hgwbeta | details]]
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| |Mark main pushQ entry as “push requested”
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| |Add to genomeClade if needed (only if this is the first release for this organism (e.g. “aaaBbb1”))
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| |[[New_Assembly_Release_Process_Details#Update_hgcentral | details]]
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| |Add line to genome-centdb.hgcentral.dbDb with active set = 0 (use checkMetaData.csh to get exact entry)
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| |[[New_Assembly_Release_Process_Details#Update_hgcentral | details]]
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| |Add the two lines to genome-centdb.hgcentral.blatServers
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| |[[New_Assembly_Release_Process_Details#Update_hgcentral | details]]
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| |Wait for pushes to RR to be complete
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| |Turn on GenBank automatic updates on on the RR. Follow instructions for turning on updates on beta, but add assembly to rr.dbs instead of hgwbeta.dbs
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| |[[New_Assembly_Release_Process_Details#genbank | details]]
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| |Test browser on RR by changing db= value in URLs
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| |[[New_Assembly_Release_Process_Details#Enable_Assembly_on_Round_Robin | details]]
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| |Request push of downloads hgwdev: /usr/local/apache/htdocs-hgdownloads/goldenPath/<db>/<appropriate folders> -> hgdownloads: /usr/local/apache/htdocs/goldenPath/<db>/<appropriate folders>. Verify that liftOver files are in /liftOver, NOT in /vsXXX directories. Remember to push pairwise alignments and liftovers (vs the new assembly) from other organisms' databases.
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| |[[New_Assembly_Release_Process_Details#Push_Downloads_from_hgwdev_to_hgdownload | details]]
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| |Request dump & autodump of database (send email to cluster-admins to ask for dump to hgdownload into htdocs/goldenPath/$db/database/)
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| |[[ New_Assembly_Release_Process_Details#autodump| details]]
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| |Double check that all appropriate /gbdb files were pushed from dev -> hgnfs1 (during beta testing), including liftOver files. (i.e. compare /gbdb/$db/* dev vs. beta)
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| |Create currentGenomes symlink and request push from hgwdev -> hgdownloads /usr/local/apache/htdocs/goldenPath/currentGenomes/<db_symlink> (this is for the FTP link)
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| |[[ New_Assembly_Release_Process_Details#currentgenomes| details]]
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| |Confirm that hgdownloads, currentGenome, and FTP links are functional
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| |[[ New_Assembly_Release_Process_Details#Push_Downloads_from_hgwdev_to_hgdownload | details]]
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| |Change line in genome-centdb.hgcentral.dbDb to be active = 1 (this makes the assembly live on RR!)
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| |[[New_Assembly_Release_Process_Details#Enable_Assembly_on_Round_Robin | details]]
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| |Enable liftOver on the RR Follow instructions for enabling liftOver on beta, but make changes to hgcentral (not hgcentralbeta): (on hgwdev)"hgsql -h genome-centdb" then in mysql type "use hgcentral" Test hgLiftOver and hgConvert immediately
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| |[[New_Assembly_Release_Process_Details#Update_hgcentral | details]]
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| |Complete testing in RR: tracks, PCR, Blat, liftOver, etc. (that required active=1).
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| |Change or add line in genome-centdb.hgcentral.(and in hgcentraltest and hgcentralbeta).defaultDb to point to new DB and test
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| |[[New_Assembly_Release_Process_Details#Update_hgcentral | details]]
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| |Send email to Donna K. letting her know it has been pushed, and she will push all static documents. Test all of her files. Test links in downloads, gateway, credits, currentGenomes.
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| |[[New_Assembly_Release_Process_Details#Push_Static_Content_from_hgwdev_to_hgwbeta_and_Round_Robin | details]]
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| |For human, mouse and rat (KG assemblies), ask for push of htdocs/knownGeneList/$db/* and knownGeneLists.html
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| |Ask admins to remove your assembly from the exclude list at: hgdownload:/etc/rsyncd.conf and alert genome-mirror.
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| |If this is a new species, send an email to Branwyn (bwagman@ucsc.edu). There is no longer a place to announce new assemblies, but she said she wanted to be informed anyways in case she wants to write something about it.
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| |Notify cluster-admin that new assembly is complete and ask for push to genome-mysql. Remind them to make permissions for users "genome" and "genomep", and update the mysql.db table permissions.
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| |Push net and chain tracks in other organisms, taking care to edit and push trackDb as necessary. If these tracks are replacing nets and chains to a previous assembly, drop those tracks and notify the mirrors.
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| |[[New_Assembly_Release_Process_Details#Edit_Other_Organisms | details]]
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| |Click on “done!” in main pushQ for this assembly (the release log will be updated the next morning)
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| |Retire the assembly sub pushQ using retirePushQ.csh from hgwdev. Make sure there are release log entries for the net and chain tracks in other databases. (The script will remove release log notes for all push queue entries where dbs=$db.)
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| |Update hgcentral.sql: cd $WEEKLYBLD; Run buildHgCentralSql.csh real (can run w/o 'real' to just see diffs). hgcentral.sql will be automatically pushed to hgdownload.
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| |Double check next day: release log, database dump/autodump, genome-mysql, genbank auto-update, downloads (bigZip autodownloads)
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| |[[New_Assembly_Release_Process_Details#Maintenance | details]]
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| |}
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| [[Category:Browser QA]]
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