- v418 Preview 1 - 12 Jul 2021
- v418 Preview 2 - 19 Jul 2021
- v418 Final - 26 Jul 2021
Code changes:
- Changed all calls to system() and popen() to use our pipeline library (#27801). Brian
- Fixed hgTracks shortcut zoom keys (#27892). Max
- Added Google Analytics button click tracking to hgTracks (#27283). Max
- Implemented mysql advisory locks to prevent duplications in hubStatus table (#27581). Brian
- Allow lower case first letter of 3-letter amino acid code in pseudo HGVS gene searches (#15554). Chris
- Allow alias tables to be used with knownGene bigBed. Brian
- Fixed multi-region minor problem in GTEx and barchart handling the tracks ss list (#27855). Galt
- Undo bigDataUrl expansion changes (#27752) and (#27767). Chris
- Adding needed EPSV extended passive command for IPv6 FTP (#27860). Galt
- The local cache directory for remote files (udcCache, which is used for file types like bigBed, bigWig, VCF, and bam) now defaults to $TMPDIR/udcCache. The previous default of /tmp/udcCache will still be used if $TMPDIR is undefined in the local environment. Jonathan
- Updates to GBiB and GBiC:
- Fixed GBiC script random error messages output on startup by changing the entire handling (#27795). Max
- Stopped supporting Ubuntu 14 in GBiC. Ubuntu 14 reaches EOL in early 2022 and it does not seem possible to set passwords in a way that is compatible from mysql 5.6 up to mysql 8 (#27795). Max
- Added gtexGenev8 to list of tables always downloaded by hgMirror and GBiB, since it is a default track on hg38 (#27854). Chris
- New push location for the gbic script, /usr/local/apache/htdocs/gbic/, used for a default location for pushers to push from. Chris
- Fixed GBiB problem due to cartVerstrion string (#27752). Max
- Added support for local-only assemblies to GBiB/GBiC (#27865). Max
hgPhyloPlace. Angie
- Added summary table w/subtree links for results from pasted/uploaded IDs.
- Updated to latest Nextstrain clades & colors.
- No crash and better error message when usher rejects all input sequences.
- Now tweaks input sequence names if necessary to prevent rejection by usher.
Data changes:
- (New) Added ARTIC V4 (primers) track for wuhCor1. Angie
- (Update) Big tree for hgPhyloPlace. Angie
- More complete & consistent country names in metadata.
- Additional metadata tweaks for issues found by Theo Sanderson w/ cov2tree.org.
- Annotate clades & lineages using paths in tree instead of representative samples.