ENCODE QA Checklist: Difference between revisions

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Other functions of use?
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wigTableStats.sh
bigWigSummary
bigWigInfo
 
==Getting Started==
# Check kent/src/hg/makeDb/doc/encodeDccHg18/*.txt to determine if/how the file diverges from reality.
# Make a list of all tables (new & updated that need to be pushed to beta)
# Run qaEncodeTracks.csh and check output
# Do bigPush.csh using list created above
# Remove "release alpha" lines from subtracks in trackDb.wgEncode.ra
# Push any new .wib or .bb files from hgwdev to hgnfs1 if applicable
 
==Description Page==
# Read description page
# Make sure there is a link to the help doc (in the config section)
# Check that there is metadata by clicking on the "..." link in the tables list
# Is description page detailed enough?
# Is description page are the citations in correct format?
# Does the "Display Conventions and Configuration" section cover all track types?
# Test all hyper-links on description page.
# Test configuration section
# Test multi-view matrix
# Test "reset to defaults" button
# Make sure there's a link to the ENCODE Data Release Policy
 
==Other things to check==
# Run genePredCheck/pslCheck if applicable. (i.e. if your track is a gene prediction track)
# Release log: Check to be sure the release log entry is right.
# Make sure the tracks in the Tier1 and Tier2 Cell Lines are properly colored (no black, and all tracks from one Cell Line have the same color).
# Make sure your track is listed on the downloads page - (push from hgwdev -> hgwbeta, RR)  /usr/local/apache/htdocs/ENCODE/downloads.html
 
==Files==
===hgdownloads===
# make sure there is a preamble.html file in the /releaseN directory
# index.html
## For releaseN: run the encodeDownloadsPage.pl script directly in the /releaseN directory to generate a new index.html page
## Make sure this file is executable (because of the way the links are created)
## Preamble should include brief description and link to the trackUi
## should include a link to the files.txt and md5sum.txt files
## For releaseN: should also include the release number at end of description
## should contain the name of each file being released
 
===Pushing Files===
# Push gbdb Files:  hgwdev -> hgnfs1 (i.e.  /gbdb/hg18/wib/wgEncode*.wib)
# Push other Files: hgwdev -> hgwbeta & RR (i.e.  /usr/local/apache/htdocs/ENCODE/protocols/cell/*.pdf)
# Push download Files: hgwdev -> hgdownload (i.e. /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncode*/*) (Note: no releaseN directory on hgdownload)
# After Pushing Files: check push with: checkPushedFiles.csh
 
==Testing in the Browser==
# Test one point from table to view in GB
# Zoom into base level (at different visibilities)
# Zoom way out 1million bps (at different visibilities)
# Searching: should items be searchable?
# default visibility: should this track be on by default?
# Check URL in Release Log (should go to track description page)
# Check for lab contact (sanitize email addresses using encodeEmail.pl script)
# Does the first 'Signal' subtrack pass the chr1 test (chr1 loads in less than one minute)
# Do all views for one experiment pass chr1 test (e.g. Pol2 in GM12878 cells)?
# Test the performance in a gene-size region of the track with just the default-on subtracks
 
==Releasing to RR==
# Check the trackDb diffs to see if there is any reason that <db>.trackDb can't go out today
# If you determine that it's OK to push <db>.trackDb, then write to browser-qa "hands off <db>.trackDb"
# Check release log field in PushQ...needs to start with ENCODE
# Push track tables from mysqlbeta -> mysqlrr (not trackDb yet)
# Drop tables from hgwbeta that need to be removed (being replaced by V2 tables)
# Clean up trackDb (remove blocks for the dropped tables - currently marked release beta)
# Make strict for <db> on hgwbeta and check to make sure tracks look like you expect them to (all there and accounted for)
# Drop tables being removed from the RR
# Push trackDb, tableDescriptions and, if items are searchable (not usually for Encode), hgFindSpec
# Push download files and index.html (from hgwdev to hgdownload)
# Drop download files that need to be dropped (from hgdownload)
# Drop .wib files that need to be dropped (from hgnfs1)
# If necessary edit and push ENCODE/downloads.html from hgwdev -> hgwbeta & RR
# Push cv.ra file (only if there is a matrix)
# Cc the data wrangler for this track on all your pushes Cc encode@soe.ucsc.edu on your final push
 
[[Category:Browser_QA]]

Latest revision as of 18:43, 10 March 2011

This page is no longer maintained.